WO2013066665A1 - Method of rapidly producing improved vaccines for animals - Google Patents

Abstract

A method of quickly producing a vaccine for a biotype of pathogenic microorganism is described, where a nucleic acid molecule or fragment thereof is obtained from a biological sample from an animal exposed to the microorganism, a protective molecule is prepared based on the nucleic acid molecule of interest or fragment thereof, and administered to an animal which has been or is as risk of being exposed to the microorganism. A protective response to the biotype of the microorganism is obtained in the animal.

Description

METHOD OF RAPIDLY PRODUCING IMPROVED VACCINES FOR ANIMALS

RELATED APPLICATIONS

This application claims priority to previously filed and co-pending application USSN

13/277,076, filed October 19, 2011, to previously filed and co-pending application USSN 13/277,066 filed October 19, 2011, each of which claim priority to USSN 61/407,297, filed October 27, 2010, USSN 61/418,433, filed December 1, 2010, to USSN 61/449,940 filed March 7, 2011, to USSN 61/484,255 filed May 10, 2011, to USSN 61/508,172 filed July 15, 2011 , and to USSN 61/525,332 filed August 19, 2011 , the contents of each of which are incorporated herein by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with Government support under contract 2007-33610-18035 and 2009-33610-20299 awarded by and SBIR grant from the U.S. Department of Agriculture. The Government has certain rights in the invention.

SEQUENCE LISTING

The instant application contains a Sequence Listing which has been submitted in ASCII format via EFS-Web and is hereby incorporated by reference in its entirety. Said ASCII copy, created on October 23, 2012, is named 150003RPCT.txt and is 110,652 bytes in size. BACKGROUND

Animal vaccines are commonly produced by several routes. Commercially developed vaccines are produced for use in all animals, in many different locations. Such a vaccine would contain antigen and could be derived from a biotype of the pathogenic agent.

Different isolates can be biotyped by a variety of typing techniques where a variant of the pathogenic agent is distinguishable by a particular characteristic over other members of the pathogenic species. These variants may differ, for example, by sequence variation of a DNA sequence, RNA sequence, pathogenic response, serological type or the like. See Sambrook et al, Molecular Cloning: A Laboratory Manual, Third editions, Cold Spring Harbor

Laboratory, Cold Spring Harbor, N.Y. 2001. Another example of biotyping is glycan typing as is described at Harris et al., US Patent 7,622,254, incorporated herein by reference in its entirety. In the example of influenza virus, the viral strains are analyzed genetically and antigenically by the World Health Organization and the Center for Disease Control by screening numerous influenza viruses circulating in the human and animal populations. A vaccine strain is updated when there is an antigenic difference between the vaccine strain and newly emerged strain of two units in the hemagglutination-inhibition assay. Autogenous vaccines on the other hand are those produced for use at a particular location and group of animals. The pathogenic agent such as a virus is isolated and the whole virus used in producing a vaccine customized for the biotypes found at that location and which may be used at other locations where there may be exposure to such biotype. By way of example, an autogenous vaccine in a veterinary setting may be developed by isolating a virus at a farm to be used as a vaccine at the farm.

The present vaccine options for animals lack an ability to adapt quickly to new outbreaks of disease. Livestock animal diseases cost producers billions of dollars each year in both treatment and lost productivity. For certain diseases, such as those affecting aquatic invertebrates, there is no commercially available vaccine for the key pathogens (such as those affecting farmed shrimp). Porcine Reproductive Respiratory Virus (PRRSV) alone costs the swine industry an estimated $560 M annually. Neumann EJ, Kleibenstein J, Johnson C, Mabry JW, Bush EJ, Seitzinger AH, Green AL, Zimmerman JJ (2005), Assessment of the economic impact of porcine reproductive and respiratory syndrome on swine production in the United States, Journal of the American Veterinary Medical Association 227: 385-392. Swine producers and veterinarians lack a broadly-effective vaccine for PRRS due to the lack of cross-protection commercial vaccines provide against heterologous strains of the pathogen. Influenza is another example of costly disease that affects humans, birds, swine and other animals. Veterinarians identified influenza as a swine disease during the influenza pandemic of 1918 when a connection was made between outbreaks in humans and swine that were closely related in time. According to the International Society for Infectious Diseases, the virus was initially isolated from pigs in 1930, with isolation from humans following in 1934. Influenza is grouped into three categories, based on the absence of serologic cross reactivity between their internal proteins: influenza A, B and C. Influenza A viruses are further classified into groups by antigenic differences of hemagglutinin and neuraminidase proteins. There are sixteen subtypes of HA and nine of NAs known, including HI, H2, H3, Nl and N2. The influenza viruses change frequently as a result of changes in the HA and NA amino acid sequence, allowing the virus to escape being neutralized by the immune response of the body. For example, to date the more prevalent subtypes circulating in human, poultry and swine populations in North America are HI and H3. In 2008/2009 a new isolate was discovered which has resulted in another pandemic among humans, known as H1N1. This is why when vaccines are prepared from a particular strain it may not provide protection against an outbreak from a different strain, thus requiring vaccines to be prepared anew each year from predicted new or expected isolates.

Thus a vaccine specific for specific biotypes of pathogens in a particular location such as on a farm is highly desirable. Companies exist which specialize in such autogenous vaccines. However, currently all autogenous vaccines are whole-organism preparations which must be inactivated (killed vaccines). In brief, a pathogen is isolated from an animal/farm, purified, grown in a laboratory, formulated, and returned to the farm for vaccination of animals. These traditional autogenous vaccines attempt to address the problem of strain variation; however they are not produced fast enough to have an immediate impact on production and economic losses caused by the disease and are not compatible with diagnostic tests for differentiating infected from vaccinated animals (DIVA).

Vaccine strains in USDA Center for Veterinary Biologies approved commercial vaccines can be 'switched out' in approximately 12 months. Rapp-Gabrielspm VJ,

Sornsen S, Nitzel G, et al. Updating swine influenza vaccines. AASV 39th Annual Meeting Proceedings 2008;261:264. Vaccine strains in autogenous vaccines can be 'switched out' more quickly, possibly within 3-6 months; however, the cost of preparing vaccines with new and updated strains for limited orders may limit availability. Order size may increase with regional/adjacent autogenous networks but may be complicated to organize and implement. Henry S., Swine influenza virus - efforts to define and implement regional immunization. AASV Proceedings 2009;475:478. VCPR vaccines may be authorized/produced by veterinarians/producers. 'Switch out' of vaccine strains can be done more rapidly than by either USDA CVB approved commercial or autogenous vaccines. (See 9 CFR 107.1 regarding Veterinary Client Patient relationship arrangements (VCPR) and 9 CFR 113.113 regarding autogenous vaccines; see also Ryan Vander Veen, Kurt Kamrud, Mark Mogler, et al. Rapid Development of an Efficacious Swine Vaccine for Novel H1N1. PLoS Currents Influenza 2009 November 2RRN1123.)

In sum, there are at least three major deficiencies in current vaccines.

1. Specificity. Commercial vaccines do not account for strain variation of pathogens that change quickly in the field. Strain variation and lack of adequate cross-protection lead to vaccine failure and thus production/economic losses.

2. Timeliness. It can take one year to change a commercial vaccine to account for strain variation. Current autogenous vaccines seek to address the problem of specificity, but can take months to prepare from the time a new strain is identified to the time the first animals are vaccinated. For example, traditional killed autogenous vaccines for PRRSV currently available can take up to six months to prepare. In this time frame a new strain of the pathogen can emerge, thus decreasing the value/effectiveness of the autogenous vaccine. A faster way to produce autogenous vaccines is thus needed.

3. Components. All current autogenous vaccines are whole-organism in that the entire pathogen is included in the vaccine. In most diseases this is unnecessary since the specific antigens needed for protection are already known. Also, since the whole virus is contained in the vaccine, they are not compatible with differential diagnostic tests.

Thus there is a need for improved vaccines for animals.

All references cited herein are incorporated herein by reference. Examples are provided by way of illustration and not intended to limit the scope of the invention.

SUMMARY

A method of producing a vaccine is provided which protects the animal from adverse effects of a pathogenic microorganism. A biological sample is obtained from an animal which has been exposed to a microorganism, a nucleic acid molecule of interest or fragment thereof of the microorganism is obtained from the sample and a protective molecule produced from the nucleic acid of interest. The protective molecule may be a nucleic acid molecule comprising the sequence or a fragment of the nucleic acid molecule of interest, may be a polypeptide or fragment produced by the nucleic acid molecule of interest, or may be an RNA molecule that is antisense to the nucleic acid molecule of interest or forms a dsRNA that corresponds to all or a portion of the nucleic acid molecule of interest. Vaccines so produced and a method of protecting an animal using the vaccine are also provided.

DESCRIPTION OF THE DRAWINGS

Figure 1 is a schematic representation of the autogenous recombinant protein vaccine production process.

Figure 2 is a schematic representation of the Backbone Biological Agent pVEK DNA plasmid vector.

Figure 3 is a schematic representation of the pVEK Plasmid Vector with Autogenous Donor Gene (ADG) insert.

Figure 4 is a schematic representation of the Autogenous Donor Gene (ADG)/GOI and backbone biological agent/RNA replicon construction.

Figure 5 is a schematic of the VEE genome organization and replication strategy.

Figure 6 is a schematic of the VEE replicon particle vaccine and packaging system. Figure 7 is a diagram of the IMNV genome transcription and translation products showing regions targeted for RNAi, predicted protein products are indicated by dark gray lines or gray shading, with target regions for dsRNA production indicated as thick black lines.

Figure 8 is a map of the vector pERK-3/M/GP5.

Figure 9 is a graph showing total gross lung score in different treatment groups. Treatment groups with different letters are significantly different (ANOVA, p<0.05).

Figure 10 is a graph showing interstitial pneumonia scores in different treatment groups. Treatment groups with different letters are significantly different (ANOVA, p<0.05).

Figure 11 is a graph showing a summary of lung lymphoid hyperplasia scores. Treatment groups with different letters are significantly different (ANOVA, p<0.05).

Figure 12 is a graph showing a summary of heart pathology scores. Treatment groups with different letters are significantly different (ANOVA, p<0.05).

Figure 13 is a graph showing mean IDEXX ELISA S/P titer per group. Groups with different letters are significantly different (ANOVA, p<0.01) within day post challenge. The bars of each group are in the order listed: strict negative, placebo, ARP, inacivated and MLV. Figure 14 is a graph showing the number of pigs out of ten per group with a FFN titer > 4. Groups with different letters are significantly different (Chi-square, p<0.05) within day post challenge. The bars of each group are in the order listed: strict negative, placebo, ARP, inacivated and MLV.

Figure 15 is a graph showing geometric mean FFN titer by group. Groups with different letters are significantly different (ANOVA, p<0.01) within day post challenge. The bars of each group are in the order listed: strict negative, placebo, ARP, inacivated and MLV. Figure 16 is a graph showing live virus titration at 7 DPC. Groups with different letters are significantly different (ANOVA, p<0.01).

Figure 17 is a graph showing the number of pigs out of ten per group PRRSV positive serum via RT-PCR. Groups with different letters are significantly different (Chi-square, p<0.05) within day post challenge. The bars of each group are in the order listed: strict negative, placebo, ARP, inacivated and MLV.

Figure 18 is a Western blot confirming recombinant HA expression. Lane 1 is the ladder; lane 2 the Vero lysate (negative control); lane 3, recombinant HA (28^g/ml); Lane 4:

Recombinant HA (1.14μg/ml); Lane 5: Recombinant HA (0.57μg/ml); Lane 6: Recombinant HA (0.38μ^πι1). Figure 19 is a graph showing a study measuring neutralizing antibodies against FMDV A24 at defined days post vaccination or challenge. The control is the first bar in each grouping, Dose A is the second bar and Dose B the third bar.

Figure 20 is a graph showing serial dilution of clarified inoculum diluted in 2% saline. Sham inoculation received an equivalent dose of 2% saline. N= 20 shrimp per treatment.

Figure 21 is a graph showing results of Example 4, Experiment 1. Shrimp were injected with 2 μg of dsRNA construct and challenged with IMNV 48 hours following administration. N=3 groups of 20 shrimp per treatment.

Figure 22 is a graph showing results of Example 4, Experiment 2. Shrimp were inoculated with a serial dilution of dsRNA and challenged 48 hours following administration. N=10 shrimp per treatment.

Figure 23 is a graph showing results of Example 4, Experiment 2. Shrimp were injected with a serial dilution of dsRNA and challenged 10 days following administration. N=10 shrimp per treatment.

Figure 24A is a graph showing results of Example 4, Experiment 3. Shrimp were injected with .02 μg of dsRNA#3, 5' truncate of dsRNA3, or a 5' truncate of dsRNA3 and challenged 10 days following administration. N= 3 groups of 10 shrimp per treatment.

Figure 24B is a graph showing results of Example 4, Experiment 3, where shrimp were injected as in Figure 24 A, but with further truncates of dsRNA#3.

Figure 25 is a graph showing results of Example 4, Experiment 4. Shrimp were inoculated with replicons or dsRNA and challenged 3 days following administration. N= 3 groups of 10 shrimp per treatment.

Figure 26 is a graph showing results of Example 4, Experiment 5 Shrimp were inoculated with replicon and challenged 3 days following administration. N= 3 groups of 10 shrimp per treatment.

Figure 27 is a graph showing results of Example 4, Experiment 5. Shrimp were inoculated with replicon and challenged 10 days following administration. N= 3 groups of 10 shrimp per treatment.

Figure 28 is a graph showing results of Example 4, Experiment 7. WSSV survival following primary challenge.

Figure 29: Is a graph showing survival following secondary WSSV challenge 21 days following primary challenge. Figure 30 is a graph showing survival following vaccination via injection or reverse gavage. Animals were challenged 14 days post vaccination. Figure 31 is a graph showing survivorship of animals following challenge that were administered dsRNA 2 days post challenge. X-axis is days post challenge. Y-axis is percent survival. dsRNA3 and eGFP dsRNA groups were treated with 5 μg dsRNA and the challenge control was treated with an equivalent volume sterile water.

Figure 32 is a graph showing percent survivorship of shrimp following treatment with feed containing different solutions. X-axis is days post infection with WSSV and Y-axis is percent of animals surviving. n=30 animals with 3 replicates of 10/treatment

Figure 33 is a graph showing shrimp survival post-vaccination with dsRNA of varying lengths (day 0) and post IMNV infection (day 10). dsRNA target position on the IMNV genome and length are indicated in the key.

Figure 34 is a graph showing percent survivorship of shrimp following treatment with feed containing different solutions. The mean percent survival of animals 20 days following injection challenge with 10 virion dose of IMNV IMJ is represented. Animals were vaccinated at PL9 and reared for 30 days prior to challenge.

Figure 35 is a graph showing percent survivorship of shrimp following treatment with feed containing different solutions. The X-axis is days post challenge. The Y-axis is percent survival (after subtracting background mortality in first 24 hours post injection from trauma as compared to water injected control). Animals were challenged 15 days post vaccination with a 10 virion dose IM (PL33).

Figure 36 is a graph showing survival of shrimp receiving dsRNA and RP administrations as indicated.

Figure 37 is a graph showing paired comparison of the H3- and nsp2-specific IFAs. Each bar represents the average titer obtained by twelve independent titrations performed on two separate days.

Figure 38 is a graph showing cumulative average titers for the same H3 RP control lot of the H3-specific (47 IFA titers determined by two different technicians over 6 separate days = 94 total IFA titers) and nsP2-specific (24 independent titrations done over 4 separate days) IFAs. Figure 39 is a graph showing the group mean (Log₂ conversion of inverse HI titers) against each relevant strain at 19 days post-boost. The horizontal line at approximately 4.3 indicates an HI titer of 20.

Figure 40 is a plasmid map of a vector PVEK1 K5

DESCRIPTION

The invention relates to an improved vaccine to protect animals against a pathogen which can be prepared very rapidly and which addresses the problem of providing protection to animals against a new or evolving biotypes. The vaccine is a new type of autogenous vaccine, that is, it is created from a nucleic acid molecule derived from an infectious agent present on a specific farm, flock, herd, pond or geographic region. It is not necessary to isolate the infectious agent in the laboratory to obtain the gene. It is prepared from the nucleic acid of microorganism(s) present in an animal or a group of animals which have been exposed to a biotype of a pathogenic microorganism. Such animals from which the nucleic acid molecule is obtained are those living in an environment in which one can expect are likely to have been exposed to the same pathogen biotype. By way of example, without limitation, where such animals are livestock animals, they may be found living in a ranch, feed yard, farm, flock, pond or region and with sufficient contact such that one skilled in the art would expect such animals to have come into contact or are likely to come into contact with the same pathogen. Upon preparation of the autogenous vaccine, these animals would then be vaccinated with the vaccine. As provided for with by the American Veterinary Medical Association (AVMA), adjacent or non-adjacent groups of animals considered to be at risk may also be vaccinated. See www.avma.org/issues/policy/autogenous_biologics.asp "Guidelines for Use of Autogenous Biologies" (Oversight: COBTA; EB approved- 1993; reaffirmed 11/97; reaffirmed 4/01 ; revised 3/06, 11/09). When referring to an autogenous vaccine is meant to include this current definition of the AVMA in which animals considered to be at risk may be vaccinated. Also, an individual animal, (often times a dog, cat, horse, or the like) may be the sole animal for which the autogenous vaccine is prepared. The source of the microorganism nucleic acid molecule of interest is any convenient biological sample such as animal tissue, fluid or cell which are expected to have the nucleic acid of the

microorganism present, whether blood, skin, organ tissue, body fluids or the like.

The term biotype refers to distinguishing a pathogenic agent by one or more characteristics over other members of the pathogenic species. The invention is particularly useful in providing a process to quickly produce a vaccine that is useful with different and/or new biotypes of a pathogen, and in an embodiment is especially useful where a biotype is found in a particular group of exposed animals or with potential for exposure to that biotype. Using current methods, a vaccine that is available may not be helpful against a different or newly evolving biotype. This invention provides a process where a vaccine that is useful with the new or different biotype is quickly developed. A biotype variant of a species can be distinguished by a variety of one or more characteristics, such as ribosomal RNA sequence variation, DNA polymorphisms, pathogenic response, response of the exposed animal to a specific vaccine, serological typing of toxin production or many other possible variations depending upon the pathogenic agent (see e.g., Sambrook et al. Molecular Cloning: A Laboratory Manual, 2^nd Edit., Cold Spring Harbor Laboratory, cold Spring Harbor, New York 2001 ; DNA cloning A Practical Approach, Vol. I and II, Glove, D.M. edit. IRL Press Ltd., Oxford, 1985; Harlow and Lane, Antibodies a Laboratory Manual, Cold Spring Harbor Publications, N.Y. 1988). By way of example, without limitation, influenza can be biotyped by distinguishing it by subtype and cluster. The category is determined by differences of their internal proteins, and further by differences of the hemagglutinin and neuraminidase proteins. A hemagglutinin inhibition test can be used, in one example, where a sample of specified dilution is applied to red blood cells and the titer determined by the maximum dilution that produces agglutination. Antibodies to the virus prevent attachment to red blood cells and thus hemagglutination is inhibited when antibodies to influenza virus are present. Results are reported as the reciprocal of maximum dilution that provides visible

agglutination. See.e.g., Katz et al.(2009) Morbid. Mortal. Weekly Rep. 58 (19) 521-524. Another example of biotyping is glycan typing where genotypes are grouped based on their glycosylation patterns. Such a process is described at Harris et al., US Patent 7,622,254, incorporated herein by reference in its entirety (see especially, for example, table 7 columns 48 and 49). For example, the strains of PRRSV (Porcine Reproductive Respiratory Virus) are classified based on whether they are European or North American strains. In another aspect of typing the PRRSV strains, the first letter is either EU (European like) or NA (North American like) to designate the genotype cluster. EU refers to isotypes of PRRSV characterized by conserved glycans at position 46, 53, or both in GP5. As used herein, NA refers to isotypes of PRRSV characterized by conserved glycans at position 44, 51, or both in GP5. Each strain is given a number corresponding to the number of glycosylation sites located in the ectodomain of GP5 amino acid sequence shown in Table 7 of '254, but excludes highly conserved glycans located at aa44 and 51 for NA strains and aa46 and 53 for EU strains. Thus, NA-0 refers to the ectodomain of GP5 of NA strain that has no glycan and EU-0 refers to the ectodomain of GP5 of an EU strain that has no glycan. For example, NA-1 refers to the ectodomain of GP5 of a North American strain that has 1 glycan located on the ectodomain of GP5 excluding highly conserved glycans located at aa44 and 51 for NA strains. Table 1 represents such a glycantyping of PRRSV.

Table 1

PRRS

NA-1 1 NA-2 2

NA-3 3

NA-4 4

NA-n n

EU-0 0

EU-1 1

EU-2 2

EU-3 3

EU-4 4

EU-n n

aNA+ North American, EU = European

^Number of glycans located on the ectodomain of GP5 excluding highly conserved glycans located at aa44 and 51 for NA strains and aa46 and 53 for EU strains. When these glycans are absent they should be noted as follows: if an NA-1 strain lacks a glycan at aa44 it is described as NA-1 (Δ44).

As the number of predicted glycans increases so does the resistance to inducing protective (neutralizing) antibodies and/or susceptibility to such antibodies.

NA-0 and EU-0 are predicted to be the parent strains for all NA and EU strains respectively. Thus these viruses should be included in attempts to generate cross-reacting antibodies. After NA-0 and EU-0, glycantyping may be a predictor of heterology which is currently poorly defined for PRRSV.

Any biotyping method to distinguish a pathogen from another of the species may be used in the invention.

The inventors provide for a new approach to the generation of autogenous vaccines. In current processes used, the whole organism is isolated, then attenuated or killed, and the animal vaccinated with the prepared virus. By way of example, US Patent 4,692,412 to Livingston et al. describes a method for preparing an autogenous vaccine for neoplastic diseases by mixing a sterile blood sample containing Progenitor cryptocides with sterile distilled water, incubating the admixtures, killing or inactivating the Progenitor cryptocides in the admixtures, microfiltering the admixture to remove blood cells and diluting the filture to form the vaccine.

In the present work of the inventors, rather than use the whole organism (either live or inactivated) as the vaccine, one uses only one or more microorganism individual gene(s) of interest (GOI) also referred to as the nucleic acid molecule of interest (NOI) or fragments thereof, derived from the pathogen and/or the protein such gene(s) encode that makes up the autogenous vaccine. Surprisingly, it is possible to produce a vaccine using such nucleic acid molecules and to provide an effective vaccine which protects the animal. The gene of interest refers to a nucleic acid molecule which may or may not represent an entire gene and may be one from which an RNA interfering molecule is produced, or encodes a polypeptide or fragment thereof that produces a protective and/or immune response in the animal when administered to the animal. As one skilled in the art appreciates, the actual vaccine uses a protective molecule and may contain the gene of interest or fragment thereof, or may contain the polypeptide or fragment thereof producing the protective response, or may contain the interfering RNA or may contain a combination. A fast and effective vaccine can be produced, since the NOI to be obtained has been identified, having been predetermined prior to being obtained from the sample.

For many pathogens the protective molecule(s) needed to induce protection are known. The gene of interest of a pathogen is first amplified from a diagnostic sample originating from the farm. While one can isolate and purify the pathogen, it is not necessary with this method. Not only in such an embodiment does this eliminate an unnecessary step and speed the production process, it removes the need to have an isolated pathogen. The gene may be isolated or any protective portion of it isolated by using any available method such as PCR. The gene is then used to prepare the vaccine and ultimately used to vaccinate animals that have been or may be exposed to the pathogen. These vaccines when compared to currently available vaccines would be faster, biotype specific, and compatible with diagnostic tests. These attributes would allow vaccines to quickly enter the market. By way of example, there are even further advantages in the livestock industry such as the swine industry or farmed aquatic invertebrates or in any other situations in which there is a high level of consolidation.

Further advances in quick production of such vaccines is achieved in one embodiment by producing the antigen via Replicon subunit (referred to in some instances as autogenous protein) or Replicon Particle (referred to in some instances as RNA particle) technology. Prior to using the NOI as a protective molecule or to produce a protective molecule, it must be obtained from the location of the disease outbreak (such as an individual farm or geographic region). Once that genetic information is obtained in an embodiment the

Replicon Subunit or Replicon Particle approach may be used to generate an autogenous vaccine. In sum, one approach is to generate an RNA subunit (RS) vaccine by introducing the replicon RNA that expresses the NOI into cells in culture. Once the replicon carrying the NOI has been introduced into cells each of the individual cells express the NOI. Alphavirus replicon vectors express heterologous proteins at very high levels (up to 20% of the total cell protein). The protective antigen, derived from the NOI, that is expressed in the cells is harvested by lysing them. The NOI/cell lysate then constitutes the autogenous vaccine. Another approach is to generate an RNA particle (RP) vaccine. RP are produced by introducing into cell in culture a replicon RNA that expresses the foreign gene and two helper RNAs, one that codes for the alphavirus capsid protein and the other that codes for the alphavirus glycoproteins (E2 and El). These RNAs can be introduced into cells using a number of methods such as lipid transfection or electroporation. After the three RNAs have been introduced into cells the replicon RNA replicates itself in-cis and the helper RNAs in- trans. The helper RNAs produce the structural proteins which recognize the replicon RNA and package it into RP. RP expressing the foreign gene constitutes the autogenous vaccine.

The methods and variations of same used to produce such replicons are known to one skilled in the art. Illustrative methodology can be found at US patent 6, 156,558, incorporated herein by reference in its entirety, and also at US patents 6,521,235; 6,531,135; and US

Patents 7,442,381 ; 6,541,010; 7,045,335; and 5,792,462 all of which are incorporated herein by reference in their entirety.

Alphavirus vectors and alphavirus replicon particles are used in embodiments of the invention. The term "alphavirus" has its conventional meaning in the art, and includes the various species of alphaviruses which are members of the Togaviridae family. This includes alphaviruses such as Eastern Equine Encephalitis virus (EEE), Venezuelan Equine

Encephalitis virus (VEE), Everglades virus, Mucambo virus, Pixuna virus, Western Equine Encephalitis virus (WEE), Sindbis virus, South African Arbovirus No. 86, Semliki Forest virus, Middelburg virus, Chikungunya virus, O'nyong-nyong virus, Ross River virus, Barmah Forest virus, Getah virus, Sagiyama virus, Bebaru virus, Mayaro virus, Una virus, Aura virus, Whataroa virus, Babanki virus, Kyzylagach virus, Highlands J virus, Fort Morgan virus, Ndumu virus, and Buggy Creek virus. The viral genome is a single-stranded, messenger- sense RNA, modified at the 5'-end with a methylated cap, and at the 3'-end with a variable- length poly (A) tract. Structural subunits containing a single viral protein, C, associate with the RNA genome in an icosahedral nucleocapsid. In the virion, the capsid is surrounded by a lipid envelope covered with a regular array of transmembranal protein spikes, each of which consists of a heterodimeric complex of two glycoproteins, El and E2. See Pedersen et al., J. Virol. 14:40 (1974). The Sindbis and Semliki Forest viruses are considered the prototypical alphaviruses, and have been studied extensively. See Schlesinger The Togaviridae and Flaviviridae, Plenum Publishing Corp., New York (1986). The VEE virus has also been studied. See U.S. Pat. No. 5,185,440 to Davis et al.

As the above patents illustrate, preparation of replicon subunits by using alphavirus replicon vectors to obtain polypeptides and using alphavirus replicon particles to produce protective molecules are processes known to one skilled in the art. There are many modifications to the process available, and any process using a replicon subunit or replicon particle methodology can be used with the invention. In a certain embodiment an alphavirus replicon RNA vector that expresses the gene of interest in a host cell and the expressed product is harvested. In another embodiment a replicon RNA comprising the gene of interest is introduced into a cell along with two helper RNAs coding for the alphavirus capsid protein and for the glycoproteins. The replicon RNA is packaged into a Replicon Particle. This Replicon Particle can be the protective molecule.

Thus the system in one embodiment provides for infectious, defective, alphavirus particles, wherein each particle comprises an alphavirus replicon RNA, and wherein the replicon RNA comprises an alphavirus packaging signal, one or more heterologous RNA sequence(s), and a sequence encoding at least one alphavirus structural protein, and wherein the replicon RNA furthermore lacks a sequence encoding at least one alphavirus structural protein; wherein the population contains no detectable replication-competent alphavirus particles as determined by passage on permissive cells in culture. For example, in US patent 6,531,135, incorporated herein by reference in its entirety is shown in an embodiment an RP system which uses a helper cell for expressing an infectious, replication defective, alphavirus particle in an alphavirus-permissive cell. The helper cell includes (a) a first helper RNA encoding (i) at least one alphavirus structural protein, and (ii) not encoding at least one alphavirus structural protein; and (b) a second helper RNA separate from the first helper RNA, the second helper RNA (i) not encoding at least one alphavirus structural protein encoded by the first helper RNA, and (ii) encoding at least one alphavirus structural protein not encoded by the first helper RNA, such that all of the alphavirus structural proteins assemble together into alphavirus particles in the cell. Preferably, the alphavirus packaging segment is deleted from at least the first helper RNA.

There are many variations that are available to one skilled in the art when preparing such replicons. For example, in another embodiment described in the patent, the helper cell also includes a replicon RNA, which encodes the alphavirus packaging segment and an inserted heterologous RNA. In the embodiment wherein the helper cell also includes a replicon RNA, the alphavirus packaging segment may be, and preferably is, deleted from both the first helper RNA and the second helper RNA. For example, in the embodiment wherein the helper cell includes a replicon RNA encoding the alphavirus packaging segment and an inserted heterologous RNA, the first helper RNA includes the alphavirus El glycoprotein and the alphavirus E2 glycoprotein, and the second helper RNA includes the alphavirus capsid protein. The replicon RNA, first helper RNA, and second helper RNA in an embodiment are all on separate molecules and are cotransfected into the host cell.

In an alternative embodiment, the helper cell includes a replicon RNA encoding the alphavirus packaging segment, an inserted heterologous RNA, and the alphavirus capsid protein encoded by the second helper RNA, and the first helper RNA includes the alphavirus El glycoprotein and the alphavirus E2 glycoprotein. Thus, the replicon RNA and the first helper RNA are on separate molecules, and the replicon RNA and the second helper RNA are on a single molecule. The heterologous RNA comprises a foreign RNA.

The RNA encoding the structural proteins, i.e., the first helper RNA and the second helper RNA, may advantageously include one or more attenuating mutations. In an embodiment, at least one of the first helper RNA and the second helper RNA includes at least one attenuating mutation. The attenuating mutations provide the advantage that in the event of RNA recombination within the cell, the coming together of the structural and nonstructural genes will produce a virus of decreased virulence.

As another aspect a method of making infectious, non-living replication defective, alphavirus particles is provided. The method includes transfecting a helper cell as given above with a replication defective replicon RNA, producing the alphavirus particles in the transfected cell, and then collecting the alphavirus particles from the cell. The replicon RNA encodes the alphavirus packaging segment and a heterologous RNA. The transfected cell further includes the first helper RNA and second helper RNA as described above.

As another aspect, a set of RNAs is provided for expressing an infectious,non-living replication defective alphavirus. The set of RNAs comprises, in combination, (a) a replicon RNA encoding a promoter sequence, an inserted heterologous RNA, wherein RNA encoding at least one structural protein of the alphavirus is deleted from the replicon RNA so that the replicon RNA is replication defective, and (b) a first helper RNA separate from the replicon RNA, wherein the first helper RNA encodes in trans, the structural protein which is deleted from the replicon RNA and which may or may not include a promoter sequence. In this embodiment, it is preferred that an RNA segment encoding at least one of the structural proteins is located on an RNA other than the first helper RNA. Thus, for example, the set of RNAs may include a replicon RNA including RNA which encodes the alphavirus packaging sequence, the inserted heterologous RNA, and the alphavirus capsid protein, but both the alphavirus El glycoprotein and alphavirus E2 glycoprotein are deleted therefrom; and a first helper RNA includes RNA encoding both the alphavirus El glycoprotein and the alphavirus E2 glycoprotein.

In another embodiment, the set of RNAs also includes a second helper RNA separate from the replicon RNA and the first helper RNA. In this embodiment, the second helper RNA encodes, in trans, at least one structural protein, which is different from the structural protein encoded by the replicon RNA and by the first helper RNA. Thus, for example, the set of RNAs may include a replicon RNA including RNA which encodes the alphavirus packaging sequence, and the inserted heterologous RNA; a first helper RNA including RNA which may encode a promoter sequence and an RNA encoding both the alphavirus El glycoprotein and the alphavirus E2 glycoprotein; and a second helper RNA including RNA which encodes the alphavirus capsid protein, with the replicon RNA, the first helper RNA, and the second helper RNA being in trans from each other, on separate molecules.

As another aspect, is provided a pharmaceutical formulation comprising infectious alphavirus particles as described above, in an effective immunogenic amount in a

pharmaceutically acceptable carrier. See, for example, the Ί35 patent at column 2, line 10 - column 11 line 52 which includes examples 1-5.

The phrases "structural protein" or "alphavirus structural protein" as used herein refer to the encoded proteins which are required for production of particles that contain the replicon RNA, and include the capsid protein, El glycoprotein, and E2 glycoprotein. As described hereinabove, the structural proteins of the alphavirus are distributed among one or more helper RNAs (i.e., a first helper RNA and a second helper RNA). In addition, one or more structural proteins may be located on the same RNA molecule as the replicon RNA, provided that at least one structural protein is deleted from the replicon RNA such that the replicon and resulting alphavirus particle are replication defective. As used herein, the terms "deleted" or "deletion" mean either total deletion of the specified segment or the deletion of a sufficient portion of the specified segment to render the segment inoperative or

nonfunctional, in accordance with standard usage. See, e.g., U.S. Pat. No. 4,650,764 to Temin et al. The term "replication defective" as used herein, means that the replicon RNA cannot produce particles in the host cell in the absence of the helper RNA. That is, no additional particles can be produced in the host cell. The replicon RNA is replication defective inasmuch as the replicon RNA does not include all of the alphavirus structural proteins required for production of particles because at least one of the required structural proteins has been deleted therefrom.

The helper cell for production of the infectious, replication defective, alphavirus particle comprises a set of RNAs, as described above. The set of RNAs principally include a first helper RNA and a second helper RNA. The first helper RNA includes RNA encoding at least one alphavirus structural protein but does not encode all alphavirus structural proteins. In other words, the first helper RNA does not encode at least one alphavirus structural protein; that is, at least one alphavirus structural protein gene has been deleted from the first helper RNA. In one embodiment, the first helper RNA includes RNA encoding the alphavirus El glycoprotein, with the alphavirus capsid protein and the alphavirus E2 glycoprotein being deleted from the first helper RNA. In another embodiment, the first helper RNA includes RNA encoding the alphavirus E2 glycoprotein, with the alphavirus capsid protein and the alphavirus El glycoprotein being deleted from the first helper RNA. In a third, preferred embodiment, the first helper RNA includes RNA encoding the alphavirus El glycoprotein and the alphavirus E2 glycoprotein, with the alphavirus capsid protein being deleted from the first helper RNA.

The second helper RNA includes RNA encoding the capsid protein which is different from the structural proteins encoded by the first helper RNA. In the embodiment wherein the first helper RNA includes RNA encoding only the alphavirus El glycoprotein, the second helper RNA may include RNA encoding one or both of the alphavirus capsid protein and the alphavirus E2 glycoprotein which are deleted from the first helper RNA. In the embodiment wherein, the first helper RNA includes RNA encoding only the alphavirus E2 glycoprotein, the second helper RNA may include RNA encoding one or both of the alphavirus capsid protein and the alphavirus El glycoprotein which are deleted from the first helper RNA. In the embodiment wherein the first helper RNA includes RNA encoding both the alphavirus El glycoprotein and the alphavirus E2 glycoprotein, the second helper RNA may include RNA encoding the alphavirus capsid protein which is deleted from the first helper RNA.

In one embodiment, the packaging segment or "encapsidation sequence" is deleted from at least the first helper RNA. In a preferred embodiment, the packaging segment is deleted from both the first helper RNA and the second helper RNA.

In an embodiment wherein the packaging segment is deleted from both the first helper RNA and the second helper RNA, preferably the helper cell contains a replicon RNA in addition to the first helper RNA and the second helper RNA. The replicon RNA encodes the packaging segment and an inserted heterologous RNA. The inserted heterologous RNA may be RNA encoding a protein or a peptide. The inserted heterologous RNA may encode a protein or a peptide which is desirously expressed by the host, alphavirus-permissive cell, and includes the promoter and regulatory segments necessary for the expression of that protein or peptide in that cell.

For example, in one preferred embodiment of the present invention, the helper cell includes a set of RNAs which include (a) a replicon RNA including RNA encoding an alphavirus packaging sequence and an inserted heterologous RNA, (b) a first helper RNA including RNA encoding the alphavirus El glycoprotein and the alphavirus E2 glycoprotein, and (c) a second helper RNA including RNA encoding the alphavirus capsid protein so that the alphavirus El glycoprotein, the alphavirus E2 glycoprotein and the capsid protein assemble together into alphavirus particles in the host cell.

In an alternate embodiment, the replicon RNA and the first helper RNA are on separate molecules, and the replicon RNA and the second helper RNA are on a single molecule together, such that a first molecule, i.e., the first helper RNA, including RNA encoding at least one but not all of the required alphavirus structural proteins, and a second molecule, i.e., the replicon RNA and second helper RNA, including RNA encoding the packaging segment, the inserted heterologous DNA and the capsid protein. Thus, the capsid protein is encoded by the second helper RNA, but the second helper RNA is located on the second-molecule together with the replicon RNA. For example, in one preferred embodiment of the present invention, the helper cell includes a set of RNAs including (a) a replicon RNA including RNA encoding an alphavirus packaging sequence, an inserted heterologous RNA, and an alphavirus capsid protein, and (b) a first helper RNA including RNA encoding the alphavirus El glycoprotein and the alphavirus E2 glycoprotein so that the alphavirus El glycoprotein, the alphavirus E2 glycoprotein and the capsid protein assemble together into alphavirus particles in the host cell.

In one embodiment of the present invention, the RNA encoding the alphavirus structural proteins, i.e., the capsid, El glycoprotein and E2 glycoprotein, contains at least one attenuating mutation. The phrases "attenuating mutation" and "attenuating amino acid," as used herein, mean a nucleotide mutation or an amino acid coded for in view of such a mutation which result in a decreased probability of causing disease in its host (i.e., a loss of virulence), in accordance with standard terminology in the art, See, e.g., B. Davis, et al., Microbiology 132 (3d ed. 1980), whether the mutation be a substitution mutation or an in- frame deletion mutation. The phrase "attenuating mutation" excludes mutations which would be lethal to the virus. Thus, according to this embodiment, at least one of the first helper RNA and the second helper RNA includes at least one attenuating mutation. In a more preferred embodiment, at least one of the first helper RNA and the second helper RNA includes at least two, or multiple, attenuating mutations. The multiple attenuating mutations may be positioned in either the first helper RNA or in the second helper RNA, or they may be distributed randomly with one or more attenuating mutations being positioned in the first helper RNA and one or more attenuating mutations positioned in the second helper RNA. Appropriate attenuating mutations will be dependent upon the alphavirus used. For example, when the alphavirus is VEE, suitable attenuating mutations may be selected from the group consisting of codons at E2 amino acid position 76 which specify an attenuating amino acid, preferably lysine, arginine, or histidine as E2 amino acid 76; codons at E2 amino acid position 120 which specify an attenuating amino acid, preferably lysine as E2 amino acid 120; codons at E2 amino acid position 209 which specify an attenuating amino acid, preferably lysine, arginine, or histidine as E2 amino acid 209; codons at El amino acid 272 which specify an attenuating mutation, preferably threonine or serine as El amino acid 272; codons at El amino acid 81 which specify an attenuating mutation, preferably isoleucine or leucine as El amino acid 81 ; and codons at El amino acid 253 which specify an attenuating mutation, preferably serine or threoinine as El amino acid 253.

In an alternate embodiment, wherein the alphavirus is the South African Arbovirus No. 86 (S.A.AR86), suitable attenuating mutations may be selected from the group consisting of codons at nsPl amino acid position 538 which specify an attenuating amino acid, preferably isoleucine as nsPl amino acid 538; codons at E2 amino acid position 304 which specify an attenuating amino acid, preferably threonine as E2 amino acid 304; codons at E2 amino acid position 314 which specify an attenuating amino acid, preferably lysine as E2 amino acid 314; codons at E2 amino acid position 376 which specify an attenuating amino acid, preferably alanine as E2 amino acid 376; codons at E2 amino acid position 372 which specify an attenuating amino acid, preferably leucine as E2 amino acid 372; codons at nsP2 amino acid position 96 which specify an attenuating amino acid, preferably glycine as nsP2 amino acid 96; and codons at nsP2 amino acid position 372 which specify an attenuating amino acid, preferably valine as nsP2 amino acid 372. Suitable attenuating mutations useful in embodiments wherein other alphaviruses are employed are known to those skilled in the art. Attenuating mutations may be introduced into the RNA by performing site-directed mutagenesis on the cDNA which encodes the RNA, in accordance with known procedures. See, Kunkel, Proc. Natl. Acad. Sci. USA 82:488 (1985). Alternatively, mutations may be introduced into the RNA by replacement of homologous restriction fragments in the cDNA which encodes for the RNA, in accordance with known procedures.

To develop the autogenous recombinant proteins, specific primers are used to amplify gene(s) derived from the disease agent (directly or using affected tissue or other sample) via polymerase chain reaction (PCR). The PCR products are then cloned into the pVEK expression system plasmid vector, creating a recombinant plasmid. The pVEK plasmid vectors are transcribed to create RNA. Electroporation of the purified RNA into Vero cells leads to the production of the autogenous recombinant proteins. The proteins are harvested by lysis of the electroporated cells using a nonionic detergent. A schematic of the production process may be found in Figure 1. Specific primers, derived from the disease agent, are used to create a cDNA Autogenous Donor Gene (ADG), sometimes referred to as a Gene of Interest (GOI). The ADG is then cloned into a vector, such as the pVEK plasmid vector shown here, creating a recombinant plasmid. The pVEK recombinant plasmid is then transcribed, creating RNA. The purified RNA is electroporated into Vero cells, leading to the production of autogenous recombinant proteins. The proteins are harvested by cell lysis. The vaccine itself consists of autogenous recombinant protein(s) derived from genes whose sequence(s) are obtained from diagnostic isolates. The proteins are mixed with an adjuvant.

A synthetic plasmid vector is used called pVEK. The pVEK plasmid vectors incorporate derivatives of the nonstructural genes from the attenuated Venezuelan equine encephalitis VEE virus vaccine, TC-83. The pVEK plasmid vectors have been modified for optimal donor gene expression (Kamrud, K. I., Custer, M., Dudek, J. M., Owens, G., Alterson, K. D., Lee, J. S., Groebner, J. L. & Smith, J. F. (2007). Alphavirus replicon approach to promoterless analysis of IRES elements. Virology. 360, 376-87. Epub 2006 Dec 6.). The plasmids are linearized and RNA is transcribed from the plasmid DNA with T7 Express enzyme in the presence of Cap analog (Promega, Madison, WI) and purified. The purified RNA is electroporated into Vero cells (derived from Master Cells) for translation into autogenous recombinant proteins. Neither the pVEK plasmid vector nor the transcribed RNA contain the structural, capsid, or glycoprotein genes for TC-83.

The nonstructural genes aid in the expression of the autogenous recombinant proteins by forming a complex which transcribes additional autogenous recombinant gene RNA. Nspl serves as the capping enzyme and is believed to play a major role in the binding and assembly of the complex. Nsp2 is an RNA binding protein that has NTPase activity and likely functions as a RNA helicase to unwind duplex RNA. Nsp2 also functions as a protease that is required for post-translational processing of the nonstructural polyproteins. Nsp3 is a phosphoprotein whose role has not been determined. Nsp4 has been identified as the RNA polymerase. Rayner, J. O., Dryga, S. A. & Kamrud, K. I. (2002). Alphavirus vectors and vaccination. Rev Med Virol 12, 279-96.

The pVEK vectors control protein expression at the level of translation by incorporating internal ribosome entry site (IRES) elements associated with each donor gene (Kamrud, K. I., Custer, M., Dudek, J. M., Owens, G., Alterson, K. D., Lee, J. S., Groebner, J. L. & Smith, J. F. (2007). Alphavirus replicon approach to promoterless analysis of IRES elements. Virology. 360, 376-87. Epub 2006 Dec 6.) as depicted in Figure 2. The sequence differs from the TC-83 genomic sequence by four mutations and the absence of all TC-83 structural genes. In addition, a kanamycin resistance Open Reading Frame has been inserted into the plasmid backbone as a selective marker to amplify E. coli that contain the replicon plasmid DNA. A multiple cloning site has also been inserted in place of the structural protein genes. The resulting plasmid, pVEK, is replicated in bacteria using the COLE1 origin of replication and contains a 5' untranslated region, TC-83 nonstructural protein sequences, a 26S promoter, a multiple cloning site and a 3' untranslated region, all placed downstream of a T7 polymerase promoter for in vitro RNA transcription. Figure 3 shows the pVEK plasmid vector with the autogenous donor gene insert. Typically, restriction enzymes Ascl and Pad are used to specifically digest the ADG cDNA at appropriate sites outside of the ADG prior to ligation with the pVEK plasmid vector. Figure 4 is a schematic representation of the ADG insertion into the pVEK plasmid vector. Because the electroporated RNA produce the autogenous recombinant protein in the cytoplasm without any DNA intermediate forms, the autogenous recombinant protein vaccine avoids the concerns of chromosomal integrations. As such no nuclear recombination events can occur.

In another embodiment, replicon particle (RP) vaccines are prepared. The RP vector has numerous advantages for vaccine development including accurate production of native proteins, tropism for lymphoid cells, lack of viral replication and transmission, induction of mucosal and systemic immunity, sequential immunization potential, and lack of preexisting immunity to VEE in animals although they clearly can respond to the virus immunologically. Dickerman RW, Baker GJ, Ordonez JV, cherer WF (1973), Venezuelan Equine

Encephalomyelitis Viremia and Antibody Responses of Pigs and Cattle, American Journal of Veterinary Research 34: 357-361

The replication strategy of VEE is similar to that of other alphaviruses. Strauss J, Strauss E (1994), The alphaviruses: gene expression, replication, and evolution, Microbiol Rev 58: 491- 562 From positive-sense genomic RNA, four non- structural proteins (nsPl - nsP4) are translated and function to replicate a full-length negative-sense RNA. The negative-sense RNA serves as a template for replication of additional genomic RNA, and for synthesis of a subgenomic messenger RNA (26S mRNA), produced in 10-fold molar excess compared to genomic RNA, which directs the synthesis of the VEE structural proteins. The structural proteins are translated initially as a polyprotein that is co-translationally and

post-translationally cleaved to release the capsid (C) protein and the two mature envelope glycoproteins (El and E2). Since VEE is a positive-sense RNA virus, full-length cDNA clones of VEE can be used to generate RNA transcripts that, when introduced into susceptible cells, will initiate a complete virus replication cycle and generate infectious virus. (Davis NL, Willis LV, Smith JF, Johnston RE (1989), In vitro synthesis of infectious Venezuelan equine encephalitis virus RNA from a cDNA clone: analysis of a viable deletion mutant, Virology 111 : 189-204.)

Using site-directed mutagenesis of the DNA plasmid, VEE viruses can be generated containing mutations in the envelope glycoproteins that result in attenuated phenotypes. When inoculated into animals, such attenuated variants of VEE do not cause illness or significant viremia but are able to induce protective immunity against subsequent virulent VEE challenge in mice, horses and primates. (Davis N, Powell N, Greenwald G, Willis L, Johnson B, Smith J, Johnston R (1991)) Attenuating mutations in the E2 glycoprotein gene of Venezuelan equine encephalitis virus: construction of single and multiple mutants in a full- length cDNA clone, Virology 183 : 20-31 Grieder F, Davis N, Aronson J, Charles P, Sellon D, Suzuki K, Johnston R (1995), Specific restrictions in the progression of Venezuelan equine encephalitis virus-induced disease resulting from single amino acid changes in the glycoproteins, Virology 206: 994-1006

Similarly, foreign genes can be inserted in place of the VEE structural protein gene region in the cDNA plasmid, and an RNA transcript from such a plasmid, when introduced into cells, will replicate and express the heterologous genes as shown schematically in Figures 5-6. This self-amplifying replicon RNA will direct the synthesis of large amounts of the foreign gene product within the cell, typically reaching levels of 15-20% of total cell protein. Pushko P, Parker M, Ludwig GV, Davis N, Johnston RE, Smith JF (1997),

Replicon-Helper Systems from Attenuated Venezuelan Equine Encephalitis Virus:

Expression of Heterologous Genes in vitro and Immunization against Heterologous

Pathogens in vivo, Journal of Virology 239: 389-401 Because the replicon RNA does not contain the structural genes for VEE, it is a single-cycle, propagation-defective RNA and replicates only within the cell into which it is introduced. The replicon RNA can be packaged into RP by supplying the structural protein genes of VEE in trans (Figure 5). Replicon RNA is packaged into RP when cells are co-transfected with replicon RNA and two separate helper RNAs, which together encode the full complement of VEE structural proteins. Pushko, supra. Importantly, only the replicon RNA is packaged into VRP, as the helper RNAs lack the packaging sequence required for encapsidation. Thus, the RP are propagation-defective, in that they can infect target cells in culture or in vivo, can express the foreign gene to high levels, but they lack critical portions of the VEE genome {i.e. , the VEE structural protein genes) necessary to produce virus particles which could spread to other cells. The "split helper" system greatly reduces the chance of an intact genome being regenerated by RNA-RNA recombination and, the possibility of functional recombination with helper RNAs was further reduced by removal of the 26S promoter from helper RNAs altogether (Kamrud et al 2010 Development and Characterization of

Promoterless Helper RNAs for Production of Alphavirus Replicon Particles. Journal of General Virology. 91 :pp. 1723-1727.). As an independent and additional layer of safety, attenuating mutations have been incorporated in the glycoprotein helper. (Pushko et al 1997) Journal of Virology 239:389-401. Figure 6 shows the VEE replicon particle vaccine and packaging system process. Expression of the nucleic acid molecule of interest can be varied up or down by introducing spacer elements upstream of the IRES/NOI cassette but downstream of the 26S promoter. (Kamrud et al. 2007, "Alphavirus Replicon Approach to Promoterless Analysis of IRES Elements" Virology 360(2), pp.376-387) Also, where the gene of interest produces a potentially toxic protein, introducing a phosphoramidite morpholino oligomers at the same time the replicon and helper RNAs are electroporated into cells shuts down expression. The PMO blocks translation of the gene of interest during packaging of RP.

The vaccine of the present invention would be ideal for the following reasons:

1) The new vaccines do not contain live virus. Current modified live virus (MLV)

vaccines could not be used in an eradication effort due to their ability to spread, revert to virulence, or recombine with field strains. Practices (such as "serum therapy" for

PRRSV in pigs) in which live virus on a farm is deliberately spread and used to infect naive animals will also not be part of a successful disease control and eradication program. 2) The new vaccines can differentiate infected from vaccinated animals. Current MLV and killed vaccines use the whole virus. Here the entire infective agent is not included. As an illustration, only a portion of the PRRSV is included in the RP vaccine allowing differentiation based on serology. For example, because the nucleocapsid is not part of the ARP vaccine the current IDEXX ELISA could be used to detect pigs/herds that were infected as opposed to just vaccinated.

3) The new vaccines are autogenous and can be produced quickly. Autogenous vaccines are desirable for animal disease treatment due to strain/biotype variation and lack of cross-protection. It is shown here that ARP vaccines can be produced faster (1 month and even less) than traditional autogenous vaccines (3 months) allowing for a quicker response.

In a yet further embodiment, one can optionally first determine if preparation of a new autogenous vaccine as described is more advisable by determining the antigenic drift of the pathogen. In such an embodiment, one obtains a sample comprising the microorganism as described above, and may optionally determine what biotype it is. Using influenza as an example, the subtype and cluster may be determined. In general, influenza viruses are made up of an internal ribonucleoprotein core containing a segmented single-stranded RNA genome and an outer lipoprotein envelope lined by a matrix protein. The genome of influenza viruses is composed of eight segments of linear (-) strand ribonucleic acid (RNA), encoding the immunogenic hemagglutinin (HA) and neuraminidase (NA) proteins, and six internal core polypeptides: the nucleocapsid nucleoprotein (NP); matrix proteins (M); non- structural proteins (NS); and three RNA polymerase (PA, PB1, PB2) proteins. During replication, the genomic viral RNA is transcribed into (+) strand messenger RNA and (-) strand genomic cRNA in the nucleus of the host cell. Each of the eight genomic segments is packaged into ribonucleoprotein complexes that contain, in addition to the RNA, NP and a polymerase complex (PB1, PB2, and PA). As noted, influenza is grouped into three categories, based on the absence of serologic cross reactivity between their internal proteins: influenza A, B and C. Influenza A viruses are further classified into groups by antigenic differences of hemagglutinin and neuraminidase proteins. Examples of subtypes and further classification into clusters are shown in Table 2 below. The hemagglutinin antigens of influenza viruses change frequently in antigenic specificity as a result of changes in the HA and NA amino acid sequence.

Table 2 Subtype Representative HA sequence Cluster

H3N2 A/Swine/Indiana/7688/2007 4

(H3N2)

cHlNl A/swine/Iowa/15/1930(HlNl) a

rHINI A/swine/Illinois/4661/2009 β

(H1N1)

H1N2 A/Swine/Illinois/11678/2008 Ί

(H1N2)

2009 A/Calif ornia/04/2009(H 1 N 1 ) Ί

H1N1

huHlNl A/Swine/Illinois/49271/2008 δ

huHlNl (H1N2)

In an embodiment of the invention, the antisera is obtained, and determined if it is the same biotype - in the present example if it reacts in the same manner as a standard obtained using existing vaccine. This can be measured in the case of influenza by using an hemagluttinin inhibition test as a standard, as described infra. If it reacts the same, then the existing vaccine can be used, if it does not match, then a new vaccine may be prepared. This is a means of measuring drift, that is change in the antigenic components. This is more effective than measuring shift, that is a major change to a new subtype. By measuring antigenic components, the virus may still fall within the same cluster, yet demonstrate a sufficient drift that a new vaccine would be more effective. While presented by way of example regarding an influenza virus, clearly one could apply such a process to any microorganism.

In addition to determining if an existing vaccine can be effectively utilized or if a new vaccine should be developed to provide protection after a change in the microorganism, fast and effective production of such vaccines can be further aided by ongoing monitoring in a group of animals of interest for any change in biotype, whether shift or drift, change in a nucleic acid of interest, or other change of the pathogen. Means of determining change in biotype are discussed infra. In one example comparing the antigenic response using the biological sample to known standards is determined. In another example homology of the NOI with known sequences is determined. By way of example without limitation, in an embodiment, a biological sample is obtained from the animal, and a nucleic acid sequence of the pathogenic microorganism obtained. It is amplified, where necessary, and the sequence compared with prior sequences obtained and/or with a sequence already known of the pathogen. In an embodiment, the sequence may be compared with sequences available from a database of such sequences. If the sequence is different from known sequences, this can signal that a new vaccine may need to be prepared. In another example, the antigenic response is determined, by using the sample to assess antigenic response compared to standards and known responses. Such monitoring can provide for early detection of need to prepare a new vaccine and accommodate changes in the microorganism.

The sample obtained can be any sample which may contain a sequence of the pathogenic organism. As also noted herein, the sample can come from serum, samples, nasal swabs, tissues samples and the like and from live and dead animals. A biological sample may be obtained and the sequence detected by any convenient method. In an embodiment of the invention, a cost effective, easily implemented means of ongoing monitoring can be collection of oral fluid from the animal. By way of example without limitation, in one embodiment, saliva from pigs may be obtained by providing to the pig a rope. Pigs will chew on the rope and saliva may be collected and analyzed. (See. e.g., Prickett et al. (2008) "Detection of Porcine reproductive and respiratory syndrome virus infection in porcine oral flud samples: a longitudinal study under experimental conditions" /. Vet Diagn. Invest. 20: 156.) This is one of many examples of quick and convenient methods to collect a sample which may have a pathogenic sequence. Ongoing monitoring of pathogenic organism provides a number of advantages.

In another embodiment, a vaccine can be further customized to provide an autogenous vaccine that is protective for a biotype of pathogen a group of animals is exposed to, that is developed at a speed responsive to urgency of the situation, and/or that also takes into consideration potential exposure to a biotype of a pathogen for another group of animals where the groups of animals may have contact.

By way of example, without limitation, an influenza vaccine may be prepared by obtaining a biological sample from an animal in a group of animals and either the NOI compared to known NOIs, and/or results of a hemagglutinin inhibition assay compared to known standards.

In an embodiment, the preparation of a vaccine may be based on only the NOI from the biological sample, may include the HI assay, or both. This allows for modification of vaccine development in response to the urgency of the situation. Where animals are showing signs of illness, a protective molecule based solely on the NOI from the biological sample may be quickly prepared within a week. Where the situation is less urgent, time can be taken for an HI assay to allow more selective development of a vaccine.

By way of example without limitation, when measuring antigenic response, where there is more than two antigenic units difference between a circulating strain and the current vaccine strain, the current vaccine strain is replaced with the new strain. By way of example without limitation, in measuring hemagglutinin inhibition response for influenza, where the HI assay is 320 inverse titers there is one antigenic unit difference at 160 HI titer, and two unit difference at 80 HI titers. Where the difference is two or more antigenic units, a new vaccine is created.

The following table shows HI results obtained using two different HI beta cluster isolates against the same two antiserum control samples from a Beta subtype isolated in 2009 from Farm X. The homology of the homologous isolate to the isolates A and B is 97% and 96% respectively. Isolate A had an identical HI titer to the control antiserum as the homologous beta isolate. However, the titer obtained using isolate B is >2 antigenic units, thus indicating that a vaccine prepared using the homologous beta isolate would likely not protect as effectively against isolate B. In this instance, an autogenous vaccine should be prepared from isolate B for that particular herd of animals. Where the herds would have sufficient contact, a vaccine would include the Beta subtype protective molecule as well as the Farm B obtained protective molecule.

Table 3

This allows one to even further refine the vaccine.

When delivering the vaccine to the same group of animals living together one is assured the vaccine will be effective with that group. Where another group of animals will come into sufficient contact with a group of animals or a biological sample from the animals, a further customized vaccine may be prepared.

In an embodiment, a sample is obtained from at least one animal in a first group of animals and the biotype determined, then compared with a sample from at least one animal in a second group of animals where it is anticipated there may be exposure between two groups to each other. Where there is a similar antigenic response or NOI, such that one could expect cross protection for both microorganisms, a single protective molecule may be produced based on the NOI. Where the two NOIs are dissimilar, two protective molecules may be produced, one based on one NOI, the other based on the second NOI. The protective molecules may be provided in a single vaccine, or separately administered, administered separately simultaniously or sequentially, and the manner of administration can take any convenient form.

By way of example without limitation, a customized vaccine can be produced which protects animals in a herd (commonly defined as a group of animals living together). In an example, biological samples are obtained from two herds, which are separate but expected to have exposure to the Rotavirus microorganisms due to use of a common transport area. The VP7 protein of Rotavirus and is a major glycoprotein of the outer shell. See, e.g., Sahara et al., US Patent 6,086,880. Biological samples are collected from each herd and via PCR a NOI obtained for the VP7 gene of Rotavirus C and Rovavirus B. The VP7 NOI of Rotavirus C is 97% homologous between herds I and II. The VP7 gene of Rotavirus B is 69% homologous between herds I and II. A protective molecule from the VP7 Rotavirus C NOI, and two protective molecules from each of the VP7 gene of Rotavirus B are produced. Both herds are administered all three protective molecules to provide a customized protection for the two groups.

The invention can be applied to any microorganism/pathogen that causes adverse impact in an animal and is not limited to any particular such microorganism or animal. In particular, the present invention provides for methods to immunize against, or to prevent or to reduce the symptoms caused by, infection of such an animal with a pathogenic organism. Thus when referring to a microorganism it is meant to include any such disease-causing agent, for example, a virus, bacteria, fungus, or protozoan parasite. Protection from disease is provided by the vaccine of the invention, that is, protection from all or some of the adverse impact on the animal's health. In particular, the present invention provides for methods to immunize against, or to prevent or to reduce the symptoms caused by, infection of an animal with a pathogenic organism (for example, infection by a virus, bacteria, fungus, or protozoan parasite).

The method of the present invention is useful in vertebrate animals including, but not limited to, humans, canine (e.g., dogs), feline (e.g., cats); equine (e.g., horses), bovine (e.g., cattle), ovine (e.g. sheep), caprine (e.g. goat) porcine animals (e.g., pigs) and rabbit, as well as in avians including, but not limited to, chickens, turkeys, ducks, geese, a quail, a pheasant, parrots, finches, hawks, crows and ratites (ostrich, emu, cassowary, and the like) as well as domestic fur animals such as ferrets, minks, mustilids, and fish such as fin-fish, shellfish, and other aquatic animals. Fin-fish include all vertebrate fish, which may be bony or

cartilaginous fish. Further examples of fin-fish include salmonid fish, including salmon and trout species, such as coho salmon (Oncorhynchus kisutch), brook trout (Salvelinus fontinalis), brown trout (Salmo trutta), chinook salmon (Oncorhynchus tshawytscha), masu salmon (Oncorhyncus masou), pink salmon (Oncorhynchus gorbuscha), rainbow trout (Oncorhynchus mykiss), Arctic charr (Salvelinus alpinus) and Atlantic salmon (Salmo salar). However, any other fish species susceptible to disease may benefit, such as ornamental fish species, koi, goldfish, carp, catfish, yellowtail, sea bream, sea bass, pike, halibut, haddock, tilapia, turbot, wolffish, and so on. Examples of shellfish include, but are not limited to clams, lobster, shrimp, crab and oysters. Other cultured aquatic animals include, but are not limited to eels, squid and octopi. Examples, without intending to be limiting, include Bovine Viral Diarrhea Virus (BVDV), Border Disease Virus (BDV), bovine herpes Virus 1 (BHVl), bovine respiratory syncytical virus (BRSV), bovine parainfluenza-3 virus (PI-3), adenovirus, Mycoplasma bovine, Clostridium difficile, Enterotoxic E. coli Pasteurella haemotytica, Bovine spongiform encephalopathy, Bovine Respiratory Syncytial Virus (BRSV); Foot and Mouth Disease virus (FMDV); African Swine fever virus (ASFV); Leptospirosis (e.g.

Leptospira interrogans serovar hardjo); Dictyocaulus viviparous (lungworm); Hemophilus somnus; Pasteurella haemotytica; Classical Swine Fever virus (CSFv); Porcine Parvo Virus (PPV); Pseudorabies virus; Swine Vesicular Disease virus (SVDV), porcine respiratory and reproductive syndrome virus (PRRSV), porcine circovirus 1 and 2 (PCV), Swine Influenza Virus (SIV); and Brucella, optionally subdivided in B. abortus and B. melitensis; feline herpesvirus (FHV), feline calicivirus (FCV), feline leukemia virus (FeLV), feline immunodeficiency virus (FIV), rabies virus; canine herpesvirus (CHV), canine parvovirus (CPV), canine coronavirus, Leptospira canicola, Leptospira icterohaemorragiae, Leptospira grippotyphosa, Borrelia burgdorferi, Bordetella bronchiseptica; equine arteritis virus (EAV) and equine herpesvirus (type 1 or type 4).

The invention may also be used with invertebrates, and in an embodiment is used with aquatic invertebrates. The examples provided here show use of the invention with shrimp, and it is considered to be particularly useful in protecting shrimp (as in the class Malacostraca which includes Decapods including Dendrobranchiates such as prawns and Carideans such as shrimp) from disease or disorders. However, other invertebrates and in particular aquatic invertebrates, freshwater and marine, are expected to benefit from protection from disease and disorder provided by the invention including, by way of example without limitation, crustacean (e.g. lobsters, crabs, shrimp, crayfish), mollusks (e.g., squid, clams, octopus, snails, abalone, mussels), Porifera (sponges), Cnidaria (e.g., jellyfish, sea anemones), Ctenophora, Echinodermata and aquatic worms. The invention is particularly useful in aquatic invertebrates having commercial value, and especially useful with farmed aquatic invertebrates (as opposed to those living in the wild at sea), as explained herein. As shown herein, it is possible to deliver the nucleic acid molecules and/or polypeptides or fragments thereof of the invention to the digestive tract of the animal (which can be found after administration throughout the digestive tract or a portion thereof), whether by immersion, oral delivery or the like. This greatly aids the delivery of a vaccine to the animal, as opposed to methods such as injection, and provides a practical and effective means of vaccinating the animals, especially with mass vaccination of a multitude of animals.

Clearly the invention is most useful in one embodiment where the animals are grouped in a ranch, feed yard, farm, pond or region. However, it is also useful to treat an individual animal. For examples, in the pet industry a cat or dog may be exposed to a particular biotype of a microorganism and a vaccine prepared that provides protection for the biotype affecting that animal, as well as litter mates or others exposed to the microorganism. The same would apply to humans.

The methods of the invention include means of interference with expression of a nucleic acid molecule of the disease-causing agent or nucleic acid molecule of the disease- causing agent. When referring to interference with expression, it is meant that expression of the nucleic acid molecule is inhibited, disrupted, or otherwise interfered with such that the animal is protected from the disease. In one embodiment, the method uses an antisense RNA that is complimentary to a nucleic acid molecule of the disease-causing agent (target nucleic acid molecule). Antisense RNA is RNA that is complementary to a target, usually a messenger RNA (mRNA) of a target nucleic acid molecule. By antisense is intended a sequence that is in inverse orientation to the 5'-to-3' normal orientation of the target nucleic acid molecule. When delivered into a cell, expression of the antisense RNA sequence prevents normal expression of the protein encoded by the targeted nucleic acid molecule. When referring to RNA being a complement is meant to include that the polynucleotide for use in antisense suppression may correspond to all or part of the complement of the sequence encoding the target polypeptide, all or part of the complement of the 5' and/or 3' untranslated region of the target polypeptide transcript, or all or part of the complement of both the coding sequence and the untranslated regions of a transcript encoding the target polypeptide. A complementary nucleic acid molecule is that which is complementary to an mRNA transcript of all or part of a target nucleic acid molecule. In addition, the antisense polynucleotide may be fully complementary (i.e., 100% identical to the complement of the target sequence) or partially complementary (i.e., less than 100% identical to the complement of the target sequence) to the target sequence. Antisense suppression may be used to inhibit the expression of multiple proteins in the same cell. Furthermore, portions of the antisense nucleotides may be used to disrupt the expression of the target nucleic acid

molecule. Generally, antisense sequences of at least 10 nucleotides, 20 nucleotides, 50 nucleotides, 100 nucleotides, 200 nucleotides, 300, 500, 550, 500, 550, or greater and any amount in-between may be used. The sequence may be complementary to any sequence of the messenger RNA, that is, it may be proximal to the 5'-terminus or capping site, downstream from the capping site, between the capping site and the initiation codon and may cover all or only a portion of the non-coding region, may bridge the non-coding and coding region, be complementary to all or part of the coding region, complementary to the 3'- terminus of the coding region, or complementary to the 3 '-untranslated region of the mRNA. The antisense sequence may be complementary to a unique sequence or a repeated sequence, so as to enhance the probability of binding. Thus, the antisense sequence may be involved with the binding of a unique sequence, a single unit of a repetitive sequence or of a plurality of units of a repetitive sequence. Methods of preparing antisense nucleic acid molecules are known. See, e.g. Shewmaker et al, US Patent No. 5,759,829 incorporated herein by reference.

In another embodiment of the invention, RNA interference is used and in a preferred embodiment double-stranded RNA molecules (dsRNA) are employed. In this process, in summary, RNA which is double stranded, in part, or completely, is produced based upon the sequence of the target nucleic acid molecule. Specifics of the means of producing the dsRNA may vary as one skilled in the art appreciates, and include, by way of example without intending to be limiting, the approach of Graham et al., US Patent No. 6,573,099 where two copies of a sequence corresponding to a target sequence is used, or that of Fire et al., US Patent 6,326,193 (both incorporated herein by reference), where the first strand is an RNA sequence corresponding to the target nucleic acid, and the second is one which is

complementary to the target sequence, each of which are incorporated herein by reference in their entirety. These strands hybridize with each other to form the inhibiting dsRNA. The strand which corresponds to the target nucleic acid molecule can correspond to all or a portion thereof, so long as a dsRNA is formed. Where a strand is used which is the complement (antisense) of the target nucleic acid is used, it can be complementary to all or a portion of the target nucleic acid molecule, so long as the dsRNA formed interferes with the target nucleic acid molecule. The dsRNA triggers a response in which the RNAse III Dicer enzyme process dsRNA into small interfering RNAs (siRNA) of approximately 21 - 23 nucleotides, which are formed into a RNA-induced silencing complex RISC which destroys homologous mRNAs. (See, Hammond, S. M., et al., Nature (2000) 404:293-296). When referring to a target nucleic acid molecule it is meant a nucleic acid molecule or fragment thereof of the disease agent, the expression of which is interfered with. Generally, sequences of at least 10 nucleotides 20 nucleotides, 30 nucleotides, 40 nucleotides, 50 nucleotides, 100 nucleotides, 200 nucleotides, 300, 500, 550, 500, 550, or greater and any amount in-between may be used.

The inventors have shown examples of dsRNA sequences that can be used in the invention, and have discovered that fragments of such dsRNA can be used to provide a protective response. For example, dsRNA#3 that interferes with IMNV and provides a protective response is a 380 base pair sequence. However, fragments of the dsRNA provide a protective response. Thus when referring to dsRNA of the invention, fragments of the dsRNA that provide such a protective response are included.

As discussed below, the inventors have also demonstrated that a nucleic acid molecule encoding a polypeptide or fragment thereof of the disease-causing agent may be administered to the animal and a protective response observed.

Once that genetic information is obtained, a nucleic acid molecule or an antisense or dsRNA of such target nucleic acid molecule is provided as a vaccine.

In one embodiment, the "naked" nucleic acid molecules or naked dsRNA or antisense molecule may be administered to the animal, that is the dsRNA or antisense need not be provided in a conventional expression cassette or vector. Such a molecule may be produced by any convenient method, such as primer amplification and reverse transcription such as is described below.

In another embodiment, the protective molecule may be delivered by an expression cassette or vector which may optionally include other components. In a further embodiment, the protective molecule may be delivered by Replicon Particle. In yet another embodiment, delivery of the vaccine to the digestive tract of the animal provides protection.

In one embodiment the vaccine of the invention comprises the protective molecule. In another embodiment the vaccine is made by producing the dsRNA which can then be introduced directly into the animal cell, or placed in a vector or expression cassette and introduced into the cell. The inventors have discovered that the dsRNA can be introduced directly into the cell and a protective response is produced. The dsRNA could be delivered by a DNA vector that then produces the dsRNA from a promoter that is recognized by some cellular DNA-dependant RNA polymerase. In another embodiment, Replicon Particle technology may be employed in producing the vaccine. Where the antisense RNA is used as a vaccine, without wishing to be bound by any theory, it is believed it then forms a dsRNA in the cell into which it is introduced.

Prior to introducing the protective molecule, one identifies a nucleic acid sequence in the disease-causing agent which is to be expressed or inhibited (target nucleic acid molecule or target gene). The protective molecules may either express, inhibit, or compete for binding sites with any such target nucleic acid molecule which, when administered, results in protection to the animal from the disease causing agent. Any such protective molecule may be employed in the invention.

As used herein, the terms nucleic acid or polynucleotide refer to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double- stranded form. The protective sequence used to make the vaccine may be the same sequence obtained from the sample, or can refer to a sequence synthetically produced based upon the sequence obtained from the sample. As such, the terms include RNA and DNA, which can be a gene or a portion thereof, a cDNA, a synthetic polydeoxyribonucleic acid sequence, or the like, and can be single- stranded or double- stranded, as well as a DNA/RNA hybrid. Furthermore, the terms are used herein to include naturally-occurring nucleic acid molecules, which can be isolated from a cell, as well as synthetic molecules, which can be prepared, for example, by methods of chemical synthesis or by enzymatic methods such as by the polymerase chain reaction (PCR). Unless specifically limited, the terms encompass nucleic acids containing known analogues of natural nucleotides that have similar binding properties as the reference nucleic acid and are metabolized in a manner similar to naturally occurring nucleotides. Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g. degenerate codon substitutions) and complementary sequences as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al. (1991) Nucleic Acid Res. 19:5081 ; Ohtsuka et al. (1985) J. Biol. Chem. 260:2605-2608; Cassol et al. (1992); Rossolini et al. (1994) Mol. Cell. Probes 8:91-98). The term nucleic acid is used interchangeably with gene, cDNA, and mRNA encoded by a gene.

As used herein, a "polypeptide" refers generally to peptides and proteins. In certain embodiments the polypeptide may be at least two, three, four, five, six, seven, eight, nine or ten or more amino acids or more or any amount in-between. A peptide is generally considered to be more than fifty amino acids. The terms "fragment," "derivative" and "homologue" when referring to the polypeptides according to the present invention, means a polypeptide which retains essentially the same biological function or activity as said polypeptide, that is, act as an antigen and/or provide treatment for and/or protection against disease. Such fragments, derivatives and homologues can be chosen based on the ability to retain one or more of the biological activities of the polypeptide, that is, act as an antigen and/or provide treatment for and/or protection against the pathogen. The polypeptide vaccines of the present invention may be recombinant polypeptides, natural polypeptides or synthetic polypeptides, preferably recombinant polypeptides. One skilled in the art appreciates that it is possible that the protective polypeptide may be expressed by the gene in the host cells, lysed, and the polypeptide itself is used with the vaccine. Or, the nucleic acid molecule of interest or replicon particles may be used in the vaccine.

Thus when referring to a protective molecule is meant a nucleic acid molecule, polypeptide or fragment thereof, which when administered to the animal produces a protective response to the microorganism. Such protective molecule is produced by the autogenous methods described. A protective molecule, then may be the gene of interest found in the microorganism, whether obtained directly or produced (as synthetically) from the nucleic acid molecule of interest; the polypeptide it produces; interfering RNA derived using the nucleic acid molecule of interest; a nucleic acid molecule which produces the interfering RNA; the replicon particles which comprise or produce any of the above; or a combination of any of these which comprises the vaccine. The animal may or may not produce antibodies in response, but the animal will have decreased morbidity or mortality resulting from administration of the vaccine, and as described further herein.

Examples are provided here of valuable autogenously produced vaccines in which a portion of the gene of interest of a pathogenic microorganism is used to produce a biotype specific vaccine. One such example is a vaccine for Porcine Reproductive Syndrome Virus (PRRSV). The genome of PRRSV is 15 kb in length and contains genes encoding the RNA dependent RNA polymerase (ORFla and ORFlb) and genes encoding structural proteins (ORFs 2 to 7). ORF5 encodes the major envelope glycoprotein, designated GP5. The ORFs 2, 3, and 4 encode glycoproteins designated GP2, GP3, and GP4, respectively. These glycoproteins are less abundantly present in purified virions of the Lelystad virus isolate of PRRSV. The GP5 protein is approximately 200 amino acids in length and is 25 kDa in molecular weight and forms a di-sulfide-linked heterodimer with the matrix protein M encoded by ORF6 in the ER. The M protein is approximately 190 amino acids in length, is 19 kDa and is non-glycosylated. The nucleocapsid protein N is encoded by ORF7. The analysis of the genome sequence of PRRSV isolates from Europe and North America, and their reactivity with monoclonal antibodies has proven that they represent two different antigenic types. The isolates from these continents are genetically distinct and must have diverged from a common ancestor relatively long ago.

An example of one such effective polypeptide and sequences encoding same, is described at US Patent 7,622,254 to Harris et al., which is incorporated herein by reference in its entirety. There a protective antigenic determinant (PAD) is described for porcine reproductive and respiratory syndrome virus (PRRSV) that provides treatment for and protection against PRRSV infection. There it was identified that glycoprotein 5 (GP5), matrix (M) protein, or a heterodimer of the GP5 and M protein of PRRSV linked by a disulfide bond gives rise to a PAD that provides protection against PRRSV infections. The disulfide bond connecting the M protein with the GP5 protein results from a cysteine amino acid of the M protein at position 9 in North American and at position 8 EU PRRSV strains and a cysteine amino acid of the GP5 protein located at position 48 of North American PRRSV strains and position 50 of European PRRSV strains. Further shown was one or more isolated

polypeptides comprising an antigenic sequence comprising glycoprotein 5 (GP5) of porcine reproductive and respiratory syndrome virus (PRRSV), wherein the GP5 protein has varying N-glycosylation patterns of asparagine amino acids located at positions 1 -44 of the GP5 protein in North American PRRSV strains or at positions 1-46 of the GP5 protein in

European PRRSV strains. In yet another embodiment, is described an isolated polypeptide comprising an antigenic sequence comprising matrix (M) protein of porcine reproductive and respiratory syndrome virus (PRRSV). A further embodiment showed the antigenic sequence includes the GP5 sequence and a matrix protein (M protein) of PRRSV, wherein the GP5 protein is linked to said M protein by a disulfide bond, resulting from a cysteine amino acid of the M protein at position 9 in North American and at position 8 in EU PRRSV strains and a cysteine amino acid located at position 48 of the GP5 protein in North American PRRSV strains or from a cysteine amino acid located at position 50 in European PRRSV strains so that a GP5-M heterodimer is produced. In one aspect of the invention, the PAD includes a GP5-M heterodimer comprising the ectodomain of GP5 and the ectodomain of M. Methods for generating antibodies were demonstrated against one or more protective antigenic determinant (PAD) of PRRSV, for preparing a vaccine against at least one PAD of PRRSV, of vaccinating pigs, for preventing or treating a PRRSV infection in a pig, and for detecting antibodies against at least one protective antigenic determinant (PAD) of PRRSV in an animal.

Here, co-expression of PRRSV GP5-M proteins can in an embodiment be used to produce effective vaccines for PRRS using the methods described of producing an autogenous vaccine. The American Association of Swine Veterinarians (AASV) has recently made position statement for eradication of PRRSV from the U.S. which will likely not be possible without a safe, efficacious vaccine that also allows one to distinguish between vaccinated and infected animals. Replicon particle (RP) is an example of one effective method of this co-expression. Use of a MLV PRRSV vaccine poses the risks of reversion to virulence and recombination with field viruses and thus is not compatible with an eradication program. Traditional killed autogenous vaccines for PRRSV are also available. However these vaccines can take up to 3 months to prepare and because they contain the whole virus are not compatible with differential diagnostic tests. The RP provides numerous additional advantages over traditional vaccines including: inability to replicate and induce disease; induction of both cellular and humoral immunity; new field strains can be incorporated into vaccines quickly; potential for sequential immunization; and being effective in the presence of maternal antibody interference.

The inventors have shown feasibility of the ARP vaccine approach and validate that this method of autogenous vaccine production is safe and efficacious against PRRSV.

In another embodiment, a polypeptide of influenza virus provides protection from that disease. Thus any protective molecule, including a polypeptide, protective fragment, or nucleic acid sequence encoding same or interfering RNA found useful in producing a protective affect in animals may be isolated and used in the process of the invention. The genome of influenza viruses is composed of eight segments of linear (-) strand ribonucleic acid (RNA), encoding the immunogenic hemagglutinin (HA) and neuraminidase (NA) proteins, and six internal core polypeptides: the nucleocapsid nucleoprotein (NP); matrix proteins (M); non- structural proteins (NS); and three RNA polymerase (PA, PB1, PB2) proteins. During replication, the genomic viral RNA is transcribed into (+) strand messenger RNA and (-) strand genomic cRNA in the nucleus of the host cell (e.g., animal cell, bacterial, insect, yeast, plant fungal or whatever is convenient). Each of the eight genomic segments is packaged into ribonucleoprotein complexes that contain, in addition to the RNA, NP and a polymerase complex (PB 1, PB2, and PA). Many examples are known and will be identified by one skilled in the art of isolates from the influenza virus that are useful in producing a protective response in an animal. One of the many examples are the hemagglutinin and nucleoprotein polypeptide encoding nucleic acid molecules of Luke et al, US Patent 7,537,768. In examples shown below, HA encoding nucleotide sequences were used to provide protection to exposed animals. Use of Replicon Particle to express a human HA gene from H3N2 strain is described at Erdman et al., (2010) Vaccine 28:594-596. Using an alphavirus replicon plasmid containing the HA gene from A/Wyoming/2/2003 (H3N2) strain was constructed and pigs immunized. A robust hemagglutinin antibody response was induced in pigs receiving the RPs.

The invention is particularly useful in protecting shrimp from disease, as there is a need for vaccines for shrimp, in particular farmed shrimp. Disclosed here and at a US Patent application "Methods and compositions to protect aquatic invertebrates from disease" USSN13/277,066, US Publication No. 20120108649, and which claims priority to USSN 61/418,433, filed December 1, 2001 ; USSN 61/449,940 filed March 7, 2011 ; USSN

61/484,255 filed May 10, 2011 ; USSN 61/508,172 filed July 15, 2011 ; and USSN 61/525,332 filed August 19, 2011 is a description of using NOIs, dsRNA and antisense to protect disease from pathogenic microorganisms. The contents of each are incorporated herein by reference in their entirety. Also described and as shown in the examples below is an autogenous source of such a NOI and protective molecule.

Without intending to be limiting, examples of disease causing agents in aquatic invertebrates include Picornavirales viruses such as Marnavirdae, and Dicistroviridae, Caliciviridae such as San Miguel sea lion viruses (SMSV) which can infect invertebrates, Nodaviridae such as Penaeus vannamei Nodaviridae (PvNV) affecting shrimp, Iridovirus affecting shrimp and prawns, Ronivirdae such as Yellow Head Virus (YHV) affecting shrimp, prawns and krill, Bunyaviridae viruses, such as Mourilyan virus (MoV) impacting shrimp, Birnaviridae (such as Infectious Pancreatic Necrosis Virus (IPNV) which can impact oysters), icosahedral virus causing Oyster velar virus disease (OVVD), Nocardia sp.

bacterium infecting oysters and causing nocardiosis, Vibrio anguilarum, V. alginolyticus and V. tubiashii infecting bivalves, Aeromonas hydrophila infecting snails, Rickettsiae,

Chlamydiae and Mycoplasmis infecting bivalve molluscs, Leucothrix mucor infecting clams, Haliphthoros milfordensis infecting oyster drill, Leptolegnia or Leptoleginella marina infecting clams, Perkinsus marinus meront and Perkinsus atlanticus infecting molluscs, Haplosporidium sp., Bonamia sp. and Minchinia sp. infecting molluscs, Thraustochytrid infecting squid, nudibranch and octopus, and Perkinsus quqwadi affecting scallop. Examples of such disease causing agents in shrimp include White Spot Syndrome Virus (WSSV) Taura Syndrome Virus (TSV), Infectious Myonecrosis Virus (IMNV), Infectious hypodermal and hematopoietic necrosis virus (IHHNV) or Penaeus stylirostris densovirus (PstDV),

Baculovirus of penaeid shrimp (BP), Rhabdovirus of penaeid shrimp (RPS), Gill-associated virus (GAV), Yellow head virus (YHV), Lymphoid organ-associated virus (LOW), Lymphoidal parvolike viral disease (LPV), hepatopancreatic parvo-like virus (HPV) or Penaeus monodon densovirus (PMDV), Baculoviral midgut gland necrosis virus (BMN), Monodon baculovirus (MBV) Reo like virus diseases (REO), Rhabdovirus (RPS),

Macrobrachium rosenbergii nodavirus (MrNV), Laem-Singh virus (LSNV), Mourlyan virus (MoV), Vibrio vulnificus Vibro parahaemolyticus, Vibrio anguillarinum, Vibrio penaeicida, Necrotizing Hepatopancreatitis Bacterium (NHPB), Vibrio harveyi, Spiroplasma,

Mycobacterium, Streptococcus spp., Ciliates, Gregarines, Parasitic Helminths, Fusarium spp., Microsporidia, and Haplosporidia.

One such disease, for example, is White Spot Syndrome Virus (WSSV). Protein subunit vaccines to WSSV envelope proteins have been shown to be effective at conferring protection to WSSV infection in both shrimp and crayfish. WSSV contains 4 major envelope proteins with no known homology to other virus proteins; these include VP28, VP26, VP24, and VP19. VP28 is present on the outer membrane and is involved in cellular entry.

(McClennen, C. White Spot Syndrome Virus, The Economic, Environmental and Technical Implications on the Development of Latin American Shrimp Farming. Master of Arts in Law and Diplomacy Thesis . 2004, http://fletcher.tufts.edu.) VP28 antisera has been shown to neutralize virus in vivo (McClennen, supra.) Recent studies have demonstrated that these four major envelope proteins bind to form a complex via several pairwise protein interactions and one self-association (VP28). (Zhou, Q., Xu, L., Li, H., Qi, Y.-P., Yang, F., 2009. Four Major Envelope Proteins of White Spot Syndrome Virus Bind To Form A Complex. Journal of Virology 83, 4709-4712.)

Infectious myonecrosis virus (IMNV) is another problematic disease in shrimp and is a non-enveloped, small (40 nm) icosohedral, monosegmented, dsRNA virus, and is a member of the Totiviridae. (Poulos, B. T., Tang, K. F. J., Pantoja, C. R., Bonami, J. R., Lightner, D. V., 2006. Purification and characterization of infectious myonecrosis virus of penaeid shrimp. Journal of General Virology 87, 987-996.)

The IMNV genome contains two open reading frames (ORFs). The IMNV genome is disclosed in Nibert et al, (2007) Journal of General Virology 88: 1315-1318 and at GenBank accession Number AY570982 by Poulos et al. (2006) and also at GenBank accession Number EF061744 by Senapin et al. (2007). The two GenBank sequences differ by one nucleotide, where the Poulos et al. sequence is 7560 bp and the Senapin et al. sequence has an additional nucleotide insertion of adenine and is 7561 bp in length. The sequence of Poulos et al. is shown in SEQ ID NO: 66 and of Senapin at SEQ ID NO: 67. The sequence of Senapin contains a single nucleotide insertion of adenine at bp 7431 of the genomic sequence. The polypeptide encoded by the ORF1 sequence of Poulous et al. sequence is shown at SEQ ID NO: 68, and the polypeptide encoded by the ORF1 sequence of Senapin is shown at SEQ ID NO: 69. The polypeptide encoded by the Poulous et al. ORF2 sequence is shown at SEQ ID NO: 70 (GenBank No. AAT67231.1) and that encoded by the Senapin et al. sequence is shown at SEQ ID NO: 71 (GenBank ABN05325.1). This area of difference was not targeted in the work here. The ORF1 encodes the major capsid protein (nucleotides 136-4953 of SEQ ID NO: 66 or 67 and identified as SEQ ID NO: 72) and ORF2 (nucleotides 5241-7451 , SEQ ID NO: 73) encodes a 736 amino acid RNA dependent RNA polymerase (RdRp) (Poulos et al., 2006, supra; see also Nibert, 2007, supra.) ORF1 encodes a 179 kDa protein (1605 amino acids) including the N-terminal sequence of the major capsid protein. The capsid is isometric with a diameter of approximately 400 angstroms. Recent studies of the IMNV genome have revealed a "2A-like" cleavage and "shifty heptamer" that may contribute to a capsid protein- RdRp fusion protein as well as three cleavage proteins of ORF 1. These have been described as "Peptide 1," "Peptide 2," and "Peptide 3." There remains some speculation as to the role of these proteins. "Peptide 1" spanning bases 136-415 (SEQ ID NO: 74, is a 10 kDa, 93 amino acid region at the N-terminus of ORF 1, shares sequence similarities with known dsRNA binding proteins, and may be involved in host immune suppression. (Tang et al., 2008 Infectious myonecrosis virus has a totivirus-like 120-subunit capsid, but with fiber complexes at the fivefold axes. PNAS 105: 17526-17531.) "Pep2" a 32 kDa, 284 aa product, spanning bases 415-1266 (SEQ ID NO: 75) and "Pep3" a 38 kDa, 327 aa product, spanning 1267-2247 (SEQ ID NO: 76), together represent the first 704 amino acids of ORFl, have been speculated to be candidate minor proteins visualized on denaturing gels, however this remains speculative in nature (Tang, et al., 2008, supra).

Three target regions, spanning the length of the viral genome, were selected as initial targets for dsRNA generation. See Figure 7, a diagram of the IMNV genome transcription and translation products (modified from Nilbert (2007) supra) showing regions targeted for RNAi. Predicted protein products are indicated by dark gray lines (Peptides 1-3) or gray shading (major capsid protein and RNA-dependent RNA polymerase). Target regions for dsRNA production are indicated as thick black lines with corresponding nucleotide regions. Longer length dsRNAs that were generated to the region encoding Peptide 1 (136- 415) and 2 (415-1266) included two iterations truncated by -100 bp on either side (SEQ ID 2 and SEQ ID 3). Shorter dsRNAs generated within the Peptide 1 encoding region are magnified (bottom left)

The first were sequences corresponding to the N-terminal region of ORFl frame 1, predicted to contain two co-translationally cleaved products, spanning Peptide 1 and 2 (dsRNA95-474, here SEQ ID NO: 1). In addition portions of the major capsid protein (MCP) (dsRNA3764-4805, here SEQ ID NO: 4) and RNA dependent RNA polymerase (RdRp) dsRNA5518-6388 (here SEQ ID NO: 5) were selected for dsRNA generation. Peptide 1 (93 aa) and 2 (284 aa) are encoded by nucleotides 136-415 (SEQ ID NO: 74) and 415-1266 (SEQ ID NO: 75) of the IMNV genome within ORF 1 frame 1, respectively, and their functions remain uncharacterized. Peptide 1 shares sequence homology with previously described dsRNA binding proteins The major capsid protein (909 amino acids) of IMNV is encoded by nucleotides 2227-4953 (SEQ ID NO: 77) within ORF 1, frame 1. The RNA dependent RNA polymerase (736 amino acids) is encoded by nucleotides 5241-7451 (SEQ ID NO: 78) within ORF2, frame 3. A non-specific control dsRNA was designed to an exogenous sequence corresponding to enhanced green fluorescent protein (eGFP). Shorter dsRNAs were designed within the area of the IMNV genome that encodes Peptide 1 (Figure 7). Two dsRNAs were generated as 100 bp truncations from the 5' (bpl94-474, SEQ ID NO: 2) or 3' (bp95-376, SEQ ID NO: 3) end of the original dsRNA95-474 (SEQ ID NO: 1). The sequence dsRNA#3 (SEQ ID NO: 1) is a subset of a clone isolated from an IMNV virus obtained from infected shrimp, which sequence is found at SEQ ID NO: 80. Clearly one skilled in the art appreciates that when used with the RP or RS technology, any polypeptide, fragment of same, or nucleic acid sequence encoding same is useful in the process of the invention.

A "vector" is any means for the transfer of a nucleic acid into a host cell. A vector may be a replicon to which another DNA segment may be attached so as to bring about the replication of the attached segment. A "replicon" is any genetic element (e.g., plasmid, phage, cosmid, chromosome, virus) that functions as an autonomous unit of DNA or RNA replication in vivo, i.e., capable of replication under its own control. The term "vector" includes both viral and nonviral means for introducing the nucleic acid into a cell in vitro, ex vivo or in vivo. Viral vectors include alphavirus, retrovirus, adeno-associated virus, pox, baculovirus, vaccinia, herpes simplex, Epstein-Barr, rabies virus, vesicular stomatitis virus, and adenovirus vectors. Non- viral vectors include, but are not limited to plasmids, liposomes, electrically charged lipids (cytofectins), DNA- or RNA protein complexes, and biopolymers. In addition to a nucleic acid, a vector may also contain one or more regulatory regions, and/or selectable markers useful in selecting, measuring, and monitoring nucleic acid transfer results (transfer to which tissues, duration of expression, etc.).

A "cassette" refers to a segment of DNA that can be inserted into a vector at specific restriction sites. The segment of DNA encodes a polypeptide of interest or produces RNA, and the cassette and restriction sites are designed to ensure insertion of the cassette in the proper reading frame for transcription and translation.

A nucleic acid molecule is introduced into a cell when it is inserted in the cell. A cell has been "transfected" by exogenous or heterologous DNA or RNA when such DNA or RNA has been introduced inside the cell.

A cell has been "transformed" by exogenous or heterologous DNA or RNA when the transfected DNA or RNA effects a phenotypic change. The transforming DNA can be integrated (covalently linked) into chromosomal DNA making up the genome of the cell.

"Conservatively modified variants" applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given polypeptide. For instance, the codons CGU, CGC, CGA, CGG, AGA, and AGG all encode the amino acid arginine. Thus, at every position where an arginine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are "silent substitutions" or "silent variations," which are one species of "conservatively modified variations." Every polynucleotide sequence described herein which encodes a polypeptide also describes every possible silent variation, except where otherwise noted. Thus, silent substitutions are an implied feature of every nucleic acid sequence which encodes an amino acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine) can be modified to yield a functionally identical molecule by standard techniques. In some embodiments, the nucleotide sequences that encode a protective polypeptide are preferably optimized for expression in a particular host cell (e.g., yeast, mammalian, plant, fungal, and the like) used to produce the polypeptide or RNA.

As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a "conservatively modified variant" referred to herein as a "variant" where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. See, for example, Davis et al., "Basic Methods in Molecular Biology" Appleton & Lange, Norwalk, Conn. (1994). Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.

The following eight groups each contain amino acids that are conservative substitutions for one another: 1) Alanine (A), Glycine (G); 2) Aspartic acid (D), Glutamic acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R), Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V); 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W); 7) Serine (S), Threonine (T); and 8) Cysteine (C), Methionine (M) (see, e.g., Creighton, 1984, Proteins).

The isolated variant proteins can be purified from cells that naturally express it, purified from cells that have been altered to express it (recombinant), or synthesized using known protein synthesis methods. For example, a nucleic acid molecule encoding the variant polypeptide is cloned into an expression vector, the expression vector introduced into a host cell and the variant protein expressed in the host cell. The variant protein can then be isolated from the cells by an appropriate purification scheme using standard protein purification techniques. Many of these techniques are described in detail below. A protein is comprised of an amino acid sequence when the amino acid sequence is at least part of the final amino acid sequence of the protein. In such a fashion, the protein may be a the original polypeptide, a variant polypeptide and/or have additional amino acid molecules, such as amino acid residues (contiguous encoded sequence) that are naturally associated with it or heterologous amino acid residues/peptide sequences. Such a protein can have a few additional amino acid residues or can comprise several hundred or more additional amino acids.

The variant proteins used in the present invention can be attached to heterologous sequences to form chimeric or fusion proteins. Such chimeric and fusion proteins comprise a variant protein fused in-frame to a heterologous protein having an amino acid sequence not substantially homologous to the variant protein. The heterologous protein can be fused to the N-terminus or C-terminus of the variant protein.

A chimeric or fusion protein can be produced by standard recombinant DNA techniques. For example, DNA fragments coding for the different protein sequences are ligated together in-frame in accordance with conventional techniques. In another

embodiment, the fusion gene can be synthesized by conventional techniques including automated DNA synthesizers. Alternatively, PCR amplification of gene fragments can be carried out using anchor primers which give rise to complementary overhangs between two consecutive gene fragments which can subsequently be annealed and re-amplified to generate a chimeric gene sequence (see Ausubel et al., Current Protocols in Molecular Biology, 1992). Moreover, many expression vectors are commercially available that already encode a fusion moiety (e.g., a GST protein). A variant protein-encoding nucleic acid can be cloned into such an expression vector such that the fusion moiety is linked in-frame to the variant protein.

Polypeptides sometimes contain amino acids other than the 20 amino acids commonly referred to as the 20 naturally occurring amino acids. Further, many amino acids, including the terminal amino acids, may be modified by natural processes, such as processing and other post-translational modifications, or by chemical modification techniques well known in the art. Common modifications that occur naturally in polypeptides are described in basic texts, detailed monographs, and the research literature, and they are well known to those of skill in the art. Accordingly, the variant peptides of the present invention also encompass derivatives or analogs in which a substituted amino acid residue is not one encoded by the genetic code, in which a substituent group is included, in which the mature polypeptide is fused with another compound, such as a compound to increase the half-life of the polypeptide (for example, polyethylene glycol), or in which the additional amino acids are fused to the mature polypeptide, such as a leader or secretory sequence or a sequence for purification of the mature polypeptide or a pro-protein sequence.

Known modifications include, but are not limited to, acetylation, acylation, ADP- ribosylation, amidation, covalent attachment of flavin, covalent attachment of a heme moiety, covalent attachment of a nucleotide or nucleotide derivative, covalent attachment of a lipid or lipid derivative, covalent attachment of phosphotidylinositol, cross-linking, cyclization, disulfide bond formation, demethylation, formation of covalent crosslinks, formation of cystine, formation of pyroglutamate, formylation, gamma carboxylation, glycosylation, GPI anchor formation, hydroxylation, iodination, methylation, myristoylation, oxidation, proteolytic processing, phosphorylation, prenylation, racemization, selenoylation, sulfation, transfer-RNA mediated addition of amino acids to proteins such as arginylation, and ubiquitination.

The present invention further provides fragments of the variant proteins of the present invention, in addition to proteins and peptides that comprise and consist of such fragments, provided that such fragments act as an antigen and/or provide treatment for and/or protection against infections as provided by the present invention.

The phrase "biological sample" refers to a fluid or tissue of an animal that commonly contains antibodies or microorganism particles. Such components are known in the art and include, without limitation, blood, plasma, serum, spinal fluid, lymph fluid, secretions of the respiratory, intestinal or genitourinary tracts, tears, saliva, milk, white blood cells, and myelomas.

As used herein, an antibody is defined in terms consistent with that recognized within the art: they are multi-subunit proteins produced by a mammalian organism in response to an antigen challenge. The antibodies of the present invention include monoclonal antibodies and polyclonal antibodies, as well as fragments of such antibodies, including, but not limited to, Fab or F(ab')hd 2, and Fv fragments.

As used herein, the term "subunit" refers to a portion of the microorganism which provides protection and may itself be antigenic, i.e., capable of inducing an immune response in an animal. The term should be construed to include subunits which are obtained by both recombinant and biochemical methods.

As used herein, the term "isolate" refers to a virus obtained from a specific source. Isolate is used interchangeably with the term "strain".

As used herein, the term "vaccine" as used herein refers to a pharmaceutical composition comprising at least one protective molecule, that induces protective response in an animal and possibly, but not necessarily, one or more additional components that enhance the activity of said active component. A vaccine may additionally comprise further components typical to pharmaceutical compositions. In another form, the immunologically active component of a vaccine may comprise appropriate elements of said organisms (subunit vaccines) whereby these elements are generated either by destroying the whole organism or the growth cultures of such microorganisms and subsequent purification steps yielding in the desired structure(s), or by synthetic processes induced by an appropriate manipulation of a suitable system such as, but not restricted to, bacteria, insects, mammalian, or other species, plus subsequent isolation and purification procedures or by induction of said synthetic processes in the animal needing a vaccine by direct incorporation of genetic material using suitable pharmaceutical compositions (polynucleotide vaccination). A vaccine may comprise one or simultaneously more than one of the elements described above.

The terms "protecting", "protection", "protective immunity" or "protective immune response," as used herein, are intended to mean that the host animal mounts an active immune response to the vaccine or polypeptides of the present invention, such that upon exposure to disease challenge, the animal is able to combat the infection. Thus, a protective immune response will decrease the incidence of morbidity and mortality from exposure to the microorganism among a host animal. The animal will be protected from subsequent exposure to the disease-causing agent. In an embodiment, the animal may be protected by treating the animal which has already been exposed to the disease-causing agent by administration of the vaccine or polypeptide after such exposure. In such an instance there is also shown to be a lessening of morbidity and mortality. Those skilled in the art will understand that in a commercial animal setting, the production of a protective immune response may be assessed by evaluating the effects of vaccination on the herd as a whole, e.g., there may still be morbidity and mortality in a minority of vaccinated animals. Furthermore, protection also includes a lessening in severity of any gross or histopathological changes (e.g., lesions in the lung) and/or of symptoms of the influenza disease, as compared to those changes or symptoms typically caused by the isolate in similar animals which are unprotected (i.e., relative to an appropriate control). Thus, a protective immune response will decrease the symptoms of the disease, which will vary according to the disease. By way of example when referring to reduction of symptoms of influenza such measurements include but are not limited to a reduction in the clinical signs or symptoms of such coughing, sneezing, abnormal breathing, nasal and ocular discharge, mucopurulent, depression, gauntness, dehydration, gross lung and microscopic lung lesions, acute inflammation, edema, and necrosis, fever, anorexia, interstitial pneumonia, thickening of alveolar walls, hyperemia, thrombosis, hemorrhage, and necrosis, weight loss, decreased weight gain, lethargy, respiratory distress, "thumping" (forced expiration), fevers, roughened haircoats, sneezing, coughing, eye edema, conjunctivitis, gross lesions microscopic lung lesions, myocarditis, lymphadenitis, encephalitis and rhinitis compared to the control pig.

In certain instances the animal may not necessarily produce antibodies that can be measured, yet disease morbidity and/or mortality is reduced and where there also may be a reduced titer of infection upon exposure to the microorganism.

As used herein, "immunogenically effective amount" refers to an amount, which is effective in reducing, eliminating, treating, preventing or controlling the symptoms of the infections, diseases, disorders, or condition.

In one embodiment, the present invention relates to a polypeptide comprising a polypeptide or fragment thereof of microorganism. The present inventors contemplate that the polypeptide may be a homologue, a derivative, or a variant of the polypeptide, or an immunologically active or a functional fragment thereof. The polypeptide may be isolated, synthesized, or recombinantly expressed using the polypeptide-encoding nucleic acids described herein.

The present invention also provides isolated and/or recombinant nucleic acids that may encode a polypeptide or RNA of the invention. In addition, it should be understood based on the general state of the art that other equivalent sequences to the nucleotide or amino acid sequences of the polypeptides are covered by the present invention. For example, some deletions, insertions and substitutions in the amino acid sequence isolated from the microorganism or expressed by a nucleic acid sequence isolated from the microorganism are covered by the present invention, unless such mutation abolishes the ability of the polypeptide to induce the generation of a protective response.

Nucleic acids of the invention, include those that encode an entire polypeptide or produce an RNA sequence as well as those that encode a subsequence of the polypeptide or RNA or produce a fragment of an interfering RNA. For example, the invention includes nucleic acids that encode a polypeptide or RNA which is not full-length but nonetheless has protective activity against infection. The invention includes not only nucleic acids that include the nucleotide sequences as set forth herein, but also nucleic acids that are substantially identical to, correspond to, or substantially complementary to, the exemplified embodiments. For example, the invention includes nucleic acids that include a nucleotide sequence that is at least about 70% identical to one that is set forth herein, more preferably at least 75%, still more preferably at least 80%, more preferably at least 85%, 86%, 87%, 88%, 89% still more preferably at least 90%, 91%, 92%, 93%, 94%, and even more preferably at least about 95%, 96%, 97%, 98%, 99%, 100% identical (or any percentage in between) to an exemplified nucleotide sequence. The nucleotide sequence may be modified as described previously, so long as any polypeptide encoded or RNA or dsRNA produced is capable of inducing the generation of a protective response.

It is shown that dsRNA sequences produced can include truncated fragments. Such fragments can be 9 or more base pairs, can be 10 base pairs, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 72, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93,94, 95, 96, 97, 98, 99, 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000 base pairs or more or any number in-between, as long as a protective response is seen when administered to an animal. According to an embodiment of the invention, without wishing to be bound by any theory, at least nine bases are used to provide for sequence specificity such that interference with the target molecule occurs. A well-described mechanism of action for RNA interference (RNAi) is described for cellular microRNAs (miRNA) that is related to the action noted for the dsRNAs described above. The 5 '-most seven to 8 nucleotides of a miRNA (sometimes referred to as the seed sequence) are involved in Watson-Crick base pairing with nucleotides in the 3' untranslated region of the target mRNA. (Lewis, B. P., C. B. Burge, and D. P.

Bartel. 2005.) Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are miRNA targets Cell 120: 15-20.) RNA-induced silencing complex (RISC) cleaves target mRNA where base pairing is perfect, and where imperfect, the target mRNA is translationally inactive, and protein expression is impacted without degrading mRNA. (Bartel, D. P. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 116:281-97.)) It is likely that the same RISC-based activity is the mechanism by which the dsRNA described above are providing protection to animals. In a preferred embodiment, at least 20 bases are used, and in another preferred embodiment at least 30 bases are used, which further aids in transport into the cells. In another further preferred embodiment, higher efficacy is achieved with a dsRNA that is at least 50bp or more in length.

To test such fragments, a process employment AEM (antiviral effector molecule) development is one of many available methods. According to successes in AEM development for IMNV, this process generally proceeds as follows: a long target region for AEM development is determined, protection from disease measured according to survival post challenge with the established disease challenge model, shorter length dsRNAs will be assessed in standard disease bioassays (described by way of example in Example 4 below) by designing dsRNAs to progressively shorter target regions within the proven, longer length AEM.

For each target of interest, in an example, a set of PCR primers with 5' T7 promoter sequence is designed to produce ~400bp portions of the amplicon sequence AS. Amplicon sequence that is encompassed by the PCR primers are filtered by screening against the genome and transcriptome sequences to predict and minimize potential off-target effects. PCR products are generated from whole body cDNA derived from pooled larval and adult RNA. From this product, dsRNAs are produced using the Ambion Mega script in vitro transcription kit and yields 50-100 ug of high quality dsRNA per reaction. Typically, dsRNA yields of 50-100μg are achieved from a single in vitro transcription reaction. It should be noted that the entire process of generating dsRNA production, from generating gene specific primers with 5' T7 promoter sequence, to product is usually 3 days (including primer synthesis and O/N shipping). Heterologous dsRNA to eGFP is used to control for the physiologic impact of triggering a dsRNA response. This process is repeated with successively truncated regions of proven targets. Gene suppression is measured by any available method, including quantitative RT-PCR or RT-PCR, nucleic acid hybridization or Northern blotting of whole body or specific tissues RNA extracts, using primer sets that extend beyond or are completely removed from the region encompassed by the dsRNA generating primer set.

The nucleic acids can be obtained using methods that are known to those of skill in the art. Suitable nucleic acids (e.g., cDNA, genomic, or subsequences) can be cloned, or amplified by in vitro methods such as the polymerase chain reaction (PCR) using suitable primers, the ligase chain reaction (LCR), the transcription-based amplification system (TAS), or the self-sustained sequence replication system (SSR). A wide variety of cloning and in vitro amplification methodologies are well-known to persons of skill. Examples of these techniques and instructions sufficient to direct persons of skill through many cloning exercises are found in Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods in Enzymology 152 Academic Press, Inc., San Diego, Calif. (Berger); Sambrook et al. (2001) Molecular Cloning— A Laboratory Manual (Third ed.) Vol. 1-3, Cold Spring Harbor

Laboratory, Cold Spring Harbor Press, NY, (Sambrook et al.); Current Protocols in

Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1994 Supplement) (Ausubel); Cashion et al., U.S. Pat. No. 5,017,478; and Carr, European Patent No. 0,246,864. Examples of techniques sufficient to direct persons of skill through in vitro amplification methods are found in Berger, Sambrook, and Ausubel, as well as Mullis et al., (1987) U.S. Pat. No. 4,683,202; PCR Protocols A Guide to Methods and Applications (Innis et al., eds) Academic Press Inc. San Diego, Calif. (1990) (Innis); Amheim & Levinson (Oct. 1, 1990) C&EN 36-47; The Journal Of NIH Research (1991) 3: 81-94; (Kwoh et al. (1989) Proc. Natl. Acad. Sci. USA 86: 1173; Guatelli et al. (1990) Proc. Natl. Acad. Sci. USA 87, 1874; Lomell et al. (1989) /. Clin. Chem., 35: 1826; Landegren et al., (1988) Science 241 : 1077-1080; Van Brunt (1990) Biotechnology 8: 291-294; Wu and Wallace (1989) Gene 4: 560; and Barringer et al. (1990) Gene 89: 117. Improved methods of cloning in vitro amplified nucleic acids are described in Wallace et al., U.S. Pat. No. 5,426,039. Nucleic acids or subsequences of these nucleic acids, can be prepared by any suitable method as described above, including, for example, cloning and restriction of appropriate sequences.

"Codon optimization" can be used to optimize sequences for expression in an animal and is defined as modifying a nucleic acid sequence for enhanced expression in the cells of the animal of interest, e.g. swine, by replacing at least one, more than one, or a significant number, of codons of the native sequence with codons that are more frequently or most frequently used in the genes of that animal. Various species exhibit particular bias for certain codons of a particular amino acid.

In one aspect, the present invention relates to polynucleotides comprising nucleic acid fragments of codon-optimized coding regions which may produce RNA, encode

polypeptides, or fragments, variants, or derivatives thereof, with the codon usage adapted for optimized expression in the cells of a given animal. These polynucleotides are prepared by incorporating codons preferred for use in the genes of the host of interest into the DNA sequence. Also provided are constructs, vectors, and host cells comprising nucleic acid fragments of codon-optimized coding regions, and fragments, variants, or derivatives thereof, and various methods of using the polynucleotide expression constructs, vectors, host cells to treat or prevent disease in an animal.

A polypeptide, homologue, fragments or other derivatives, or variants thereof, or cells expressing it can be used in one embodiment as an antigen to produce antibodies thereto. The present invention includes, for example monoclonal and polyclonal antibodies, chimeric, single chain, as well as Fab fragments. Thus, the present invention also encompasses a method of generating antibodies directed against one or more polypeptides described above comprising providing a polypeptide of or a biologically functional homologue or derivative or variant thereof and administering the polypeptide to an animal subject in an amount sufficient to induce an immunological response to generate antibodies directed towards the polypeptide. Thus, the invention includes a method for generating antibodies by

administering to an animal the nucleic acid molecule and/or polypeptides or combinations thereof.

A nucleic acid may then be introduced into either a prokaryotic or eukaryotic host cell through the use of a vector, plasmid or construct and the like. A typical expression cassette contains a promoter operably linked to a nucleic acid. The expression cassettes are typically included on expression vectors that are introduced into suitable host cells, including for example, bacterial, insect, fungal, plant or animal cells. Either constitutive or regulated promoters can be used in the present invention. Promoters suitable for use in eukaryotic host cells are well known to those of skill in the art. The expression vectors of the invention can be transferred into the chosen host cell by methods known to those of ordinary skill in the art including, for example, calcium phosphate transfection, DEAE-dextran mediated

transfection, transvection, microinjection, cationic lipid-mediated transfection,

electroporation, transduction, scrape loading, ballistic introduction, infection or other methods. (See Molecule Cloning: A Laboratory Manual, 2d Ed. Vol. 1-3, ed. Sambrook et al., Cold Spring Harbor Laboratory Press (1989)). Transformed cells can be selected, for example, by resistance to antibiotics conferred by genes contained on the plasmids, such as the amp, gpt, neo and hyg genes.

In an example, the protective molecule may be expressed by a recombinant vector, viral vector, or virus. In another aspect, the recombinant vector, viral vector, or

microorganism expressing the protective molecule may itself serve as a vaccine component acting as a as an protective agent or an adjuvant and eliciting or enhancing the protective response. By way of example, suitable recombinant virus vectors include but are not limited to adenovirus, poxvirus, baculovirus, pseudorabies virus (PRV), Venezuelan equine encephalitis (VEE) vectors such as strains V3526 or TC-83, and viral replicon particles (VRPs) derived from VEE, equine arteritis virus (EAV), or transmissible gastroenteritis virus (TGE). The techniques employed to insert such a sequence into the viral vector and make ether alterations in the viral DNA, e.g., to insert linker sequences and the like, are known to one of skill in the art. (See, e.g., Molecular Cloning. A Laboratory Manual, supra.) The vaccine in an embodiment will not comprise a living pathogenic microorganism.

The nucleic acid molecule may be operably linked to a suitable promoter at the 5' end of the cDNA encoding a polypeptide or producing RNA and a termination signal and poly(A) signal at the 3' end of the cDNA. As used herein, the term "operably linked" means that the nucleic acid molecule containing an expression control sequence, e.g., transcription promoter and termination sequences, are situated in a vector or cell such that expression of the polypeptide or RNA produced by the nucleic acid molecule is regulated by the expression control sequence. Methods for cloning and operably linking such sequences are well known in the art. Examples of promoters suitable for expressing the antigen include but are not limited to are the cytomegalovirus immediate-early (CMV) promoter, the Rous sarcoma virus long terminal repeat (RSV-LTR) promoter, the simian virus 40 (SV40) immediate-early promoter, and inducible promoters such as the metallothionein promoter. Other examples of promoters include, T7 phage promoter, T3 phage promoter, beta-galactosidase promoter, and the Sp6 phage promoter. An example of a DNA having a termination and poly(A) signal is the SV40 late poly(A) region. Another example of a viral expression system suitable for producing the antigen is the Sindbis Expression system available from Invitrogen. The use of these commercially available expression vectors and systems are well known in the art. The vaccine of the present invention may also contain multiple copies of one protective molecule or a combination of protective molecules.

In another embodiment, replicon particle (RP) vaccines are prepared. The RP vector has numerous advantages for vaccine development including accurate production of native proteins, tropism for lymphoid cells, lack of viral replication and transmission, induction of mucosal and systemic immunity, sequential immunization potential, and lack of preexisting immunity to VEE in animals although they clearly can respond to the virus immunologically. (Dickerman RW, Baker GJ, Ordonez JV, Cherer WF (1973), Venezuelan Equine

Encephalomyelitis Viremia and Antibody Responses of Pigs and Cattle, American Journal of Veterinary Research 34: 357-361.)

In an optional embodiment it is possible to provide an adjuvant in the vaccine.

Adjuvants enhance the immunogenicity of an antigen but are not necessarily immunogenic themselves. Adjuvants may act by retaining the antigen locally near the site of administration to produce a depot effect facilitating a slow, sustained release of antigen to cells of the immune system. Adjuvants can also attract cells of the immune system to an antigen depot and stimulate such cells to elicit immune responses. Immunostimulatory agents or adjuvants have been used for many years to improve the host immune responses to, for example, vaccines. The vaccines of the present invention may be used in conjunction with an adjuvants, for example, lipopolysaccharides, aluminum hydroxide and aluminum phosphate (alum), saponins complexed to membrane protein antigens (immune stimulating complexes), pluronic polymers with mineral oil, killed mycobacteria in mineral oil, Freund's complete adjuvant, bacterial products, such as muramyl dipeptide (MDP) and lipopoly saccharide (LPS), as well as lipid A, and liposomes. Desirable characteristics of ideal adjuvants may include: (1) lack of toxicity; (2) ability to stimulate a long-lasting immune response; (3) simplicity of manufacture and stability in long-term storage; (4) ability to elicit both CMI and HIR to antigens administered by various routes; (5) synergy with other adjuvants; (6) capability of selectively interacting with populations of antigen presenting cells (APC); (7) ability to specifically elicit appropriate T-cell helper 1 (TH 1) or TH 2 cell-specific immune responses; and (8) ability to selectively increase appropriate antibody isotype levels (for example, IgA) against antigens. An adjuvant used with the present invention need not possess all these characteristics to be used with the present invention.

Another adjuvant which may be used is E. coli heat labile enterotoxin (LT). LT has been used to assist in preventing E. coli induced diarrhea (See for example Limjuco et al., US Patents 4,285,931 and 4,220,584). However, since its early isolation it has been found that its use of LT is greatly limited due to toxicity, and is avoided as an adjuvant unless modified in some manner to reduce toxicity. See Zhang et al. (2009) Vet. Rex. Commun. 33:735-747 DOI 10/1007/sl 1259-009-9222-7. Thus there has been effort to avoid the toxicity problem by changing the sequence of the enterotoxin or by truncation. See, e.g., Piazza et al., US Patent 7,291,588. The inventors here have found that it is possible to use a non- mutated LT as an adjuvant without toxicity. Such non-mutated LT is that which is not truncated or otherwise mutated. As a result, an adjuvant non-toxic impact is provided, and at reduced cost in its manufacture.

The means and methods of producing such a vaccine are known to one skilled in the art and many variations and approaches to such production are known and expected to be further developed. The following sets forth as examples some of the many options available to produce and administer such a vaccine. A discussion of an example of various means for producing and administering vaccines of the invention is described at Harris et al., US Patent 7,622,254, incorporated herein by reference in its entirety.

In one embodiment of the invention, a method of identifying protective sequences of the virus or nucleic acids that elicit protection is provided. This method also includes fragments, derivatives, or homologs of the protective molecule. In one aspect, the method comprises administering to a test animal such sequences. The test and control animals are subsequently challenged with an infectious amount of a microorganism that causes the disease. Various methods and techniques for determining whether protection is provided are known to those skilled in the art, including but not limited to, observing a difference between the test and control animal in the symptoms of the disease, for example. A decrease in any of the symptoms observed in the test animal compared to the control animal indicates that protective molecule(s) provide a degree of protection against disease. Similar symptoms or an increase in any of the symptoms observed in the test animal compared to those observed in the control animal indicate that the protective molecule(s) do not provide protection.

In another aspect, determining whether the protective molecules provided protection against infection includes determining the presence or absence of challenge disease in the test animal by electron microscopy or antibody or assays such as the fluorescent focusing neutralizing (FFN) test or Western blot assay may be used. PCR methods may be used to determine if the protective molecule is present. Northern blotting can detect the presence of diagnostic sequences. In another aspect, an ELISA or similar assay, such as a

hemagglutinin inhibition assay are the types of many varied assays that can determine if the protective molecule is effective. The ELISA or enzyme linked immunoassay has been known since 1971. In general, antigens solubilised in a buffer are coated on a plastic surface. When serum is added, antibodies can attach to the antigen on the solid phase. The presence or absence of these antibodies can be demonstrated when conjugated to an enzyme. Adding the appropriate substrate will detect the amount of bound conjugate which can be quantified. A common ELISA assay is one which uses biotinylated anti-(protein) polyclonal antibodies and an alkaline phosphatase conjugate. For example, an ELISA used for quantitative

determination of protein levels can be an antibody sandwich assay, which utilizes polyclonal rabbit antibodies obtained commercially. The antibody is conjugated to alkaline

phosphatases for detection. In another example, an ELISA assay to detect trypsin or trypsinogen uses biotinylated anti-trypsin or anti-trypsinogen polyclonal antibodies and a streptavidin- alkaline phosphatase conjugate.

Clearly, many such methods are available to one skilled in the art to ascertain if the protective molecule provides protection, and provides protection at the levels administered to the animal.

The present inventors also contemplate that the isolated sequences from the microorganism of the present invention may be delivered using various vectors and viruses. The vaccine composition may be introduced into an animal, with a physiologically acceptable vehicle and/or adjuvant. Useful vehicles are well known in the art, and include, e.g., water, buffered water, saline, glycine, hyaluronic acid and the like. The resulting aqueous solutions may be packaged for use as is, or lyophilized, the lyophilized preparation being rehydrated prior to administration, as mentioned above. The compositions may contain pharmaceutically acceptable auxiliary substances as required to approximate physiological conditions, such as pH adjusting and buffering agents, tonicity adjusting agents, wetting agents and the like, for example, sodium acetate, sodium lactate, sodium chloride, potassium chloride, calcium chloride, sorbitan monolaurate, triethanolamine oleate, and the like. In one embodiment of the invention, the protective molecule is encapsulated such that the resulting composition is water resistant. In an embodiment, the molecule is combined with a binder that assists in associating the molecule with feed, which is particularly useful for oral administration. Such a water resistant binding substance can be any substance having such properties. Examples include, without limitation, agarose or other sugar compounds, albumin, alginate or any similar composition.

In another embodiment, protective molecules isolated from a particular strain or biotype can be combined with other sequences and components of other strains or biotypes or diseases to achieve protection against multiple microorganisms. These different

microorganism sequences or components may be administered sequentially or progressively or alternately administered simultaneously in an admixture. Sequential or progressive administration of the vaccine compositions of the invention may be required to elicit sufficient levels of immunity to multiple microorganism strains. Single or multiple administration of the vaccine compositions of the invention can be carried out. Multiple administration may be required to elicit sufficient levels of immunity. Levels of induced immunity can be monitored by measuring amount of neutralizing secretory and serum antibodies, and dosages adjusted or vaccinations repeated as necessary to maintain desired levels of protection.

The protective molecules may be "administered" in any suitable manner, including but not limited to, by immersion in a composition or substance containing the protective molecule (as with shrimp, by providing the vaccine in liquid surrounding the shrimp, for example) parenterally, by injection subcutaneously or intramuscularly, into an organ or cavity of the animal, reverse gavage (rectally), and oral, whether per os or ingestion of feed, as well as transdermal or by gas exchange. In one example, without intending to be limiting, a bacterial strain expressing the protective molecule may be fed to the animal. In an example, bacteria may be modified to be deficient in RNase, and transfected with an inducible promoter driving a plasmid producing the protective molecule. The bacteria is inactivated and fed to the animal. The vaccine can be administered by any means which includes, but is not limited to, syringes, nebulizers, misters, needleless injection devices, or microprojectile bombardment gene guns (Biolistic bombardment), via a liposome delivery system, naked delivery system, electroporation, viruses, vectors, viral vectors, or an ingestible delivery system wherein the protective molecules are consumed, for example, in feed or water or in any other suitable manner. Oral or immersion administration provides advantages in ease of administration and the capacity to administer the protective molecules to a group of animals. The immunogenic preparations and vaccines are administered in a manner compatible with the dosage formulation, and in such amount as will be therapeutically effective, immunogenic and protective.

The quantity to be administered depends on the subject to be treated, including, for example, the capacity of the immune system of the individual to mount a protective response. Suitable regimes for initial administration and booster doses are also variable, but may include an initial administration followed by subsequent administrations. For example, it may be desirable to provide for an initial administration of the vaccine followed by additional doses. In one example, without intending to be limiting, an increased protective response may be achieved by immersing the animal in a solution comprising a Replicon Particle producing the protective molecule and orally administering the protective molecule. The need to provide an effective amount of the protective molecule will also need to be balanced with cost of providing higher amounts of the protective molecule. A cost effective vaccine is one in which the cost of producing it is less than the value one can obtain from using it. Measurement and determination of efficacy of any of the compositions and vaccines of the invention may be accomplished by any of the many methods available to one skilled in the art. By way of example, without limitation, where the process involves interference with a target molecule, target molecule suppression can be measured by quantitative RT-PCR or RT-PCR or nucleic acid hybridization or Northern blotting of whole body or specific tissues RNA extracts, using primer sets that extend beyond or are completely removed from the region encompassed by the dsRNA generating primer set.

The inventors have found that in one embodiment, a straightforward and quick method can be to perform a Western blot analysis of a sample candidate vaccine composition to quantitate the amount of polypeptide or fragment thereof in the sample. There are various options available to the skilled person, and the need for fast production may dictate which is preferred. In one embodiment, one compares the amount of polypeptide to a standard known to be effective with like polypeptides from other biotypes, and either prepares a vaccine where the level of polypeptide produced is at least at this standard or higher, or may test the vaccine with a test animal. As one measure of vaccine potency, an ELISA can be performed on a sample collected from an individual vaccinated to determine whether antibodies to a vaccine comprising the sequence, a derivative, a homologue or a variant or fragment thereof generated anti-polypeptide antibodies. The individual's sample is measured against a reference anti-polypeptide antibody. Analysis of symptoms and measurement of animal weight gain also demonstrated lessening of impact of the disease in the presence of a particular dose. Fluorescent focused neutralization assay is still another assay to detect serum neutralizing antibodies and analyze effectiveness of a vaccine and a particular dose.

When testing animals administered the influenza vaccine, for example, measuring antibody response by hemagglutinin inhibition assay of post- vaccination sera is also effective in determining efficacy of the vaccine. Sera may be collected and titer measured as the reciprocal of the maximal dilution at which hemagglutination is inhibited, as described in an example below. Other measurements post-administration of the vaccine can also be employed to determine effectiveness, whether pathological evaluation, isolation of the pathogen, measurement of symptoms, and overall health and weight gain of the animal.

Thus, the effectiveness of the present vaccine may also be evaluated quantitatively (for example, with influenza, a decrease in the percentage of consolidated lung tissue as compared to an appropriate control group) or qualitatively (e.g., isolation of influenza virus from blood, detection of influenza virus antigen in a lung, tonsil or lymph node tissue sample by an immunoperoxidase assay method, etc.). The symptoms of the influenza disease may be evaluated quantitatively (e.g., temperature/fever), semi-quantitatively (e.g., severity of respiratory distress, or qualitatively (e.g., the presence or absence of one or more symptoms or a reduction in severity of one or more symptoms, such as, pneumonia, lung lesions, etc.). Clearly one skilled in the art has many different options available for measuring effectiveness of the vaccine. With the present invention, it is possible to achieve protection against disease in an aquatic invertebrate, and which protection is provided for longer periods than have been achieved in such animals. Protection periods of more than seven days after at least one challenge or exposure to the pathogenic microorganism have been achieved, and protection of at least two weeks, at least 20 days, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35 , 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55 , 56, 57, 58, 59, 60 days or more, have been achieved using the invention. Such protection periods are also provided when using the invention with other animals. The protective response is also shown here in an embodiment to be specific to the disease as opposed to another disease, and thus demonstrates specific memory. In still another example, ranges of doses may be prepared and protective response measured. A candidate vaccine can be formulated at two or three or more different doses to determine the minimum protective dose. For example, when using RP, in addition to measuring IFA titration, qPCR assays can be used to determine the number of genome equivalents present in the vaccine and compared to IFA titer to obtain a GE:RP ratio. Such an assay helps assure uniformity as well. In still another example, such testing indicated that a swine influenza efficacious dose was about 1X10⁸ RP per 2ml dose. Further examples show efficacious dose for SIV of RP titer at >5 X 10⁷/2ml. A GE:RP ratio for the SIV vaccines ranged from 1 - 20.64. Efficacious doses included 5X10⁵/2ml. By way of another example, without limitation, two or three or more dose ranges may be prepared, as in the example below with shrimp and morbidity and mortality measured upon challenge. The dose selected in a preferred embodiment is that which provides protection to the animal which is also cost effective.

In one embodiment a method of determining the quantity of a nucleic acid molecule of interest or fragment thereof (NOI) is employed when using a Replicon Particle. As discussed herein, the Replicon Particle includes nonstructural proteins (nsp) to replicate full- length negative- sense RNA which acts as a template to replicate additional genomic RNA as well as subgenomic RNA that code for the NOI. The nonstructural sequences (nspl-4, discussed supra) aid in the expression of the autogenous recombinant proteins by forming a complex which transcribes additional autogenous recombinant gene RNA. In the process of expressing an NOI all replicons will produce nspl-4 as described above. Because

nonstructural proteins are expressed by all Replicon Particles, detection of them may be used to determine the titer of Replicon Particles in the absence of methods or reagents to detect the specific NOI encoded on the replicon. This allows for a method of determining the titer of any NOI Replicon Particle, without the necessity of preparing a separate method of analysis for each NOI. This is of particular relevance for rapid production of a vaccine. In an embodiment, an assay may be used specific for a nonstructural protein, and correlates with titer of RNA or Relicon Particle titer. Any means of detecting the nonstructural protein may be employed and a variety are known and may be developed by one skilled in the art.

Examples, without limitation, include an Immunofluorescence Assay (See, e.g., Kamrud et al (2008) PLoS One 3(7); Paradis et al. (2007) Can Vet J. 48(l):57-62) , which may be direct or indirect, quantitative PCR (Innis et al, supra) or flow cytometry (See, Ormerod, M.G. (edit) (2000) Flow Cytometry - a practical approach 3^rd Edit. Oxford University Press). Further, the detection may be of any nonstructural protein present in the Replicon Particle, such as nspl , nsp2, nsp3 or nsp4. In a preferred embodiment, nsp2 is detected. The use of such a method provides for a uniform, fast and convenient method to determine titer of the NOI Replicon Particles and is useful in preparing a vaccine having a desired dose of the NOI Replicon Particles. It may be used with other means to analyze the presence of a nucleic acid of interest, such as qRT-PCR, ELISA, antibody binding and the like. In another embodiment, the titration is used with qPCR to quantitate RNA copies and to produce a genome equivalents: Replicon particle (GE:RP) ratio to monitor consistency and dosage.

With hemagglutinin titers of at least 1 :40 expected to elicit a protective response, dosages can be modified to elicit a protective response. (Potter CW, Oxford JS. Determinants of immunity to influenza infection in man. Br Med Bull 1979;35:69-75.) By way of example, the inventors here determined that in providing a vaccine with recombinant hemagglutinin polypeptide, an effective amount as measured in micrograms per milliliter of was 0.38μg/ml to 1.14μg/ml concentration. When measured as a dilution of lysed Vero cells, an effective amount of HA was at least 1 : 150. In another embodiment, a preferred concentration was 1 :50 to 1 : 150 of lysate to liquid/buffer and in a further preferred embodiment was 1 :60 to 1 :75. Concentrations too dilute to provide a protective response were those above 1 : 150. Cost effectiveness was provided in the preferred ranges. With PRRSV reduction in symptoms occurred with a cost effective dosage of le8/ml in PBS. In one of the several experiments using dsRNA, vaccines were prepared having .02ug, 0.2 μg and 2.0 ug and even at the lowest, most cost effective dose, protection was provided. FMDV doses ranged from 5 X10⁸ to lX10⁹ IU/mL of RP comprising FMDV capsid and 3C proteinase coding regions is prepared and protective response measured.

Thus, the inventors have demonstrated that an autogenous vaccine of protective molecules is effective in protecting an animal from a pathogenic microorganism.

The following examples are presented by way of illustration and not intended to limit the scope of the invention.

EXAMPLE 1

Here described is one method of producing autogenous replicon particle (ARP also referred to by some practitioners as RNA particle or Replicon Particle) In a first experiment, it was confirmed that RP vaccines were capable of producing a foreign antigen in vivo that resulted in an induced immune response in pigs.

Pigs were obtained at 2 weeks of age, weighed, tagged, and randomized into 2 groups of 8 pigs each (Table 4). Prior to vaccination, serum was collected to assure pigs were free of influenza antibodies. Table 4: Design of replicon particle (RP) proof of concept study in pigs. Pigs received either an empty RP or an

RP expressing the influenza hemagglutinin (HA) protein.

Serum was collected throughout the study for hemagglutination inhibition (HI) assay using the AAVyoming/03/2003 virus. All pigs were HI negative prior to starting the study and Group 1 pigs remained negative during the study (individual pig data not shown). However a robust and long lasting antibody response to HA protein was induced in Group 2 (Table 5). This response started to appear following the priming dose and elevated quickly after the second dose. By Day 21 all pigs had titers between 1280 and 5120 and maintained this level through termination of the study at 62 days. Although the pigs in this experiment were not challenged with virulent virus, based on previous studies and generally accepted protective level (>40) this level of HI antibody would have been protective. Table 5: HI results (inverse titers) of pigs immunized with RP expressing the influenza HA protein (>40 considered positive). Pigs were immunized on Day 0 and 14. The trial ended on Day 62.

We have successfully shown that RP vaccines can be made that co-express both PRRSV GP5 and M proteins and that a heterodimer is formed. Erdman MM, Harris DL, Kamrud KI. Replicon particle co-expression of PRRSV GP5 and M proteins. Proc CRWAD 2006.

Following successful expression in vitro, a pig trial was conducted to determine if the GP5-M RP vaccine would induce an immune response in pigs. Pigs 2-3 weeks of age were obtained from a PRRSV negative source. Pigs were tagged, weighed, and randomized into 2 groups of 8 (Table 6). Serum was collected prior to vaccination to assure pigs had no antibodies to PRRSV. Table 6: Previous PRRSV RP proof of concept study. Pigs were vaccinated with either an empty RP or an RP co-expressing PRRSV GP5 and M proteins.

All pigs were challenged on Day 48 with a homologous PRRSV strain (HLV013) intramuscular with 2 ml of 10⁶ TCID₅₀. Neither group had virus neutralizing antibodies on Marc 145 cells prior to challenge although Western blotting indicated antibodies were present to the PRRSV proteins. Following challenge, 3 of 8 pigs in the vaccinate group and 0 of 8 pigs in the control group had neutralizing titers within 7 days. All pigs were necropsied 14 days after challenge. At necropsy 5 of 8 in the vaccinate group and 4 of 8 in the control group had neutralizing titers. However the geometric mean titers (GMT) was higher in the vaccinate group (GMT=27.8) compared to the control group (GMT=9.5). Virus titration of lung lavage indicated that 7 of 8 control pigs were virus positive and only 4 of 8 vaccinate pigs were virus positive. Lung lesion scoring showed less gross pathology in the vaccinate group (mean score of 16.3) compared to the control group (mean score of 22.3).

Results and Accomplishments

ARP vaccine construction

The entire vaccine development process took three weeks from PRRSV positive serum sample to formulated GP5 and M single promoter ARP vaccines and an additional week to produce the GP5/M double promoter ARP vaccine. Due to the fact that speed of development was important to us in this experiment we opted to conduct the trial by co- injecting the GP5 and M single promoter ARP since they took less time to produce and posed less technical challenges. However both the single promoter and double promoter approaches are viable options and that both are more rapid than the time it generally takes to develop a new conventional autogenous vaccine requiring isolation and growth of the virus.

PCR can be performed on a sample to both provide a positive diagnosis of PRRS and also generate cDNA of the genes needed to make the ARP vaccine. It is also anticipated that this entire process can be performed in less time than it generally takes for a pig producer to get a traditional autogenous vaccine made.

To develop the new ARP vaccine, a large swine producer that had pigs suffering from clinical PRRSV was identified. Serum samples from diseased animals were sent to Iowa State University. RT-PCR was used both to confirm diagnosis and produce cDNA of genes targeted for vaccine production. Specific primers were used to amplify both the PRRSV GP5 and M genes, ORF 5 and 6 respectively. Although not needed to make the vaccine, the live virus was isolated in order to prepare a traditional killed autogenous vaccine and used for challenging the pigs. The isolate was referred to as PRRSV strain Pennway.

The PRRSV GP5 and M genes were cloned into replicon vectors that are based on the live attenuated vaccine strain of VEE known as TC-83 (Figure 8). The GP5 and M replicon vectors were analyzed by both IFA and Western blot to confirm expression of desired proteins. The replicons were then packaged into particles via co-electroporation with helper RNAs to produce ARP. ARP were harvested from culture fluids and the infectious titer of the ARP preparation was measured by antigen- specific IFA and tested in a CPE assay to assure the absence of replication competent virus.

Vaccine formulations

The placebo vaccine consisted of 2 ml of sterile PBS (HyClone Laboratories).

The ARPs had initial titers of 2.1 le9/ml for the GP5 ARP and 3.56e9 for the M ARP. Each ARP was diluted to a titer of le8/ml using PBS. Each dose consisted of 1 ml of GP5 ARP and 1 ml of M ARP co-injected in the same syringe.

The inactivated PRRSV vaccine was derived from the same strain used to produce the ARP vaccine. The virus was grown to 85% CPE on Marc- 145 cells and harvested from the supernatant. The virus titer was determined to be 2.7e5 TCIDso/ml. The virus was heat inactivated at 65 degrees C for 90 minutes. A sample of the prep was inoculated onto Marc- 145 cells to confirm the lack of viable virus. The lysate was formulated with Emulsigen-D adjuvant (MVP laboratories, Ralston, NE) by adding 1.6 ml of the lysate with 0.4 ml of adjuvant per dose.

The PRRSV MLV vaccine was Inglevac PRRS ATP (Boehringer Ingelheim

Vetmedica, Inc). The vaccine was used as directed by the manufacturer which indicated giving a single 2 ml dose of vaccine.

Pig trial

Three week old pigs were obtained from a farm in Iowa with no history of PRRSV infection based on clinical signs and serology. Pigs were ear tagged, weighed, and randomized into five groups of ten pigs each in BSL-2 animal facilities at Iowa State

University. A description of groups is given in Table 7 and a timeline for the vaccination- challenge study is shown in Table 8. Group 1 contained strict negative control pigs that were neither vaccinated nor challenged. All pigs in Groups 2, 3, and 4 were vaccinated intramuscular (IM) on Day 0 and again on Day 28. Group 2 received the placebo vaccine, Group 3 the ARP vaccine, and Group 4 the inactivated PRRSV vaccine. Group 5 received one dose of the MLV vaccine on Day 0.

Table 7: Groups in PRRSV vaccination-challenge study

PRRSV= porcine reproductive and respiratory syndrome virus, M= matrix protein, GP5= glycoprotein 5, ARP= autogenous replicon particles, MLV= modified live virus NA= not applicable, IM= intramuscular, IN= intranasal

Pigs were challenged IN on Day 56 with 2 ml of lxlO⁵ TCID₅₀/ml of virulent PRRSV strain Pennway. Pigs were monitored for clinical signs including respiratory distress, lethargy, and recumbancy following challenge but none were noted. Pigs were euthanized 21 days after challenge, a necropsy performed, and tissues collected for laboratory testing including quantitative gross lung lesion scoring, histopathology, IDEXX ELISA, virus titration, and virus neutralization.

Table 8: Time course for vaccination-challenge trial

Pathology At necropsy, gross pathology lung lesions were determined by a treatment blinded, board certified veterinary pathologist as previously described by Halbur et al. Halbur PG, Paul PS, Meng XJ, Lum MA, Andrews JJ, Rathje JA. Comparative pathogenicity of nine US porcine reproductive and respiratory syndrome virus (PRRSV) isolates in a five- week-old cesarean-derived, colostrum-deprived pig model. J Vet Diagn Invest 1996;8: 11-20.

Briefly, each section of the lung was assigned a number and the lung score represents the percentage of that lobe with evidence of pneumonia. The scores for each lobe are then added together to get the overall lung score for that pig. The lung pathology in this experiment was rather mild and is summarized in Figure 9 as the total lung score by group. Histopathology was also conducted on lung and heart sections as described by Halbur et al., supra

These results are summarized in Figures 10-12. The interstitial pneumonia is the average of four different sections per pig using a scale of 0 (normal) to 6 (severe and diffuse). Results indicated no statistical differences between groups. Lung lymphoid hyperplasia was examined on the same sections with a scale of 0 (normal) to 6 (severe hyperplasia). Results indicated that both the placebo and inactivated vaccine groups had statistically (p<0.05) greater hyperplasia when compared to the strict negative group. No other statistical differences were noted. The heart section was examined for signs of infection on a scale of 0 (normal) to 3 (severe myocarditis). Results indicated no statistical differences between groups.

The pathology results indicate few statistical differences despite the fact that other assays we conducted indicate a successful challenge. Lesions and clinical signs induced in PRRSV studies can vary greatly, or be nearly absent as seen here, due to a variety of reasons including strain differences. This contributes to the fact that other measures such as virema and antibody assays discussed below are considered the gold standard for evaluating PRRSV vaccines.

IDEXX HerdChek PRRS 2XR ELISA

The IDEXX ELISA detects antibodies to the nucleopcapsid (N) protein of PRRSV. These antibodies dominate the early response to PRRSV although they do not provide protection from disease. Previous work has also correlated the S/P (sample to positive , the ratio of sample signal to background that is commonly used with IDEXX ELISA) titers to level of viremia and in this way the titers can be used to compare level of infection between groups. Johnson W, Roof M, Vaugh E, Christopher-Hennings J, Johnson CR, Murtaugh M. Pathogenic and humoral immune response to porcine reproductive and respiratory syndrome virus (PRRSV) are related to viral load in acute infection. Veterinary Immunology and Immunopathology 2004;102:233-47.

Serum samples were collected from all pigs on 0, 7, 14, and 21 days post challenge. Samples were sent to South Dakota State University for testing. An S/P ratio of > 0.40 is considered positive. The results are shown in Figure 13 as mean S/P ratio per group. The results indicate that on the day of challenge all pigs in Groups 1-4 remained negative. This assured us that we did not have lateral introduction of live virus during the study. All pigs in Group 5 were IDEXX positive on the day of challenge which is to be expected since the N protein is a major part of the MLV vaccine. All pigs in the ARP group remained negative prior to challenge reinforcing the idea that this vaccine can be used in conjunction with the IDEXX ELISA to differentiate infected from vaccinated animals (DIVA). Groups 2-4 seroconverted by 14 days post challenge. However the ARP group remained signicantly lower than the other treatment groups through necropsy indicating a lower level of infection in this group. This comparison was not possible in the MLV group since it was positive prior to challenge. The strict negatives remained negative throughout the study.

Fluorescent focused neutralization assay

The fluorescent focused neutralization (FFN) assay detects serum neutralizing antibodies against PRRSV. Serum samples were collected from all pigs on 0, 7, 14, and 21 days post challenge. Samples were sent to South Dakota State University for testing as previously described. The test virus used was PRRSV strain Pennway and an inverse titer > 4 was considered positive. The number of positive pigs in each group is summarized in Figure 14. There no positives in any group on day of challenge. However after challenge the ARP and MLV groups showed more pigs positive by necropsy when compared to to the inactivated and placebo groups. All pigs in the strict negative group remained negative throughout the study. With more positive pigs it is not surprising that the mean neutralizing titers of the ARP and MLV groups were higher than the other treatments as shown in Figure 15.

Although our previous work has indicated that expressed PRRSV GP5 and M can induce neutralizing antibody prior to challenge we did not see that in this study. However it is possible that this is due to glycosylation of the GP5 used for this study. This was a new vaccine created from a field strain that tend to be highly glycosylated. Although there were not neutralizing antibodies prior to challenge, we did note a priming effect in the ARP group similar to the MLV group as evidenced by the differences between groups post challenge. Live virus titration Serum samples collect at 0, 7, 14, and 21 DPC as well as bronchial alveolar lavage (BAL) fluid collected at necropsy were tested for the presence of live PRRSV as previously described. Briefly, samples were diluted 10-fold on 96 well plates containing confluent Marc- 145 cells. Each clinical sample was plated in quadruplicate. Plates were incubated at 37°C and 5% C0₂ for 7 days, or until no new CPE was observed. TCIDso/ml titers were calculated using the Reed-Muench equation. The detection limit was 5.6el TCIDso/ml.

All groups were negative for live virus on 0 DPC and the strict negative group remained negative throughout the study. By 7 DPC virus was detected in the four challenged groups and significant differences in viremia were noted (Figure 16). There was no detectable live virus in the serum at 14 and 21 DPC.

Testing of the BAL fluid indicated only one positive sample in Groups 2 and 5 and two positive samples in Groups 3 and 4 (Data not shown).

RT-PCR

RT-PCR was conducted on serum samples collected at 0, 7, 14, and 21 DPC as previously described. Briefly, viral RNA was extracted using the Qiagen Virus Spin Kit. The extract was then tested in duplicate using primers specific for the ORF7 gene of PRRSV which codes for the N protein. The results are summarized as the number of positive pigs in each group (Figure 17).

While PCR is another assay to detect viremia, it is not surprising that the PCR and live virus titration results do not match. One method detects live virus while the other only detects nucleic acid which could possibly be present in the absence of live virus. The PCR results indicate that by 14 DPC the ARP and MLV groups had significantly fewer viremic pigs compared to the placebo group.

EXAMPLE 2

In this study, the alphavirus replicon is derived from the TC-83 strain of the alphavirus Venezuelan Equine Encephalitis Virus (VEEV). In a previous study, a VEEV replicon vaccine expressing the HA gene from a human H5N1 isolate protected chickens from lethal challenge. Schultz-Cherry S, Dybing JK, Davis NL, Williamson C, Suarez DL, Johnston R, Perdue ML. Influenza virus (A/HK/156/97) hemagglutinin expressed by an alphavirus replicon system protects chickens against lethal infection with Hong Kong-origin H5N1 viruses. Virology. 2000 Dec 5;278(l):55-9. PubMed PMID: 11112481. Recently, our group became the first to evaluate VEEV replicon particle vaccines in swine. Erdman MM, Kamrud KI, Harris DL, and Smith J, 2010, "Alphavirus Replicon Particle Vaccines

Developed for Use in Humans Induce High Levels of Antibodies to Influenza Virus Hemagglutinin in Swine: Proof of concept", Vaccine 28:594-596. The objective of this study was to evaluate replicon-expressed recombinant novel H1N1 HA protein as a swine vaccine in a vaccination-challenge model. Materials and Methods

Novel H1N1 HA Replicon Subunit Vaccine Production

The hemagglutinin (HA) nucleotide sequence was retrieved from the Global Initiative on Sharing Avian Influenza Data (GISAID) database. The gene was synthesized by a commercial company (DNA2.0, Menlo Park, CA, USA) with unique Ascl and Pad restriction sites engineered at the 5' and 3' ends, respectively. The HA gene was cloned into the Ascl/Pacl sites of the pVEK (TC-83) replicon vector (Hooper JW, Ferro AM, Golden JW, Silvera P, Dudek J, Alterson K, Custer M, Rivers B, Morris J, Owens G, Smith JF, and Kamrud KI, 2009, "Molecular Smallpox Vaccine Delivered by Alphavirus Replicons Elicits Protective Immunity in Mice and Non-Human Primates" Vaccine 13(13)). and an optimized construct was selected as previously described. (Kamrud KI, Custer M, Dudek JM, Owens G, Alterson KD, Lee JS, Groebner JL, Smith JF. Alphavirus replicon approach to promoterless analysis of IRES elements. Virology. 2007 Apr 10;360(2):376-87. Epub 2006 Dec 6. PubMed PMID: 17156813; PubMed Central PMCID: PMC1885372). The HA gene was then sequenced to ensure the proper sequence was maintained through the cloning process. RNA transcripts were produced in vitro as previously described (Kamrud et al. (2007),

supra. Replicon RNA was mixed with Vero cells in electroporation cuvettes and

pulsed. Cells were incubated overnight and then lysed using RIPA buffer (Pierce, Rockford, IL, USA). Resulting lysate was tested for protein expression by Western blot and HA protein concentration was determined by a novel H1N1 HA-specific ELISA. Lysate was diluted to the specified HA concentration and vaccine was adjuvanted with Emulsigen-D (MVP Technologies, Omaha, NE, USA).

Western Blot Analysis

Vero cell lysate containing recombinant HA protein was separated by running on a 12% SDS-PAGE gel (Invitrogen, Carlsbad, CA, USA) and was then transferred to a PVDF membrane (Invitrogen, Carlsbad, CA). The ladder used was the SeeBlue Plus2 Pre-Stained Standard (Invitrogen, Carlsbad, CA, USA). After transfer, membrane was blocked with 5% non-fat dry milk at room temperature. Membrane was incubated with swine polyclonal anti- HA for two hours, washed three times, followed by incubation with goat anti-swine IgG horseradish peroxidase conjugate (ImmunoJackson Research Laboratories, Inc, West Grove, PA, USA) for one hour, and washed three times. Detection was performed using TMB substrate (KPL, Gaithersburg, MD, USA). Animal Studies

Pigs free of swine influenza virus (SIV) and porcine reproductive and respiratory syndrome virus (PRRSV) were obtained at three weeks of age. Pigs were randomized and separated into 4 groups of 5 pigs each. Prior to vaccination, serum was collected and tested by the homologous hemagglutination inhibition (HI) assay against the novel H1N1

A/California/04/2009 strain to confirm negative antibody status. Sera were collected throughout the study and tested by this same HI assay to monitor seroconversion post- vaccination. A prime/boost vaccination schedule was followed. The first dose of vaccine was given to pigs at approximately 4 weeks of age on day 0. On day 21 pigs received booster vaccination, with challenge on day 47 and necropsy on day 52. Pigs received either phosphate buffered saline (PBS) (Group 1) or different concentrations of novel HI HA recombinant protein (Groups 2-4,). Pigs were challenged intratracheally with virulent A/Calif ornia/04/2009 (CDC# 2009712047) at a dose of 2xl0⁵ TCID₅₀/ml. Nasal swabs were collected daily for live virus isolation beginning on day of challenge and continuing until study completion 5 days post-challenge. Pigs were weighed immediately before challenge and again at necropsy for determination of average daily gain. At necropsy, gross lung lesion consolidation was determined by a board-certified pathologist. Lung tissue was fixed in formalin for SIV immunohistochemistry (IHC) and histopathological

analysis. Bronchoalveolar lavage fluid (BALF) was collected from lungs for live virus isolation. This animal study was approved by the Iowa State University Institutional Animal Care and Use Committee.

Gross Lung Lesion Scoring, Histopathology, and SIV Immunohistochemistry

A single board-certified veterinary pathologist who was blinded to group treatments, performed gross lung scoring, histopathological analysis, and SIV Immunohistochemistry (IHC) analysis. At necropsy, each lung lobe affected by pneumonia was visually estimated, and a total percentage for the entire lung was calculated based on weighted proportions of each lobe to the total lung volume ( Halbur PG, Paul PS, Frey ML, Landgraf J, Eernisse K, Meng XJ, Lum MA, Andrews JJ, Rathje JA. Comparison of the pathogenicity of two US porcine reproductive and respiratory syndrome virus isolates with that of the Lelystad virus. Vet Pathol. 1995 Nov;32(6):648-60. PubMed PMID: 8592800). Tissue samples from the trachea and all lung lobes were collected and fixed in 10% formalin. Tissues were routinely processed and stained with hematoxylin and eosin. Lung samples were scored according to the method used by Vincent et al. (Vincent AL, Ma W, Lager KM, Janke BH, Webby RJ, Garcia-Sastre A, Richt JA. Efficacy of intranasal administration of a truncated NSl modified live influenza virus vaccine in swine. Vaccine. 2007 Nov 19;25(47):7999-8009. Epub 2007 Sep 29. PubMed PMID: 17933442; PubMed Central PMCID: PMC2099695). Swine influenza virus IHC was done according to the method described by Vincent et al. (Vincent LL, Janke BH, Paul PS, Halbur PG. Demonstration of swine influenza virus in formalin- fixed, paraffin-embedded tissues by use of an immunohistochemical test. Proceedings of the 14th IPVS Congress. 1996;97). All tissue preparation and staining was done by the Iowa State University Veterinary Diagnostic Laboratory.

Live Virus Isolation

Live virus titers were determined from nasal swabs and live virus isolation performed on bronchoalveolar lavage fluid(BALF) samples. Briefly, nasal swabs and BALF samples were thawed and centrifuged to remove cellular debris. The resulting supernatant was diluted 10- fold in 96 well plates in Dulbecco's Modified Eagle Medium (DMEM) (Gibco, Carlsbad, CA, USA) containing 1% antibiotic-antimycotic (Gibco, Carlsbad, CA, USA) and 1% L- glutamine (Mediatech, Manassas, VA, USA). After dilutions were made, ΙΟΟμΙ was transferred from each well into respective wells of a 96 well plate which contained a monolayer of swine testicle (ST) cells. Plates were incubated at 37°C until no further CPE was observed, typically 3-5 days. Wells displaying CPE were considered positive, and titers were calculated using the TCIDso/ml method of Reed-Meunch. (Reed LJ and Muench H. A simple method of estimation of 50% end points. American journal of Hygiene. 27;493-497. 1938)

Hemagluttination Inhibition Assay

Antibodies to influenza virus were measured by hemagglutination inhibition (HI) assay run by the University of Minnesota Veterinary Diagnostic Laboratory following standard laboratory protocol. Briefly, sera were treated with receptor-destroying enzyme, heat inactivated, adsorbed with 20% turkey erythrocytes, and centrifuged. Supematants were then serially diluted in V-shaped well microtiter plates with an equal volume containing 4-8 agglutinating units of A/California/04/2009 and plates were incubated at room temperature before addition of 0.5% turkey erythrocytes. Titer was defined as the reciprocal of the maximal dilution at which hemagglutination was inhibited.

Direct Antigen Capture ELISA

Unknown samples, negative controls, and purified novel HI protein (Protein Sciences, Meriden, CT, USA) were directly captured to NUNC Maxisorp (Rochester, NY, USA) 96- well microplates by diluting with capture buffer (50 mM Carbonate/Bicarbonate, pH 9.6) and incubated overnight at 4°C (100 μΐ/well). The microplates were washed four times with wash buffer (20 mM Phosphate Buffered Saline, 0.05% Tween-20, pH 7.2). The plates were blocked with 1.25% non-fat dry milk in capture buffer for 1 hour at 37°C (200

μΐ/well). After four washes, pig polyclonal anti-HA was added to wells (100 μΐ) and incubated for 1 hour at 37°C (diluted 1/500 in wash buffer containing 1.25%

NFDM). Following four washes, goat ant-pig IgG-HRP labeled (Jackson ImmunoResearch, West Grove, PA, USA) was added to the wells (100 μΐ) and incubated for 1 hour at 37 °C (diluted 1/2000 in was buffer containing 1.25% NFDM). Four final washes were performed prior to the addition of 100 μΐ of TMB substrate (KPL, Gaithersburg, MD, USA) and incubation at 37°C for 20 minutes. Absorbance values were measured at 620 nm and a standard curve was plotted with the purified novel HI protein. Linear regression analysis of the standard curve was used to calculate the novel HI concentrations in the unknowns.

Statistical Analysis

Single factor analysis of variance (ANOVA) was used to analyze homologous HI titers, macroscopic and histopathological lung scores, IHC and BALF results, loglO transformed nasal swab viral titers, and ADG (JMP 8.0.1, SAS Institute Inc., Cary, NC, USA). Statistical significance was set at p < 0.05. Results

Vaccine Preparation

The novel H1N1 HA gene was inserted into the alphavirus replicon platform according to the methods listed previously. Nucleotide sequencing after insertion confirmed the correct HA gene sequence had been maintained throughout the cloning process. Western blotting performed on protein lysate confirmed expression of the novel HA protein at all the varying HA doses (Figure 18) used in vaccine preparation for the animal study. The HA

concentration was determined by novel HA ELISA and diluted to the specified HA concentration (Table 9). See Figure 18. Table 9: Design of novel HlNl recombinant HA vaccine study. Pigs received either sham vaccine (PBS, Group 1) or varying doses of HA antigen (Groups 2-4). All vaccines were given intramuscularly as 2ml doses on days 0 and 21.

Group Vaccine HA concentration/dose

1 Sham NA

2 Recombinant HA 1.14μg

3 Recombinant HA 0.57μg

4 Recombinant HA 0.38μg

Antibody Titers

Post- vaccination sera were tested for specific antibody response by the homologous HI assay. Hemagglutination inhibition titers were not seen in vaccinated pigs after one dose, but were all positive (>1 :40), except for a single pig in Group 2, at 7 and 14 days post-boost vaccination (data not shown). On the day of challenge, homologous HI titers were significantly higher in Groups 2-4 than Group 1 (Table 10).

Table 10. Summary of serum antibody titers, average macroscopic and microscopic lung involvement, immunohistochemistry (IHC), and average daily gain (ADG).

Histopathologic

Group HI Titers³ % Pneumonia¹⁵ Score^c Lung IHC^d ADG^e

1 <10 15.6 + 5.4 1.8 + 0.1 5/5 1.76 + 0.2

2 121* 1.4 + 0.9* 0.8 + 0.2* 1/5* 2.56 + 0.68

3 184* 0.2 + 0.2* 0.6 + 0.2* 0/5* 2.64 + 0.22*

4 106* 1.8 + 1.1* 0.8 + 0.2* 1/5* 2.45 + 0.34* ^aGeometric mean homologous HI titers

bGroup mean + standard error

°0-3, group mean + standard error

dNumber of positive samples per group

eADG post-challenge in pounds, group mean + standard error

* Values are significantly different from non- vaccinates (Group 1) within a column at p <

0.05 Pathological Evaluation

At necropsy, lungs exhibited macroscopic dark purplish-red consolidated lesions located mainly in the cranioventral lobes. Lungs taken from Groups 2-4 exhibited significantly lower lesion scores and consolidation than pigs in Group 1 (Table 10). There was also a significant reduction in pathological scores in all vaccinated groups compared to the non-vaccinated group (Table 10). The lung sections taken from non- vaccinated Group 1 pigs had approximately 50% of the airways affected by bronchiolar epithelial disruption and peribronchiolar lymphocytic cuffing. The vaccinated Groups 2-4 demonstrated only occasional affected airways with light cuffing. Swine influenza virus IHC was also performed on lung sections. All 5 lungs taken from non- vaccinated Group 1 pigs were positive for influenza antigen, while only 2 pigs in total from the vaccinated Groups 2-4 were positive. Additionally, SIV IHC was done on trachea samples taken from each pig at necropsy (data not shown). Although there were positive trachea IHC samples in all groups, there was no significant differences between vaccinated and non-vaccinated groups. Positive trachea IHC results correlate with what was previously reported on pathogenesis of novel H1N1 in ferrets. (Munster VJ, de Wit E, van den Brand JM, Herfst S, Schrauwen EJ, Bestebroer TM, van de Vijver D, Boucher CA, Koopmans M, Rimmelzwaan GF, Kuiken T, Osterhaus AD, Fouchier RA. Pathogenesis and transmission of swine-origin 2009 A(H1N1) influenza virus in ferrets. Science. 2009 Jul 24;325(5939):481-3. Epub 2009 Jul 2. PubMed PMID: 19574348)

Virus Isolation

No live influenza virus was detected one day post-challenge from nasal swabs (Table 11). On day 2 post challenge live influenza virus was detected in Groups 1, 3, and 4, although there were no significant differences between mean group viral titers. On day 3 post-challenge Groups 2 and 4 had significantly lower titers than did Group 1. On both days 4 and 5 Groups 2-4 all exhibited lower titers than Group 1. No live virus was detected in nasal swabs from any pigs in Group 2 for the duration of the challenge period. Similarly, there was a significant reduction in the number of positive BAL samples between groups (Table 11). By 5 days post- challenge, only a total of 3 vaccinated pigs had detectable live virus in BAL samples, while all 5 pigs in the non-vaccinated group were virus isolation positive. Average Daily Gain

All pigs were weighed on the day of challenge and again at necropsy. Groups 3 and 4 had significantly higher average daily gain (ADG) over the 5 day period following challenge than did Group 1. Group 2 did exhibit higher ADG but was not significantly higher than Group 1 (p=0.08).

Table 11. Summary of live virus isolation from nasal swabs and bronchoalveolar lavage

(BAL).

Nasal Swab^a BAL^b

Group 1 DPC^C 2 DPC 3 DPC 4 DPC 5 DPC 5 DPC

1 0 0.85 + 0.53 2.55 + 0.66 3.05 + 0.18 3.05 + 0.24 5/5

2 0 0 0* 0* 0* 2/5

3 0 1.05 + 0.07 0.65 + 0.65 0.9 + 0.57* 1.0 + 0.62* 0/5

4 0 0.45 + 0.45 0.5 + 0.5* 0.65 + 0.65* 0.65 + 0.65* 1/5 ^aLogio mean virus titers + standard error in nasal swabs post-challenge

bNumber of positive BAL samples per group

°Days post-challenge (DPC)

* Values are significantly different from non- vaccinates (Group 1) within a column at p < 0.05

A similar study was designed that did not involve an influenza virus challenge or associated analysis; only immunogenicity of recombinant HA vaccines produced in this manner was measured in vaccinated animals. For this study the HA genes for four other influenza viruses (HI -beta, HI -delta, HI -gamma and H3) were inserted into the alphavirus replicon platform using methods as described above. Nucleotide sequencing after insertion confirmed the correct HA gene sequences had been maintained throughout the cloning process. Western blots were performed on protein lysates generated with each of the HA constructs to confirm expression of the HA protein (data not shown). In this experiment varying dilutions of the resultant HA vaccines were used to vaccinate groups of pigs (vaccines used and schedule described in the Tables 12 and 13 below); the dilutions used to vaccinate pigs are shown in Table 14. The immune responses induced by the different recombinant HA vaccines were analysed by homologous HI titers, using the method described above where endpoint titer is shown as the reciprocal of the last dilution of serum capable of inhibiting hemagglutination of the virus in the assay. A summary of the HI titers determined in this study can be found Table 14 .

Table 12

Table 13

Vaccine schedule

Discussion

The outbreak of novel H1N1 in the human population has highlighted the zoonotic potential that influenza viruses possess. Even before the pandemic of this decade, there were many reported cases of swine to human transmission of influenza. As such, part of controlling this zoonotic threat is vaccination of swine against swine influenza viruses. In this study, we demonstrate how rapidly an efficacious swine influenza vaccine based on the alphavirus replicon expression system can be produced in response to an outbreak of a novel zoonotic strain. This reports on immunization of swine with a recombinant protein produced via an alphavirus replicon expression system. Replicon particle (RP) vaccines produced with this system have recently been utilized to induce protection against swine influenza virus (SIV) and porcine reproductive and respiratory syndrome virus (PRRSV) in swine. (Erdman MM, Kamrud KI, Harris DL, Smith J. 2010, Alphavirus Vector Vaccines Developed for Use in Humans Induce High Levels of Antibodies to Influenza Virus Hemagglutinin in Swine: Proof of Concept. Vaccine 28:594-596; Bosworth B, Erdman M, Stine D, Harris I, Irwin C, Jens M, Loynachan A, Owens G, Kamrud K, Harris DL. 2010, Virus-like replicon particle vaccine protects pigs against influenza. Comparative Immunology, Microbiology and Infectious Diseases 33 (2010) e99-el03.) The first proof of concept study demonstrated that a replicon particle vaccine administered to swine was able to induce high antibody HI titers against a human influenza strain. A subsequent study using an RP vaccine expressing the HA gene of a clade IV H3N2 SIV isolate confirmed that influenza HA RP vaccines given to swine are not only able to induce an antibody response, but also provide significant protection against a homologous viral challenge. In contrast to these earlier studies, this study used an alphavirus replicon expression system to produce recombinant HA protein in vitro; however, similar antibody response and protection from viral challenge was demonstrated.

The results demonstrate that influenza infection in swine with A/California/04/2009 is able to induce clinical symptoms and gross lesions comparable to other strains of SIV. (Vincent AL, Ma W, Lager KM, Janke BH, Webby RJ, Garcia-Sastre A, Richt JA. Efficacy of intranasal administration of a truncated NS 1 modified live influenza virus vaccine in swine. Vaccine. 2007 Nov 19;25(47):7999-8009. Epub 2007 Sep 29. PubMed PMID: 17933442; PubMed Central PMCID: PMC2099695 ; Vincent AL, Lager KM, Ma W, Lekcharoensuk P, Gramer MR, Loiacono C, Richt JA. Evaluation of hemagglutinin subtype 1 swine influenza viruses from the United States. Vet Microbiol. 2006 Dec 20;118(3-4):212-22. Epub 2006 Aug 1. PubMed PMID: 16962262; Sreta D, Kedkovid R, Tuamsang S, Kitikoon P,

Thanawongnuwech R. Pathogenesis of swine influenza virus (Thai isolates) in weanling pigs: an experimental trial. Virol J. 2009 Mar 25;6:34. PubMed PMID: 19317918; PubMed Central PMCID: PMC2678088.) In contrast with a previous study, several pigs (primarily in the non- vaccinated group) in this study exhibited clinical signs, mainly coughing and sneezing. This discrepancy may be due to the miniature pig model used in the previous study (Itoh Yet al. In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses. Nature. 2009 Aug 20;460(7258): 1021-5. PubMed PMID: 19672242; PubMed Central PMCID:

PMC2748827). In this study, vaccine administration induced specific antibody titers, reduced macroscopic and histopathologic lung lesions, and reduced viral load in both the nose and lung. Vaccinated pigs also demonstrated a higher average daily gain than non- vaccinates. These results demonstrate that this recombinant novel HA protein is efficacious when used as a vaccine against novel H1N1 swine influenza.

This study also demonstrated the quickness and flexibility with which a vaccine can be produced using the alphavirus replicon expression system. It took less than two months from the time the novel HA sequence was retrieved from GISAID database until pigs were administered the first vaccine dose. Traditional methods for producing influenza vaccines take much longer and are dependent on viral replication in embryonated eggs or on tissue culture cells with subsequent inactivation. In the face of an influenza epidemic, a quick turnaround is important in preventing further transmission and decreasing the zoonotic potential. The alphavirus replicon platform allows for rapid insertion of any influenza HA (or other) gene, making it an attractive influenza vaccine technology due to the constant antigenic shift and drift among influenza viruses.

Tissue or fluids from animals at a location where pigs have been exposed to influenza virus is obtained. Using the RT-PCR approach as described in Example 1 , HA of the virus is isolated. The sequence encoding HA is introduced into a vector and lysis of vero cells infected with the replicon for production of HA antigen (and mixed with an appropriate adjuvant) or, in another experiment, an RP vaccine produced using the procedures described in Example 1. Pigs are administered a vaccine and morbidity and mortality results measured. EXAMPLE 3

Foot-and-mouth disease (FMD) is a highly infectious disease of cloven-hoofed animals that rapidly spreads by contact and aerosol. (Bachrach HL. Foot-and-mouth disease: world-wide impact and control measures. In: Kurstak E, Maramorosch K, editors. Viruses and environment. New York: Academic Press; 1978. p. 299-310.) Outbreaks of FMD in Taiwan, Japan, South Korea, the United Kingdom, and the Netherlands, countries that had been FMD-free for many decades, resulted in significant adverse economic consequences including slaughter of large numbers of animals and loss of export markets. Even the very limited FMD outbreak in the United Kingdom in the summer of 2007, which resulted from the escape of FMDV from the Pirbright facility that houses both the government Institute of Animal Health and the Merial vaccine manufacturing laboratory, resulted in significant economic losses (~$100 million US). These outbreaks demonstrate the vulnerability of FMD- free countries, such as the US, to this disease. Disease control procedures include restriction of animal movement, slaughter of infected and exposed animals, and vaccination in certain situations. However, current vaccines, which are chemically inactivated preparations of live virus, have a number of shortcomings including the inability to induce rapid protection.

An RP vaccine that co-expresses the FMDV capsid and 3C proteinase coding regions was produced by engineering the capsid-3C proteinase cassette into a replicon vector and generating RP that could be used to immunize cattle. See GenBank Accession No.

AY593768 (2005). The capsid-3C proteinase cassette was obtained from officials at the USDA, ARS, ARS, NAA Plum Island Animal Disease Center Foreign Animal Disease Research Unit. Data from these vaccinations is shown.in the Figure 19 and Table 15. Table 15 Lesion scoring 5 Days post-FMDV challenge

Cattle vaccinated one time with lxlO⁹ IU A24 RP showed nearly complete protection from systemic disease after FMDV challenge (one animal showed lesions on one hoof while all others remained symptom free). Half of the animals that received 5xl0⁸ IU of A24 RP were protected from significant systemic disease. Dose A: lxlO⁹ IU. Dose B: 5xl0⁸ IU. Numbers shown over the columns pre-challenge represent the # positive animals /total # animals. Virus neutralization assays were run on serum collected at 0, 7, 14 and 21 days post vaccination. Results are shown below. All of the animals in the highest dose group demonstrated FMDV neutralizing antibodies by day 7 that were maintained through the day of challenge (day 21). Two candidate rapid response vaccine approaches against foot and mouth disease virus (FMDV) are described here. The first consists of replicon RNAs that express FMDV genes packaged into particles (RP). A similar RP as described above is prepared using an autogenous source and animals vaccinated as outlined below. The purified RP represent the vaccine. The second consists of a protein lysate generated by introducing replicon RNAs that express FMDV genes into cells; a recombinant subunit (RS) lysates vaccine is then harvested by lysing the transfected cells after vaccine antigen has been produced. Both replicon-based approaches provide the ability to differentiate between vaccinated and infected animals.

Replicon vectors co-expressing the FMDV capsid and 3C proteinase coding regions of FMDV are prepared. Expression of these FMDV proteins produces virus-like particles (VLP) because the 3C proteinase processes the coat proteins allowing them to self-assemble into antigenic VLP. The P1-2A capsid coding region, the 2B coding region and the complete 3C protease coding region will be expressed. (Moraes MP, Mayr GA, Mason PW, Grubman MJ. Early protection against homologous challenge after a single dose of replication- defective human adenovirus type 5 expressing capsid proteins of foot-and-mouth disease virus (FMDV) strain A24. Vaccine 2002;20: 1631-9.) Because most of the FMDV

nonstructural proteins are not included in the genes engineered into the replicon vector animals vaccinated with this can be unequivocally differentiated from infected animals.

Replicon clones expressing at the highest relative level and which product the highest titer RP are selected. Monoclonal antibodies are used that are cross reactive with all seven serotypes of FMCV in yield and expression analysis.

The first approach is to generate an RNA subunit (RS) vaccine by introducing the replicon RNA that expresses the FMDV capsid and 3C proteinase coding regions into cells in culture. Once the replicon carrying the FMDV genes has been introduced into cells each of the individual cells express the FMDV proteins. The FMDV proteins expressed in the cells are harvested by lysing the cells creating an FMDV protein lysate that constitutes the RS vaccine. In brief, RNA transcripts will be produced in vitro (Promega RiboMAX

transcription system) from the replicon plasmid and purified by either spin-column (gel binding and elution) or size exclusion chromatography, followed by agarose gel analysis to assess integrity, and quantification by ultraviolet (UV) absorbance. Specified mass amounts of the replicon RNA will be mixed with certified Vero cells in electroporation chambers and pulsed using optimal conditions for transfection efficiency and protein expression.

Electroporated cell suspensions will be seeded into individual roller bottles with media containing serum and incubated at 37°C in 5% C0₂ for 18-24 hr. Following incubation, cells are trypsinized and pelleted by centrifugation. Cells are then lysed by resuspending the cell pellet with a mammalian cell lysis buffer (RIPA Lysis and Extraction buffer, Thermo Scientific). The resultant lysate is tested for potency via Western blot analysis to confirm protein expression.

In RS potency assays, densitometry analysis of Western blots specific for FMDV VP2 capsid protein will be used to determine a relative concentration of FMDV antigen. The relative antigen concentration will be associated with a total cellular protein concentration determined using the BCA Protein Assay Reagent (bicinchoninic acid, Pierce, Rockford, IL) method and a bovine serum albumin protein standard curve. The maximum concentration of FMDV antigen will be based on the minimum formulation dilution possible and volume restrictions linked with practical vaccination of the test animals. In addition to the most concentrated FMDV antigen dose, two additional dilutions of FMDV antigen lysates will be formulated. The two additional dilutions will represent a 1 :5 and a 1 : 10 dilution of the highest dose.

The second approach is to generate an FMDV RP vaccine. FMDV RP vaccines are produced by introducing into Vero cells by electroporation a replicon RNA that expresses the FMDV genes and two helper RNAs. FMDV RP are then harvested from the cells approximately 18 hours post electroporation; the RP express the FMDV capsid and 3C proteinase coding regions when introduced into animals by vaccination. In brief, RNA transcripts will be produced in vitro as described above from the replicon and helper plasmids and purified by either spin-column (gel binding and elution) or size exclusion

chromatography, followed by agarose gel analysis to assess integrity, and quantification by UV absorbance. Specified mass amounts of the replicon and helper RNAs will be mixed with certified Vero cells in electroporation chambers and pulsed using various electroporation parameters to identify the optimal conditions for transfection efficiency and RP yield.

Electroporated cell suspensions will be seeded into individual roller bottles containing serum- free medium and incubated at 37°C in 5% C0₂ for 18-24 hr. Following incubation, media and cells from the roller bottles will be combined and pumped through a charged depth filter. RP will be eluted from the cells and filter using a high NaCl concentration buffer and stored at - 80°C until ready for use. The infectious titer of the RP preparation will be measured by antigen-specific IFA and tested at defined MOI in a CPE assay to assure the absence of detectable replication-competent virus. After a negative result is obtained from the CPE assay, the RP preparation is considered devoid of detectable RCV and can subsequently be handled under BL 1 laboratory conditions. Potency assays are used to determine RP titer based on an IFA assay and qRT-PCR analysis to determine the number of RNAs associated with each RP. Determining the total number of RNA copies helps to assure vaccine consistency from serial to serial. The method for calculating the potency is based upon an IFA specific for the vaccine H3 antigen. The H3 positive cells are observed and quantified. Individual wells of the IFA tissue culture plate are visualized under 10X magnification and wells containing 20 to 50 H3 positive cells per grid field are used. A total of five fields per well are counted. A duplicate well is counted in the same manner. An average of the ten readings is used to calculate the potency, or RP/ml. The total number of H3 positive cells is determined by inserting the average of the ten counts into the following equation: potency = (average)x(dilution)x(100)/(0.12) where average represents the average of ten positive H3 cell counts for the sample, dilution represents the well in which the average H3 positive cells were counted, 100 is a constant representing the surface area of the wells in the tissue culture plate and 0.12 is a constant representing the volume of RNA particle vaccine tested (ml).

Densitometry analysis of Western blots specific for FMDV VP2 capsid protein will be used to determine a relative concentration of FMDV antigen. The relative antigen concentration will be associated with a total cellular protein concentration determined using the BCA Protein Assay Reagent (bicinchoninic acid, Pierce, Rockford, IL) method and a bovine serum albumin protein standard curve. The maximum concentration of FMDV antigen will be based on the minimum formulation dilution possible and volume restrictions linked with practical vaccination of the test animals. In addition to the most concentrated FMDV antigen dose, two additional dilutions of FMDV antigen lysates will be formulated. The two additional dilutions will represent a 1:5 and a 1 :10 dilution of the highest dose. Animals

Species/Breed/Strain: Bovine, no restriction on breed or strain

Sex: No restrictions

Approximate Initial Age: 3-6 months at time of vaccination. No weight restriction and/or weight (Day 0).

Approximate Number: 10 enrolled

Source of Supply/Origin: Animals sourced from commercial farm or production system Identification: Each animal will be identified by a uniquely numbered ear tag

Conditioning/ Acclimation: Acclimated > 5 days prior to administration of investigational veterinary product (IVP) Management/Housing: Animals will be fed and watered in accordance with the

standard procedures of the study site. Animals will be handled in compliance with site Institutional Animal Care and Use Committee (IACUC) approvals and site facility regulations. Exclusion: Only clinically healthy, animals will be enrolled in the study.

Unsuitable animals will be excluded from the study at the discretion of the Investigator and/or the attending veterinarian prior to the administration of the IVP. Reasons for any animal being removed from the study will be included in the final report.

Allotment: The identification number of each enrolled animal will be recorded on the allocation plan prior to the administration of the IVP. Table 16 Investigational Veterinary Product

Storage < -70°C

IDL Challenge Dose Approximately 1-2 x 10⁴ bovine infectious dose 50 (BID₅₀) per animal

IDL Challenge Intradermal inoculation at multiple sites in the tongue/0.5 1.0 total mL. Route/Volume This route of challenge in cattle is one recommended by the OIE.

Table 18 Study Groups

Vaccination and Challenge

On Day 0, blood from all cattle will be collected (baseline). Cattle will be vaccinated once with test article (T02, T03) or sham-immunized (T01) at Day 0. On Day 7 and 14 blood from all cattle (T01-T03) will be collected and tested for the presence of serum virus neutralizing (SVN) antibodies to FMDV A24. Cattle will be challenged with FMDV serotype A24

Cruzerio SGD strain according to OIE guidelines. For challenge administration, each animal will be sedated and then receive intradermal inoculations at multiple sites (0.5-1.0 total mL) in the upper surface of the tongue.

An RP or RS vaccine is especially useful as there currently is no approved FMDV vaccine in the US. Rather, the US would have to rely upon sources in other countries, and those vaccines would be unlikely to be effective in US strains and biotypes. With the present invention, a US based FMDV could be biotypes, and vaccine prepared quickly.

Tissue or fluids from animals at a location where animals have been exposed to FMDV virus is obtained. Using the RT-PCR approach as described in Example 1 , FMDV capsid and 3C proteinase coding regions of the virus are isolated. The sequences are introduced into a vector and lysis of vero cells infected with the vector or, in another experiment, an RP vaccine produced using the procedures described in Example 1. Animals are administered a vaccine and morbidity and mortality results measured. EXAMPLE 4

The following demonstrates use of interfering RNA and autogenously sourced as a vaccine for animals. Those experiments below in which IMNV vaccines and WSSV VP28 vaccines were prepared using a shrimp farm as the source of the nucleic acid of interest, first amplified in disease free animals before sequencing.

Determination of RNAi Sequences

In order to evaluate candidate sequences that would induce RNAi in response to IMNV, in vitro dsRNA was synthesized corresponding to regions of viral genome. Template DNA for in vitro transcription was created by extracting viral RNA using a commercial nucleic acid purification kit (Qiagen RNeasy Mini). cDNAs to IMNV genome were created using specific oligionucleotide primers designed from sequences available (GenBank accession no.EF061744). (Senapin, S., Phewsaiya, K., Briggs, M., Flegel, T. W., 2006. Outbreaks of infectious myonecrosis virus (IMNV) in Indonesia confirmed by genome sequencing and use of an alternative RT-PCR detection method. Aquaculture 266, 32-38.) Reverse transcription (Thermoscript RT Invitrogen) was performed by adding 5 uL of RNA extract to the reaction mix and incubated at 50 degrees for 60 minutes per manufacturer's instructions. Following reverse transcription, template cDNA (-50 ng) was added to a PCR master mix (PuReTaq Ready-To-Go PCR Beads) and thermocycling was performed using oligonucleotideprimers to specific regions of the IMNV genome (Table 19). Cycling conditions were 95 ° C for 4:00 followed by 35 cycles at 94° C for :30, 55°C for :30, 72° CI :00 and a final extension of 10:00 at 72° C

dsRNA sequences used in experiments 1-3 (see list of sequences at end): dsRNA#3 (SEQ ID NO: 1)

dsRNA#3 5' Truncate (SEQ ID NO: 2)

dsRNA#3 3 'Truncate (SEQ ID NO: 3)

dsRNA #2 (SEQ ID NO: 4)

dsRNA#l (SEQ ID NO: 5)

GFP dsRNA (SEQ ID NO: 6)

Table 19: Oligonucleotide Primer Sequences

Primer Sequence 5 '-3' eGFPT7F TAATACGACTCACTATAGGGAGAATGGTGAGCAAGGGCGAG (SEQIDNO: 7) GAGCTGT

eGFPT7R TAATACGACTCACTATAGGGAGATTACTTGTACAGCTCGTCC (SEQIDNO: 8) ATGCCG

Pepl95F AGAAAGTTTGTTTCGTAGAGCGAGA

(SEQIDNO: 9)

Pe l474R AAAGGTGGCAGGTGTCCATACTGA

(SEQIDNO: 10)

Pe l 95 T7F TAATACGACTCACTATAGGGAGAAGAAAGTTTGTTTCGTAGA (SEQIDNO: 11) GC

Pe 1474 T7R TAATACGACTCACTATAGGGAGAAAAGGTGGCAGGTGTCCA (SEQIDNO: 12) TAC

Capsid4 F AATTTGGGTGGTTGGGACACATGG

(SEQIDNO: 13)

Capsid 4 R CCCGACTTTCGTGCACACAACTTT

(SEQIDNO: 14)

Capsid4T7 F TAATACGACTCACTATAGGGAGAAATTTGGGTGGTTGGGAC (SEQIDNO: 15) ACA

Capsid4 T7R TAATACGACTCACTATAGGGAGACCCGACTTTCGTGCACAC (SEQIDNO: 16)

RdRPl F TCAACTCACTCGCAGCTGAAGGTA

(SEQIDNO: 17)

RdRPl R AATATAGCAACGTCGTCTCCGCGT

(SEQIDNO: 18)

RdRPl T7 F TAATACGACTCACTATAGGGTCAACTCACTCGCAGCTGAAG (SEQIDNO: 19)

RdRPl T7 R TA AT AC G ACTC ACTATAGGG AATAT AGC A AC GTC GTCTC CG (SEQIDNO: 20)

VP19 T7 F TAATACGACTCACTATAGGGAGACGAAGCTTGGCCACCACG (SEQIDNO: 21) ACT

VP19 T7 R TAATACGACTCACTATAGGGAGACGGAGCTCCTGCCTCCTCT (SEQIDNO: 22) TGGGGTAA

VP28F CGGGATCCATTGAAGGCCGCGCCATGGATCTTTCTTTCACTC (SEQ ID NO: 23) T

VP28R CGGAGCTCTTACTCGGTCTCAGTGCCAGA

(SEQ ID NO: 24)

VP28 Ascl F GAGAGGCGCGCCATGGATCTTTCTTT

(SEQ ID NO: 25)

VP28 Pad R TCTCTTAATTAACTACTCGGTCTCAGT

(SEQ ID NO: 26)

AscPe lanti F CTAAGGCGCGCCTAAAGGTGGCAGG

(SEQ ID NO: 27)

-ssdsRNA#3 CGCGTTAATTAAAGAAAGTTTGTTTCG

(SEQ ID NO: 28)

Products were then cloned into pCR4.0 vectors (Zero Blunt TOPO PCR cloning kit, Invitrogen) and transformed into E. coli (TOP 10, Invitrogen). Plasmids preparations from these transformants were used as the template source for in vitro dsRNA synthesis. dsRNA was prepared using Ambion MEGAscript® RNAi Kit following manufacturer's directions. Briefly, opposing T7 RNA polymerase can be used at 5 ' ends of one DNA template or a single T7 promoter at opposite ends of a region to be transcribed is used with two templates, or two templates transcribed to make complementary RNA molecules that are annealed. DNA templates for transcription were PCR products with addition of T7 promoter sequences amplified using the primer sequences described. (See, e.g. Ujvari, A and Martin, CT.

Identification of a Minimal Binding Element within the T7 RNA Polymerase Promoter. /. Mol. Biol. (1997) 273, 775-781 ; Sousa et al. (2003) "T7RNA polymerase" Prog Nucleic Acid Res Mol Biol 73: 1-41.). PCR cycling conditions were 95 ° C for 4:00 followed by 35 cycles at 94° C for :30, 61°C for :30, 72° C 1 :00 and a final extension of 10:00 at 72° C. These clones were then incubated overnight (16 hours) at 37° C forming dsRNA. dsRNA products were then incubated with DNase I and RNase for 1 hour and purified using the provided columns. dsRNA synthesis was confirmed by gel electrophoresis in comparison with a molecular weight ladder (pGEM ladder, Promega) and product was quantified

spectrophotometrically (BioRad SmartSpec).

Animal Rearing Specific pathogen free (SPF) postlarvae were received from Shrimp Improvement Systems (Plantation Key, Florida) and reared in a biosecure animal holding facility. Animals were placed into 1000L Poly tanks containing artificial seawater (Crystal Sea Marine Mix), an oystershell airlift biofilter, and an activated carbon filter. Animals were fed a commercial growout diet (Rangen 35/10, Buhl, Idaho) until 5 grams in weight.

Preparation of Viral Inoculum

A modification of the methods from Hasson et al (Hasson, K. W., Lightner, D. V., Poulos, B. T., Redman, R. M., White, B. L., Brock, J. A., Bonami, J. R., 1995. Taura syndrome in Penaeus vannamei: demonstration of a viral etiology. Disease of Aquatic Organisms 23, 115- 126) was used to make a clarification for viral inoculation. Briefly, whole frozen animals that tested positive for infection with IMNV by PCR were received from Shrimp Improvement Systems. Tail muscle was removed from these animals, diluted 1 :3 in TN buffer (.02 M Tns-HCl , 0.4 M NaCl, pH 7.4) and homogenized in a sterilized Waring blender for 5 minutes. The macerate was placed into centrifuge tubes and centrifuged at 4000 x g. The supernatant was then removed and centrifuged again at 15,000 x g for 30 minutes. A final centrifugation step was performed at 25,000 x g for 60 minutes. This supernatant was diluted 1 : 10 in sterile 2% saline and filtered through 0.2 micron syringe filters (Whatman). This clarification was then aliquoted into cryotubes and frozen at -80° C for challenge studies.

Determination of Challenge Dose

A dilution series of inoculum was prepared by diluting the prepared stock virus 10 fold and 100 fold into sterile 2% saline. Stock virus, a ten fold dilution, and a 100 fold dilution were injected into the third abdominal segment into groups of 20 naive SPF animals weighing 5-8 grams each. Animals were observed twice daily for mortality. All doses resulted in 100% mortality at varying time points. 100% mortality took 2 days for stock concentration, 7 days for ten fold dilution, and 12 days for 100 fold dilution (Figure 20). The 100 fold dilution of the stock virus was used as the viral challenge dose for the described challenge experiments.

Histopathology

Moribund animals that were found prior to death were fixed in Davidson's fixative for 24 hours before being transferred to 70% EtOH. Tissues were embedded in paraffin, cut into slides and stained with Hematoxylin and Eosin and evaluated for the presence of IMNV lesions.

Inoculation of animals

Double stranded RNA (dsRNA) was prepared by diluting dsRNA into RNase free water to the specified concentration. 50 [iL was injected into the muscle of the third abdominal segment of animals using a tuberculin syringe.

Study Design #1

Two hundred liter tanks containing synthetic seawater and an oystershell airlift biofilter were stocked with 20 SPF juveniles weighing 5-7 grams and allowed to acclimate for 72 hours. Following acclimation, four separate dsRNA constructs corresponding to three different segments of the IMNV genome were evaluated by comparison to a hetereologous dsRNA control. A total of 2 μg of in vitro synthesized dsRNA was inoculated into animals into randomized tanks. Following vaccination animals were challenged 48 hours later with IMNV. Animals were counted daily for mortality. Moribund animals were fixed for histopathology. Following this treatment, surviving animals from vaccination and challenge with dsRNA #3 were reared (n=16) for an additional 60 days and then rechallenged with undiluted viral stock.

Study Design #2

Two hundred liter tanks containing synthetic seawater were stocked with 10 animals weighing 5-7 grams that were allowed to acclimate for 72 hours. Following acclimation, 6 experimental groups received a dose (2, .2 or .02 μg) of a dsRNA construct (dsRNA #2 or dsRNA #3), control groups received 2 ug of a heterologous eGFP dsRNA control. These groups were then split with one being challenged 2 days following vaccination, and another being challenged 10 days following vaccination. Mortality was assessed daily and moribund animals were fixed for histopathology. Results

Experiment #1

Two of the dsRNA constructs demonstrated protection against IMNV challenge. dsRNA#2 (SEQ ID NO: 4) had 62% survival (38% mortality) in comparison to only 3%(97% mortality) for the non- vaccinated controls at 30 days post vaccination. The effect of dsRNA #3 (SEQ ID NO: 1) was even more robust with over 80% survival (Figure 21). Significant differences (P<.05) were calculated between dsRNA #2 and #3-injected animals as compared to controls according to Oneway ANOVA followed by Tukey's multiple comparison test using SPSS software. No significant differences were evident between animals injected with dsRNA #1, dsRNA GFP or the 2% saline control. Non-challenge controls remained at 100% survival throughout the duration of the study. Animals receiving non-sequence specific dsRNA had similar mortalities to the non-vaccinate group.

The surviving animals from dsRNA#3 (SEQ ID NO: 1) group had 100% (16/16) survival following the second challenge (60 days after the primary virus challenge) with one hundred fold higher virus concentration. This indicates that protection from challenge is robust even after an extended period of time has passed between the first and second viral challenge.

Experiment #2

The construct dsRNA #3 (SEQ ID NO: 1) showed excellent protection even at the lowest dose and longest interval between vaccination and challenge at 80% survival. (Figure 23) In comparison, low doses of dsRNA#2 (SEQ ID NO: 4) appeared to have little impact on survival with survival rates of 10% and 30% following challenge. However, non-vaccinated groups had no survival in either group and non-sequence specific administered group had 10% survival when challenged at 48 hours (Figure 22). Non-challenged controls had survivals of 100%. After 30 days, significant differences (P<.05) were noted with dsRNA #2 and #3 -injected animals as compared to controls according to Oneway ANOVA followed by Tukey's multiple comparison test using SPSS software. No significant differences were evident between animals injected with dsRNA #1, dsRNA GFP or the 2% saline control. Experiment #3

To determine whether the entire dsRNA#3 sequence was required to provide the protection noted above two additional dsRNAs that are simple truncations of the full length dsRNA#3 were tested (dsRNA#3 5' truncate and dsRNA#3 3' truncate). Animals weighing 5-7 grams were used as described above to test the new dsRNA#3 sequences (2 μg of each dsRNA were used). The construct dsRNA #3 3' truncate (SEQ ID NO: 3) was shown to be 100% protective when delivered 10 days post vaccination at a dose of .02 μg (Figure 24 A). dsRNA 5' truncate (SEQ ID NO: 2) and the original dsRNA3 (SEQ ID NO: 1) were shown to be 90% protective at 25 days (15 days post challenge) when challenged 10 days following vaccination. These experiments show preferred sequences having a very strong effect on dose and duration of RNAi trigger components that will be delivered through the described following vector systems.

Further truncations also showed protection (Figure 24B), using the same procedures described above. A 154bp sequence (dsRNA#3 223-376, SEQ ID NO: 61) showed 100% protection, a 82bp sequence (dsRNA#3 194-275, SEQ ID NO: 56) showed 100% protection and a 57bp sequence (dsRNA#3 219-275, SEQ ID NO: 51) 73% protection.

Replicon Particles

Replicon particles were produced as described, supra.

Alphavirus Replicon Proof of Concept

Alphavirus replicon particles expressing structural proteins and antisense sequences of WSSV and IMNV virus were created by cloning genes from a commercially synthesized gene sequence (GeneArt) into an existing alphavirus backbone vector. The WSSV genes of interest, in this case VP19, VP28, and the complementary sequence to VP19 (VP19 antisense) were created using a sequence derived from a virulent WSSV isolate from

Thailand (AF369029.2 GI:58866698). In the case of IMNV sequences were derived from available sequence from an Indonesian isolate downloaded from GenBank (EF061744.1 01: 124303516), and reverse complement of the region spanning from 95-474 bases of the published sequence. Gene constructs were designed to include appropriate restriction sites on both the 5' and 3' ends to facilitate cloning onto the replicon plasmid. Following insertion of the protective molecule into the replicon vector, the insert was sequenced to confirm the identity of the construct (Iowa State University DNA Sequencing Facility). The replicon plasmid DNA was linearized and used to generate RNA transcripts by run-off transcription using a commercially available in vitro transcription kit (RiboMAX T7 Express, Promega). Replicon RNA containing the target gene (VP28, VP19, VP19 antisense, IMNV -ssRNA of dsRNA#3), and the two helper RNAs that code for the VEE capsid or glycoprotein genes were prepared using the same run-off transcription method. Specified (previously optimized) mass amounts of the replicon and helper RNAs were mixed with Vero cells in electroporation chambers and pulsed using previously optimized square wave electroporation parameters.

Electroporated cell suspensions were seeded into roller bottles containing serum-free medium and incubated at 37°C in 5% C0₂ for 16-18 hours. Replicon particles (RP) were harvested from culture fluids and the infectious titer of the RP preparation was measured by antigen- specific IFA and tested in a cytopathic effect (CPE) assay to assure the absence of detectable replication-competent virus. RP was purified by size exclusion/ ionic exchange filtration. The potency (infectious titer) of the purified bulk RP will be determined by IFA and the preparation will be formulated and frozen at -80 °C.

Sequences insertions used in replicon plasmids (see list of sequences at end): VP28 (SEQ ID NO: 29)

VP19 (SEQ ID NO: 30) encoding the protein, and also transcribed to produce dsRNA VP19-antisense (SEQ ID NO: 31)

VP19-IR (inverted repeat DNA producing dsRNA) (SEQ ID NO: 32)

DNA transcribed to produce antisense strand of dsRNA#3) (SEQ ID NO: 33)

Red Florescent Protein (RFP) (SEQ ID NO: 34) The titer (IU/ml) of the RP preparations generated was measured. A representative example of the IU/ml titer of the RP preparations generated is: VP- 19 RP =1.4E8 IU/mL, VP-28 RP = 1.2E8 IU/mL, and VP19-Anti RP = 5.86E7 IU/mL, IMNV RNA3 antisense =3.49E8/ml IU/mL The RP preparations all passed the CPE assay by demonstrating the absence of detectable replication competent virus. Following release assays the RP were considered appropriate for use in the studies described below. For experiment #5 an additional group of antisense VP19 replicons were created that allowed for an increase titer of 1.26E8IU/mL. Preparation of WSSV for use as a challenge stock virus were amplified utilizing SPF stocks of L. vannamei with a virulent strain of WSSV (Don Lightner, University of Arizona). Fifty (50) SPF juvenile shrimp weighing approximately 12 grams were exposed per os with infected tissue from moribund shrimp that were PCR positive for WSSV (infected tissues used were stored at -80 °C prior to use). Infected tissues were diluted 1 :3 in TN buffer (.02 M Tris-HCl , 0.4 M NaCl, pH 7.4) and homogenized in a sterilized Waring blender for 5 minutes. The macerate was placed into centrifuge tubes and centrifuged at 4000 x g. The supernatant was then removed and centrifuged again at 15,000 x g for 30 minutes. A final centrifugation step was performed at 25,000 x g for 60 minutes. This supernatant was diluted 1 : 10 in sterile 2% saline and filtered through 0.2 micron syringe filters (Whatman). This clarification was then aliquoted into cryotubes and frozen at -80 °C for challenge studies. Challenge dose was then optimized by injecting SPF animals with serial dilutions of viral inoculum in 2% saline. A challenge dose of 1 part inoculum and 10,000 parts 2% saline resulted in 10-20% survival 14 days after challenge and was used for the viral challenge dose for the described studies.

Viral Challenge: Experimental animals were challenged by injection 3 days after the initial injection with RP. Experimental and control groups will be observed for mortality over a 21 day period. At the termination of the experiment the remaining individuals were sedated and euthanized in an ice slurry, fixed whole in Davidson's fixative, and submitted for histological analysis. A gill tissue sample was taken and frozen at -20 °C for PCR testing if needed. Experiment #4 Experimental Design

SPF juvenile L. vannamei weighing approximately 5 grams were placed into 16 tanks containing 10 animals and synthetic seawater (Crystal Sea Marine Mix) at 30 ppt salinity and maintained at 25 °C. Three replicate tanks were provided for each experimental group. Experimental animals were injected with 50 μΕ of RP expressing VP28 (SEQ ID NO: 28) or VP19 (SEQ ID NO: 30) at a concentration of 10E8 IU/mL or VP19 antisense RP (SEQ ID NO: 31) at a concentration of 10E7 IU/mL into the ventral sinus. A sham injection control group was injected with 50 uL of cell culture media used as a control. VP19 naked double stranded RNA (SEQ ID NOs: 49 and 50) was used as a positive vaccine control as it had provided 100% protection in previous experiments.

Experiment #5 Experimental Design

SPF juvenile L. vannamei weighing approximately 5 grams were placed into 15 tanks containing 10 animals and synthetic seawater (Crystal Sea Marine Mix) at 30 ppt salinity and maintained at 25 °C. Experimental animals were injected with 50 uL of RP expressing VP19 at a concentration of 10E8 IU/mL or VP 19 antisense RP at a concentration of 10E7 IU/mL into the ventral sinus. A sham injection control group was injected with 50 uL of cell culture media used as a control. VP19 naked double stranded RNA was used as a positive vaccine control of 10 days post vaccination as it had provided 100% protection in previous experiments

Experiment #6 Experimental Design

SPF larvae and postlarvae were be placed into petri dishes containing 25 mL seawater and 10E7 IU/mL of RP expressing the RFP reporter protein. Immersion exposure was done at room temperature for 2 hours. Animals were then transferred to 500 mL flasks containing seawater and an airstone. Whole larvae were sacrificed at 24, 48, and 72 hours post-exposure and evaluated for fluorescence using epifluorescence microscopy. Control animals were immersed into tanks containing cell culture media, and evaluated using the same method. This study was used to determine if a) RP infectivity remains intact through the digestive tract and b) RP are able to infect and express a foreign protein in larval and post larval animals.

Experiment #7

SPF juvenile L. vannamei weighing approximately 5 grams were placed into tanks containing 10 animals and synthetic seawater (Crystal Sea Marine Mix) at 30 ppt salinity and maintained at 25 °C . To evaluate the duration of immune response for extended periods of time in animals administered specific dsRNA or non-specific dsRNA animals were given specific dsRNA (VP19 or VP28) or non-specific (eGFP) by IM injection (5 μg) and challenged 3 days following administration. Following the primary challenge in which only slight mortality was observed, a second challenge was performed 21 days later.

Experiment #8

In order to compare methods of delivery, and determine if an orally delivered sequence was protective, SPF juvenile L. vannamei weighing approximately 5 grams were placed into tanks containing 10 animals and synthetic seawater (Crystal Sea Marine Mix) at 30 ppt salinity and maintained at 25 °C. Experimental animals were fasted for 24 hours, injected with 5 ug of dsRNA VP 19 or reverse gavaged (enema) with 5 μg VP 19 dsRNA diluted in sterile water. Animals were challenged 14 days after vaccine administration.

Results

Experiment #4

At 21 days post challenge, VP19 dsRNA (Control), VP19 RP, VP19 antisense RNA-RP or VP28 RP showed 100%, 70%, 40% and 40% survival respectively. The positive control group showed 20% survival (Figure 25). This study demonstrates that VP19 dsRNA and VP19 expressed by RP provide protection against mortality due to WSSV. As seen in Experiment 1 and 7, protection up to at least 24 days was observed. Referring to Figures 21, 22, 23 and 24B. protection up to at least 30 and at least 40 days is provided. This study will be repeated and duration of this protection following inoculation will be assessed. Experiment #5

For the group that was challenged 3 days post vaccination, VP19 RP, VP19 antisense -RP and positive control group showed 5%, 35% and 0% survival, respectively 14 days post challenge as shown in Figure 26. For the group that was challenged 10 days post vaccination VP19 dsRNA (Control), VP19 RP and VP19 antisense RNA-RP showed 95%, 5% and 60% survival 21 days post challenge, respectively, as shown in Figure 27. The positive control group for the 10 day post vaccination group showed 20% overall survival. See Figures 26 and 27.

Experiment #6

Fluorescence was difficult to evaluate in the post larval stages due to autofluorescence present in the gut tissue in both controls and experimental groups. In contrast, the larval stages evaluated (Mysis and Zoea) demonstrated strong specific RFP fluorescence in both gut and gills when compared with controls at 48 and 72 hours post inoculation with RFP RP. This shows that protein can be delivered to the aquatic invertebrate digestive tract and that immersion vaccination of larval animals provides a feasible delivery system for replicon particles. Experiment #7

Differences in survival were observed between VP19 (100% survival), VP28 (83%), Nonspecific dsRNA (33.3%) and unvaccinated control (20%) (Figure 28, 29) following challenge at 21 days. This demonstrates the differences between specific and non-specific dsRNA in the duration of the protective response.

Experiment #8

Animals administered VP 19 dsRNA via IM and reverse gavage demonstrated protection (95% and 100% survival respectively) versus controls. (Figure 30) Experiment #9

Study Design:

200L tanks were stocked with 3-5 gram SPF growth line animals and allowed to acclimate for 24 hours. Tanks were equipped with an oystershell airlift biofilter that has been allowed to mature in an LT tank with ammonia. Animals were divided into three groups, one receiving dsRNA3 82 bp dsRNA fragment, one receiving eGFP (green fluorescent protein (GFP) gene (Sheen et al., Plant J. (1995) 8(5):777-84) as a heterologous dsRNA control treatment , and one receiving sterile water as a no dsRNA treatment. The dsRNA treatment groups received a 100 uL injection containing 5 μg of in vitro synthesized dsRNA 2 days following challenge with IMNV. Animals were challenged 2 days prior to dsRNA

vaccination with a 1 : 100 dilution of IMNV clarification. Groups were counted daily for 30 days and evaluated for mortality. Moribund animals were fixed in Davidson's solution for histopathology and muscle tissues taken for qPCR analysis. Animals were frozen at -80 degrees at termination of study.

Primers used for producing the dsRNA #3 were SEQ ID NO: 59, SEQ ID NO: 60, to produce SEQ ID NO: 56. Primers for producing GFP included SEQ ID NO: 7, SEQ ID NO: 8 and SEQ ID NO: 6 is the DNA producing GFP dsRNA for control.

Table 20

Results

Animals receiving a treatment of dsRNA3 82 bp demonstrated a 50% survival following challenge with IMNV. In comparison, animals receiving either eGFP dsRNA or sterile water as a control demonstrated 0% survival (Figure 31).

Conclusions dsRNA#3 82 bp can successfully reduce mortality when administered 2 days post infection with IMNV.

Experiment #10

Experimental Animals

Specific pathogen free (SPF) juvenile L. vannamei weighing 3-5 grams were stocked into 200 L tanks (10 animals/tank) and allowed to acclimate for 48 hours. Each tank contained artificial seawater with oystershell biofilter and activated carbon.

Feed formulation

Chitosan encapsulated particles were prepared using VP19 dsRNA, supra SEQ ID NO: 30), or IMNV dsRNA3 (not truncated, SEQ ID NO: 1). 0.2 grams chitosan was dissolved in 100 ml sodium acetate buffer. 1.0 mL of this solution was then transferred to a new bottle with 99 ml of 50 mM sodium acetate buffer (1 : 100 dilution), resulting in a 0.002% w/v solution of chitosan. 120 ug of each dsRNA (VP 19 and dsRNA3) were diluted in a sodium sulfate solution (0.2 M sodium acetate and 0.2 M acetic acid) to a total volume of 300 ul. 300 ul dsRNA solution was combined with 300 ul 0.002% chitosan solution. The solution was heated in a 55° C water bath for 1 minute, and promptly vortexed for 30 seconds. The tubes were then centrifuged at 13,200 x g for 10 minutes. Following the centrifugation, the solution was resuspended by pipetting and top coated onto 1 gram ground feed. The entire 600 ul of the chitosan-dsRNA solution was added first, followed by 600 ul 2% agarose. The feed was then blended with pipette tip to create evenly mixed clumps, which solidified after several minutes.

Experimental Design

Table 21

3. VP 19 dsRNA 10 3 67%

without chitosan

4. Positive control 10 3 0

After 3 days shrimp in each treatment group were challenged 100 uL with .2 micron filtered WSSV clarification diluted in 2% sterile saline at WSSV 1: 1 x 10⁵. Daily feeding of 10% biomass and 10% water exchange was performed daily to remove molts, excess food and fecal material. Mortality was observed for 21 days and samples of dead animals were frozen at -80 for further testing.

Results

Following challenge with WSSV, animals that were treated with feed coated with VP 19 dsRNA demonstrated 67% survival. In addition, groups that were treated with feed coated with chitosan nanoparticles containing VP19 dsRNA demonstrated 33% survival following challenge with WSSV. Animals that received sham treatment in the feed (Positive Control) had 0% survival following challenge. (See Figure 32). Experiment #11

HV156: dsRNA duration

The experiment demonstrated dsRNA82(l 94-275) (SEQ ID NO: 56) and dsRNA3 (95-474) (SEQ ID NO: 1) vaccination efficacy at 30 days post vaccination

15 x 200L tanks were stocked with 3-5 gram SPF growth line animals and allowed to acclimate for 24 hours. Tanks were equipped with an oystershell airlift biofilter that has been allowed to mature in an LT tank with ammonia. The dsRNA treatment groups received a 100 μΕ injection containing 2.0 μg of dsRNA (DE3 fermentation production lots see Timmons et al (2001) Gene 263: 103-112) . In this method DE3 was used (referring to E. coli

DE3HT115) in which the bacteria has been transfected with the T7 polymerase, and plasmids producing the dsRNA, followed by inactivation of the bacteria diluted in RNase free water. Animals were then challenged 30 days after dsRNA administration with a lethal dose of IMNV via injection. Groups were evaluated daily for 21 days following challenge and evaluated for clinical signs and mortality. Table 22

Results

The study was terminated on Day 51 (21 days post challenge). Upon termination survival in treatment groups was significantly higher (P<.0001 using Tukey' s HSD following One- Way ANOVA) than controls. Animals administered dsRNA3 had 100% survival following administration of dsRNA3, animals given dsRNA82 had a mean survival of 93.33% (90%, 90%, and 100%). Sham administration controls had 6.67% mean survival at termination (0%, 10%, and 10%) (Figure 33).

Conclusions

dsRNA3 and dsRNA82 production lots made in DE3 E. coli are highly protective against lethal IMNV challenge up to 30 days post administration. Experiment #12

Objectives: Determine if dsRNA induced and inactivated DE3 E. coli can prevent mortality caused by IMNV and determine if dsRNA82 feeding in PL9 can prevent mortality caused by IMNV. Animals were fed prepared feed containing 45 ug of dsRNA82 (15 ug per feeding over 3 days for 300 PLs) or inactivated DE3 biomass at a rate of 0.1 gram cells (per feeding for three feedings for 300 PLs). Following the three days of feeding with dsRNA, animals were reared under normal conditions for an additional 20 days, prior to challenge. For challenge with IMNV, animals were split into three replicates of 10 individuals per tank and challenged via an intramuscular injection with 10 virions of IMNV. See Figure 34 for results. Conclusions: PL9 animals fed dsRNA82/Ag coated feed demonstrated a statistically significant increase in survival (55%) (P<.05) when compared to feed coated with agarose alone (10%).

Experiment #13

Objectives: Determine if induced and inactivated DE3 E. coli producing dsRNA380can prevent mortality caused by IMNV and determine if dsRNA380 feeding in PL15-PL18 can prevent mortality caused by challenge with IMNV

Methods: Feed preparations used a 0.2 gram mixture of dry feed mixed with 20 uL of liquid dsRNA followed by a top coat mixture of 20 uL 2% agarose mixture. Dosages levels at feeding were 60 ug of dsRNA380 or 0.1 gram equivalent biomass cells (300 ng/PL) Feed consumption was measured and -80% of feed was consumed. Animals were reared an additional 15 days before being challenged. For challenge with IMNV, animals were split into three replicates of 10 individuals per tank and challenged via an intramuscular injection with 10 virions of IMNV. Negative control groups consisted of a placebo IM injection of 2% saline and a strict negative control with no treatment. Results are shown in Figure 35.

Conclusions: dsRNA380 biomass treatment group showed just over 30% survival whereas top coated liquid dsRNA showed just over 20% survival. Survival in control animals was less than 10%.

Experiment #14

Objective: Determine impact of dsRNA#3 (380bp) feeding to shrimp following challenge with IMNV when boosted prior to or after feeding with RP producing dsRNA administered by immersion.

Objective: Determine if dsRNA induced and inactivated DE3 E. coli can prevent mortality caused by IMNV 250 Animals at post larval stage 20 (PL20) were placed into a 10L aquaria and acclimate for 24-48 hours. Animals were held without food for 8-12 hours prior to immunization.

Animals were fed shrimp feed top coated with either inactivated DE3 biomass bacteria producing the 380 bp dsRNA#3, or purified dsRNA#3. Animals were immunized over two successive days. Each day vaccination took place over the span of two hours; feed was administered to tanks at 15 minute intervals during that time to increase the likelihood that all of the feed would be consumed. The amount of inactivated DE3 biomass, used to top coat feed was such that the total amount of dsRNA in the biomass would correspond to the amount of purified dsRNA#3 used to directly top coat feed. Based on this normalization animals received 20 ug dsRNA#3 per feeding.

RP vaccination was carried out by placing 250, PL20 animals in 250 mL of water containing 2e6 IU RP/mL. Two RP were used (each at a concentration of 2e6 RP/mL). One RP (Pep3 sense RP) produced a positive sense IMNV Pep3 RNA (SEQ ID NO: 76) and the other (Pepl antisense RP, the antisense of dsRNA#3, that is complement of SEQ ID NO: 1) produced a negative sense IMNV Pepl RNA. Animals were immersed in RP 24 hr before vaccination with top coated feed (prime) or 24 hr after vaccination with top coated feed (boost). Negative controls consisted of a placebo challenge (2% saline groups) or a strict negative that received no injection.

Survival at 14 days post injection challenge with 10 IMNV virions is shown. As can be seen from Figure 36, priming animals with RP followed by boosting with either biomass or dsRNA top-coated feed resulted in better survival than using RP as a boost after dsRNA vaccination on feed. Prime indicates animals were immersed in RP prior to feeding dsRNA, Boost indicates animals were immersed in RP following feeding of dsRNA. Error bars indicate standard error between replicates.

EXAMPLE 5

The experiment shows an nsP2-specific assay (here Immunofluorescent Assay or IFA) can be utilized to determine titer uniformly for all Replicon Particle (RP) vaccines. In addition to the nsP2-specific IFA, a vaccine gene-specific qRT-PCR can be used to determine identity and RNA copy number (genome equivalents).

Methods and Results An influenza H3 RP vaccine was prepared using methods as described in Example 2 . Many replicate samples of the H3 IFA assay control RP were tested. In total, this sample was titrated a total of 47 times and was read by two different technicians, for a grand total of 94 titrations. This historical data was compared to current nsP2 IFA titers obtained from the same H3 RP reference lot. In addition, paired comparisons were also performed testing the same RP lot using the two different antibodies in the IFA assay.

The H3-specific IFA was performed as follows. Briefly, the IFA uses confluent Vero cells in a 48-well tissue culture plate format. The plate is seeded with 5xl0⁶ total Vero cells and placed in a 37°C/5 C0₂ incubator until all the wells have formed a confluent monolayer (typically 6 to 8 hours). Dilutions of the H3 RP vaccine samples are made in media and range from 1 :400 to 1:97,656.25. A known positive control RP sample is used on all plates. The RP samples are allowed to incubate for 18 to 24 hours in a 37°C/5 C0₂ incubator to allow protein expression. During this time, the RP will produce the SIV HA protein. The cells are then fixed with an equal volume acetone/methanol solution. After removing the fixing solution, and washing with phosphate buffered saline (PBS), a primary mouse anti- influenza monoclonal antibody, specific for H3, is added to each well. A FITC labeled anti- mouse IgG is added after incubation and additional PBS washes. After another incubation step and final washes with PBS, the plate is examined with a fluorescence microscope. Using a standardized field size, fluorescent cells are counted and the functional RP per ml value is determined. This will represent the RP potency. Defective RP will not result in the expression of H3, making the assay an accurate model of vaccine potency. The RP concentration is calculated using the following equation:

(Average) x (Dilution) x (100)

RP/ml = (0.12)

Where Average represents the average of ten positive H3 cell counts for the sample

Where Dilution represents the well in which the average H3 positive cells were counted Where 100 is a constant representing the surface area of the wells in the tissue culture plate Where 0.12 is a constant representing the volume of RNA particle vaccine tested (ml)

The nsP2-specific IFA was performed with minor variations in the procedure to adapt to specifics of the materials used. A goat anti-nsp2 antibody and a secondary anti-goat fluorescent antibody were used. Dilution amounts depends, for example, on the lot of nsp2 antibody used and can change with variations in the lot.

The results of the paired comparison of the titers determined with the H3 and nsP2 IFA antibodies are shown in Figure 37 and Table 22. Six independent titrations were completed of the H3 RP control, and all six titrations were tested by both H3- and nsP2- specific IF As. This test was repeated on a second day for a total of 12 independent titrations for each antibody. There was no significant difference observed between the RP titers obtained with the H3- and nsP2-specific antibody IF As by paired t-test (p>0.05).

Table 22. Raw data from the paired comparison shown in Figure 37. No significant difference was observed between the two IFAs when analyzed by paired t-test (p>0.05).

Twelve additional titrations of the same H3 control RP lot were completed on two additional days and titer was determined using the nsP2-specific IFA. Thus, a total of 24 independent nsP2 IFA titrations were completed on four different days. The results are shown in Figure 38. These titers were compared to the 94 titers obtained previously for the same H3 RP control lot. There was no significant difference between titers obtained using the two different IFA tests when analyzed by ANOVA (p>0.05).

Conclusions

The data included support the conclusion that RP titers obtained using a gene of interest or NOI or NOI-specific primary antibody are the same as titers obtained using a replicon or nsP2-specific primary antibody in the quantitative IFA. The nsP2-specific IFA may be used alone and/or with gene of interest qRT-PCR for quantitation of genome equivalents and gene identity. EXAMPLE 6

The IFA described above is used in this potency assay experiment. The second aspect of the potency assay is a quantitative real-time polymerase chain reaction (qRT-PCR) analysis of the vaccine to determine the number of RNA copies in each serial. Determining the total number of RNA copies helps to assure vaccine consistency from serial to serial. We have developed a qRT-PCR assay specific for the replicon nsP2 gene that allows quantitation of RNA genomes in a serial, and when compared to the H3-specific IFA titer, a genome equivalents (GE) to RP titer can be calculated (GE:RP). Statistical analysis of the resultant potency determinations in each section of this report was performed with t-tests as appropriate. Significant differences between assays or technicians are defined as p<0.05 for a given test statistic. For p values greater than 0.05, it's concluded that no statistical difference exists between assays or technicians.

SPECIFICITY AND SELECTIVITY

The ability of the IFA potency assay to selectively detect the H3 positive cells without being affected by cross-reactive substances was evaluated by testing various media used throughout the production process, as well as other non-specific RP formulations. The vaccine diluent (RP diluent) consists of Phosphate Buffered Saline (PBS) with 5% (w/v) sucrose and 1% (v/v) normal swine serum. General growth media , OptiPro media , and 5% Sucrose Buffer were also tested as samples because they are used during the manufacturing process and may contribute matrix effects. Three non-specific RP formulations were also included to further demonstrate the specificity of this assay. These three samples included RP expressing the swine influenza virus nucleoprotein (NP) and HI genes, as well as shrimp infectious myonecrosis virus pep3 (IMNV pep3) gene. All samples were tested on two separate days. No detectable fluorescence was observed with any of the samples, indicating that these sample matrices do not contribute any positive signal to the potency values of the serials, nor does the assay have any cross-reactivity with non-specific RP formulations.

ANALYTICAL SENSITIVITY

The Limit of Detection (LOD) for the potency assay can be derived theoretically because of its design. Protocol A specifies that an average of 20 to 50 H3 positive cells need to be observed in each grid field. With a minimum sample dilution in the assay of 1:400, and the lowest number of H3 positive cells being 20, the theoretical LOD is 6.67xl0⁶ RP per ml [(20 x 400 x 100)/(0.12)]. Experimental samples from two different serials, formulated to be near the LOD, were tested and plates read by two technicians to assess the sensitivity of the assay at this theoretical limit. The expected result was 6.67xl0⁶ RP/ml. The actual results were 7.13xl0⁶ and 6.19xl0⁶ RP/ml, so the % errors were 6.85 and -7.25%, respectively. Due to the design of the IFA assay, the LOD can be decreased by changing the initial RP dilution scheme.

The Limit of Quantitation (LOQ) for this potency assay can be derived theoretically as well. Since the maximum sample dilution is 1 :97, 656.25, and the highest number of H3 positive cells is 50, the theoretical LOQ is 4.07xl0⁹ RP per ml [(50 x 96,656.25 x

100)/(0.12)]. Experimental samples, formulated to be near the LOQ, were tested and plates read by two technicians to assess the theoretical limit. The expected result was 4.07xl0⁹ RP/ml. The actual results were 4.65xl0⁹ and 3.84xl0⁹ RP/ml, so the % errors were 14.17% and -5.57%, respectively. Due to the design of the IFA assay, the LOQ can be increased by changing the initial RP dilution scheme.

This assay uses general growth media as the negative control on each sample plate. No detectable fluorescence is observed, so there is no background contribution, making it impossible to measure the Signal to Background (S/B). One of the criteria for a successful potency test is the absence of fluorescence in the negative control . qPCR GENOME ANALYSIS

The assay to quantitate the number of RNA genomes associated with each RP serial is performed by quantitative RT-PCR (qRT-PCR). Briefly, replicon RNA is extracted using the Qiagen Viral RNA Mini kit. A standard one-step qRT-PCR protocol is performed on a BioRad CIOOO thermocycler with the CFX96 detection system. Amplification is detected by means of a fluorogenic probe designed to anneal to a region of the nsP2 gene on the replicon between the two primers. A 5' reporter dye (6-FAM) and a 3' quencher dye (BHQ-1) are attached to the nsP2 probe. Proximity of the reporter and quencher dyes results in the suppression of reporter fluorescence prior to amplification. Upon successful amplification of the target region, the 5 ' exonuclease activity of DNA polymerase releases the reporter dye from the hybridized probe, resulting in a fluorescent signal. Purified replicon pVEK RNA is used to generate a standard curve in the assay, and the fluorescent signal of each RP sample is measured up to thirty PCR cycles and compared to the fluorescent signal of the standards to quantify RNA copies in each RP sample. Copies of RNA per RP serial are compared to the IFA titer and used to determine RNA genome equivalents to RP titer ratio (GE:RP ratio).

Different replicons typically yield different GE:RP ratios, but RP batches produced using the same replicon typically yield comparable GE:RP ratios. Because of this, GE:RP ratios can be used to monitor the consistency of individual products.

Two different serials of H3 RP vaccine (091410 and 092810) were formulated at different doses and tested by both H3 -specific IFA and the qPCR assay. Two additional H3 serials were also tested (020711 and 021511). The qPCR assay was run by two different technicians on two separate days. No statistical significant difference was observed between the two technician' s results using the Student' s t-test. In addition, six samples from another lot of RP (111710 A-F) were extracted and tested in triplicate in the qRT-PCR assay. The IFA RP titer of the lot used was 5.85xl0⁷/ml.

The data presented from the 5 different lots of H3 RP used here demonstrate that the GE:RP ratios are consistent between all H3 RP lots, and does not change based on the titer of a specific RP lot. For comparison, Sample 091410 A has an IFA titer of 1.20xl0⁹, 34 times higher than the titer of Sample 021511, which has an IFA titer of 3.55x10⁷. Even though the IFA titers of these lots are significantly different, the GE:RP ratios are relatively similar (15.42 and 13.21).

Table 24. qRT-PCR and GE:RP results multiple replicates of one H3 serial Serial GE/ml GE:RP

111710 A 6.57E+08 11.23

111710 A 9.55E+08 16.32

111710 A 7.1E+08 12.14

111710 B 6.6E+08 11.28

111710 B 1.12E+09 19.15

111710 B 6.71E+08 11.47

111710 C 9.94E+08 16.99

111710 C 8.96E+08 15.32

111710 C 7.28E+08 12.44

111710 D 1.11E+09 18.97

111710 D 7.23E+08 12.36

111710 D 6.54E+08 11.18

111710 E 7.22E+08 12.34

111710 E 6.8E+08 11.62

111710 E 9.12E+08 15.59

111710 F 7.26E+08 12.41

111710 F 8.88E+08 15.18

111710 F 8.11E+08 13.86

Average 13.88

SERIAL RELEASE

The method for calculating the potency is based upon an IFA specific for the vaccine H3 antigen. The H3 positive cells are observed and quantified. Individual wells of the IFA tissue culture plate are visualized under 10X magnification and wells containing 20 to 50 H3 positive cells per grid field are used. A total of five fields per well are counted. A duplicate well is counted in the same manner. An average of the ten readings is used to calculate the potency, or RP/ml. The total number of H3 positive cells is determined by inserting the average of the ten counts into the following equation.

(Average) x (Dilution) x (100)

Potency = (0.12)

Where Average represents the average of ten positive H3 cell counts for the sample Where Dilution represents the well in which the average H3 positive cells were counted Where 100 is a constant representing the surface area of the wells in the tissue culture plate Where 0.12 is a constant representing the volume of RNA particle vaccine tested (ml) These results indicate that specific functional RP as well as replicon genomes can be quantitated using antigen- specific IFA and qRT-PCR assays, respectively. Thus, IFA titers and qRT-PCR values must fall within the empirically determined range for successful release of vaccine serials.

An efficacious dose of this vaccine is 1X10⁸ RP in a 2ml dose, or 5X10⁷ RP.ml. Overage may be included to further enhance potency as indicated from the potency validation.

Optimal RP titer and GE:RP ratio will vary for each vaccine, and the studies show this can be calculated precisely. By way of example, criteria to analyze dosage in this instance provide that RP titer is optimal at >5X10⁷/ml following a freeze/thaw cycle and a GE:RP ratio of 1.0 to 20.64.

EXAMPLE 7 Study Design: 12 groups of 5 pigs each received different HA RP vaccines at various doses as indicated in the table below. Pigs were given 2 injections at a 3 week interval in 2ml volumes delivered IM. Sera were collected for HI testing.

Table 25

Results: HI titers were obtained on prebleed, day of boost (prime only), 6 days post-boost and 19 days post-boost sera. Sera from pigs receiving the pandemic HA RP were also tested against the heterologous HV gamma SIV strain, and sera from pigs receiving delta 1 HA RP were also tested against a heterologous delta 2 SIV strain. In addition, sera samples from pigs receiving delta 1 HA RP were tested against a heterologous delta 1 strain. See Figure 39 for a graph showing titers at 19 days post boost.

Conclusions: HI titers were induced against all the different HA RP at doses as low as 5e5/dose and correlation was observed between RP dose and HI antibody levels.

EXAMPLE 8 A biological sample of lung tissue was obtained from Farm Y from an infected pig. The hemagglutinin (HA) gene of an H1N2 swine influenza virus (SIV) was sequenced at the Iowa State University Diagnostic Laboratory (SEQ ID NO: 81). Appropriate restriction site sequences were added to the 5' and 3' ends of the native sequence to facilitate cloning of the synthesized gene into the alphavirus replicon vector. This sequence was then submitted for codon optimization and de novo synthesis (SEQ ID NO: 82). Using the appropriate restriction sites enzymes the autogenous gene was cloned into the alphavirus replicon vector. Appropriate sized inserts were down selected and sequenced to ensure proper sequence. Transformed E. coli containing the plasmid with the correct HA sequence were further expanded and plasmid DNA purified using a commercial kit (Qiagen)(pVEKl K5, Figure 40). Purified DNA was linearized with endonuclease digestion and transcribed using the

RNA T7 Express system (Promega). Transcribed RNA was purified using commercial spin- columns (Qiagen). Purified RNA was held at -80°C until used for electroporations.

Vero cells were mixed with the HA RNA as well as the two alphavirus helper RNAs necessary for RP production, the Capsid and Glycoprotein RNAs. The three RNAs and Vero cells were co-electroporated in individual cuvettes and seeded back into roller bottles for overnight incubation. Following incubation, the RP were collected on a charged depth filter (Cuno) and washed with a sucrose buffer and eluted using a high NaCl concentration buffer. The RP was tested for the presence of replication-competent virus using a cytopathic effect (CPE) assay which consists of a blind passage of the RP in Vero cell cultures. In addition, RP were tested for potency using an nsp2-specific IFA, expressed as RP/ml. This titer was used to formulate the RP to the dose of 5e5/ml, for a total of le6 RP/dose. The RP were formulated in a final solution of 5% sucrose and 1% swine serum. Five pigs in four different dosage groups were administered the vaccine by intramuscular injection. One group was administered vaccine at a dose titration of le6, another group at dose titration of le7, another at 5e5 and a fourth at 5e6. HI antibody levels are determined. Piglets from a sow herd at Farm Z were identified which had been exposed to Rotavirus with select animals displaying signs of infection, including death. Biological samples were obtained from affected animals from which the VP7 gene of Rotavirus was obtained via PCR. A replicon particle vaccine was produced with this VP7 gene and delivered to Farm Z 42 days later. Vaccination of the entire herd via injection was accomplished and a whole herd booster dose administered 21 days later. Three weeks thereafter, sows were vaccinated six and three weeks pre-farrowing . As Rotavirus is a serious issue for suckling pigs, mortality of piglets was monitored. The measurements showed a statistically significant reduction in mortality correlated with vaccination, as detected by methods used for statistical process control charts. Analysis of Means (ANOM) of the prevaccination period averages compared to the averages of the post- vaccination period showed the differences to be significant (a= 0.05). Average pre-weaning mortality prior to vaccination was 7.6% and dropped to 6.4% after vaccination. The drop in mortality continued to be observed 100 days later. When comparing mortality at the same ten weeks of the year with the two prior years in which there was no vaccination, a dramatic reduction in mortality was also observed.

EXAMPLE 9

Disease diagnosis, gene sequence attainment, vaccine manufacture, use and statistical analysis of a farm specific RP vaccine in a production system. A biological sample of tissue (ex. lungs, tonsils, nasal swabs, serum, fecal content intestinal tract tissue, etc) is obtained from a farm from an infected animal. Once the pathogen affecting the farm has been identified by diagnostic methods the relevant gene of interest, capable of inducing a protective immune response, can be sequenced by state or regional or national Diagnostic Laboratories. Examples of potential pathogens and relevant genes of interest that would be sequenced from a biological sample are; influenza virus (ex hemagglutinin gene), Porcine Reproductive and Respiratory Syndrome Virus (ex GP5 gene) and Rotavirus (ex VP7 gene). Appropriate restriction site sequences can be engineered into the 5' and 3' ends of the gene sequence by PCR that facilitate cloning of either the native gene sequence or a gene sequence that has been codon optimized and de novo synthesized. The genes are then cloned into the alphavirus replicon vector using the engineered restriction sites. Individual clones are analyzed by restriction analysis and then sequenced to ensure proper sequence has been maintained through the cloning process. E. coli transformed with the replicon plasmid containing the farm specific pathogen gene are then further expanded and plasmid DNA purified using commercially available kits (ex Qiagen). Purified DNA is then linearized by endonuclease digestion and RNA is produced by in vitro transcription using the RNA T7 Express system (Promega). The transcribed RNA can then be purified using commercially available spin-columns (ex Qiagen). The Purified farm specific replicon RNA can then be stored at -80°C until used for electroporations.

In order to generate RP, Vero cells will be mixed with the farm specific replicon RNA as well as the two alphavirus helper RNAs necessary for RP production, the Capsid and Glycoprotein RNAs. The three RNAs and Vero cells are combined in cuvettes and subjected to electroporation. Once the RNA has been electroporated into the cells, the cells can be seeded into roller bottles for overnight incubation. Following incubation, the RP are collected on a charged depth filter (Cuno), washed with a sucrose buffer and eluted using a high NaCl concentration buffer. The RP are then tested for the presence of replication-competent virus using a cytopathic effect (CPE) assay which consists of blind passage of the RP in Vero cell cultures. In addition, RP are tested for potency using an nsp2-specific IFA and titer is expressed as RP/ml. This titer will be used to formulate the RP to the dose of 5e5 RP/ml, for a total of le6 RP/dose. The RP will be formulated in a final solution of 5% sucrose and 1% normal serum (serum source dependant on the species source of the pathogen gene).

Statistical Process Control (SPC) charts for assessment of animal performance following on-farm interventions, including administration of farm-specific vaccines

Animal performance (production) data are collected daily within food animal production systems and analyzed by management who work within the systems. Animal health must be maintained at a high level to achieve a high level of animal performance.

A swine production system may consist of several different sites designated for pigs of different ages. Sow farms within a system produce weaned pigs that are moved from the sow farm to an off-site location for the purpose of additional growth. The population of these sow farms can be as large as 10,000 (or more) animals that produce up to 240,000 (or more) pigs per year. When a disease infects pigs on these farms death losses can be economically devastating and unsustainable. Thus assurance of healthy swine is essential for the economic survival of the system. Healthy pig growth management is accomplished by appropriate bioremediation such as farm-specific vaccines, made from the pathogen-of-interest demonstrated to be present on the farm. These vaccines are administered to females 2-3 weeks prior to farrowing in order to transfer protective antibodies and/or cells to offspring. Or, in some cases, the offspring may receive the farm-specific vaccine in order to be protected from the pathogen of interest. The benefits of these vaccines are assessed by the magnitude of reduction in the levels of dead and cull pigs or other key production metrics as determined by management's analysis of key production parameters. Results from analyses are used to identify areas for production improvement, define when improvements occur and quantify the amount of improvement achieved.

Statistical process control (SPC)( Wheeler, D. J. (1995). Advanced Topics in Statistical Process Control. The Power of Shewhart's Charts. Knoxville, TN, SPC Press.) charts can be used to determine if an objective has been met following its definition, measurement method, and assessment of data according to rules of data pattern distribution within calculated limits (an operational definition^ Wheeler, D. J. and S. R. Poling (1998). Building Continual Improvement. A Guide for Business. Knoxville, TN, SPC Press.)).

In order for data to be properly analyzed with SPC, they are rationally subgrouped (Wheeler, 1995, supra). Subgroups are constructed with some reasonable criterion for association within a subgroup. The two most-often SPC charts are called individuals and moving range (XmR) and the average and range ( -bar) charts. Each of these SPC Chart consists of two graphs: a graph of location (individual (X) or subgroup average ( -bar) and a graph of dispersion (moving range (mR), or range (R)). Data dispersion is the basis for estimating standard deviation (σ) and thus calculating 1-, 2-, and 3-sigma limits. Limits for location and dispersion graphs are calculated as follows: X-bar R Charts: Upper Control Limit for Averages = UCL_X = X + A₂ff

Average Central Line = CL_X = X

Lower Control Limit for Averages = LCL_X = X - A₂ff

Range Upper Control Limit

Range Central Line = R

Range Lower Control Limit

Where A₂, D₄, and D₃ are defined by subgroup in) size and summarized in Table 26. Table 26. SPC Chart Factors for Calculating Limits

XmR Charts:

Upper Control Limit for Averages =

Upper Natural Process Limits for Individual Values = UNPL_X = X + E₂ mR

Central Line for Individual Values = CL_X = X Lower Control Limit for Averages =

Lower Natural Process Limits for Individual Values = LNPL_X = X - E₂ mR Upper moving Range Limit = UmRL = D₄mR

Where E₂ = 2.660 and D₄ = 3.268 are defined by the two-point moving range, thus subgroup size = 2.

These limits are used to assess data distribution patterns (representing economically- meaningful process changes) as follows (Wheeler, 1995, supra) as follows:

• Rule 1, one data point outside the 3-sigma limit

• Rule 2, two out of three consecutive data points outside 2-sigma limit and on the same side of the average.

• Rule 3, four out of five consecutive data points outside 1-sigma limit and on the same side of the average.

• Rule 4, 8 consecutive data points on the same side of the average.

The production system includes:

1. Receipt of a gene sequence from a pathogen of interest (for instance rotavirus,

influenza virus, or porcine reproductive and respiratory syndrome virus) demonstrated to be from affected pigs on the farm.

2. Production of a farm-specific vaccine from the gene of interest.

3. Injection of the vaccine into animals to induce immunity 4-6 weeks after receipt of the sequence.

4. Establish an expected timeframe within which improvements would be expected.

5. Collection and SPC analysis of production data from the farm system; these data will include pre-weaning mortality, cull rates, and post-weaning mortality and/or other metrics which have been determined to be economically important to the farm system.

6. Use of SPC analysis to demonstrate benefit to the farm system, based on the rules outlined above.

7. On-going monitoring of the farm to determine if changes in pathogen gene sequences have occurred.

LIST OF SEQUENCES SEQ ID NO: 1 DNA producing dsRNA#3 (380bp)

SEQ ID NO: 2 DNA producing dsRNA#3 5' Truncate

SEQ ID NO: 3 DNA producing dsRNA#3 3 'Truncate

SEQ ID NO: 4 DNA producing dsRNA #2

SEQ ID NO: 5 DNA producing dsRNA#l

SEQ ID NO: 6 DNA producing GFP dsRNA

SEQ ID NO: 7: Primer eGFPT7F

SEQ ID NO: 8 Primer eGFPT7R

SEQ ID NO: 9 Primer Pep 195F

SEQ ID NO: 10 Primer Pepl474R

SEQ ID NO: 11 Primer Pep 1 95 T7F

SEQ ID NO: 12 Primer Pep 1474 T7R

SEQ ID NO: 13 Primer Capsid4 F

SEQ ID NO: 14 Primer Capsid 4 R

SEQ ID NO: 15 Primer Capsid4T7 F

SEQ ID NO: 16 Primer Capsid4 T7R

SEQ ID NO: 17 Primer RdRPl F

SEQ ID NO: 18 Primer RdRPl R

SEQ ID NO: 19 Primer RdRPl T7 F

SEQ ID NO: 20 Primer RdRPl T7 R

SEQ ID NO: 21 Primer VP19 T7 F

SEQ ID NO: 22 Primer VP19 T7 R

SEQ ID NO: 23 Primer VP28F

SEQ ID NO: 24 Primer VP28R

SEQ ID NO: 25 Primer VP28 Ascl F

SEQ ID NO: 26 Primer VP28 Pad R

SEQ ID NO: 27 Primer AscPeplanti F

SEQ ID NO: 28 Primer PacPeplanti R

SEQ ID NO: 29 DNA encoding VP28 and also transcribed to produce dsRNA

SEQ ID NO: 30 DNA encoding VP 19 and transcribed to produce dsRNA

SEQ ID NO: 31 VP19-antisense DNA

SEQ ID NO: 32 VP19-Inverted repeat DNA producing dsRNA

SEQ ID NO: 33 DNA transcribed to produce dsRNA#3 -ssRNA

SEQ ID NO: 34 DNA encoding RFP SEQ ID NO: 35 +ss RNA3

SEQ ID NO: 36 -SSRNA3

SEQ ID NO: 37 +ssRNA3 5' Truncate

SEQ ID NO: 38 -SSRNA3 5' Truncate

SEQ ID NO: 39 +ssRNA3 3' Truncate

SEQ ID NO: 40 -SSRNA3 3' Truncate

SEQ ID NO: 41 +ssRNA#2

SEQ ID NO: 42 -ssRNA #2

SEQ ID NO: 43 +ssRNA dsRNAl

SEQ ID NO: 44 -ssRNA dsRNAl

SEQ ID NO: 45 eGFP +ssRNA

SEQ ID NO: 46 eGFP -ssRNA

SEQ ID NO: 47 VP28 +ssRNA

SEQ ID NO: 48 -ssRNA VP28

SEQ ID NO: 49 VP19 + ssRNA

SEQ ID NO: 50 VP19 -ssRNA

SEQ ID NO: 51 dsRNA #3 219-275 sequence

SEQ ID NO: 52 dsRNA #3 219-275 +RNA sequence

SEQ ID NO: 53 dsRNA #3 219-275 -RNA sequence

SEQ ID NO: 54 T7 dsRNA #3 219 Forward primer:

SEQ ID NO: 55 T7 dsRNA #3 275 Reverse primer:

SEQ ID NO: 56 dsRNA #3 194-275 sequence

SEQ ID NO: 57 dsRNA #3 194-275 +RNA sequence

SEQ ID NO: 58 dsRNA #3 194-275 -RNA sequence

SEQ ID NO: 59 T7 dsRNA #3 194 Forward primer

SEQ ID NO: 60 T7 dsRNA#3 275 Reverse primer

SEQ ID NO: 61 dsRNA #3 223-376 sequence

SEQ ID NO: 62 dsRNA #3 223-376+RNA sequence

SEQ ID NO: 63 dsRNA #3 223-376 -RNA sequence

SEQ ID NO: 64 T7 dsRNA #3 223 Forward primer

SEQ ID NO: 65 T7 dsRNA #3 376 Reverse primer

SEQ ID NO: 66 IMNV genome - Poulos

SEQ ID NO: 67 IMNV genome - Senapin

SEQ ID NO: 68 IMNV polypeptide - ORF 1 of Poulos et al. SEQ ID NO 69 IMNV polypeptide - ORF1 of Senapin et al.

SEQ ID NO 70 IMNV polypeptide - ORF 2 of Poulos et al.

SEQ ID NO 71 IMNV polypeptide - ORF 2 of Senapin et al.

SEQ ID NO 72 IMNV ORF1 (nucleotides 136-4953 of SEQ ID NO: 66)

SEQ ID NO 73 IMNV ORF2 (nucleotides 5241-7451 of SEQ ID NO: 66)

SEQ ID NO 74 IMNV nucleotide sequence encoding Peptide 1 (136-415 of SEQ ID NO

66

SEQ ID NO: 75 IMNV nucleotide sequence encoding Peptide 2 (415-1266 of SEQ ID NO: 66)

SEQ ID NO: 76 IMNV nucleotide sequence encoding Peptide 3 (1267-2247 of SEQ ID NO: 66)

SEQ ID NO: 77 IMNV nucleotide sequence encoding major capsid protein (2227-4953 of SEQ ID NO: 66)

SEQ ID NO: 78 IMNV nucleotide sequence encoding RNA dependent RNA polymerase (5241-7451 of SEQ ID NO: 66)

SEQ ID NO: 79 dsRNA Pepl 474T7F

SEQ ID NO: 80 sequence of clone isolate from IMNV virus

SEQ ID NO: 81 sequence of clone isolate from influenza virus

SEQ ID NO: 82 sequence 81 after optimization

Claims

What is claimed is:

1. A method of producing a vaccine to protect an animal from a biotype of a microorganism, the method comprising,

a) identifying a nucleic acid molecule of interest or fragment thereof (NOI) of said

microorganism, said NOI known to be capable of producing a protective molecule; b) obtaining a biological sample from at least one animal where said animal has been

exposed to said microorganism;

c) obtaining from said sample said NOI of said microorganism without the need to isolate said microorganism;

d) producing a protective molecule from said NOI, said protective molecule selected from the group consisting of:

(i) a nucleic acid molecule comprising the sequence of said NOI or a fragment

thereof;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a nucleic acid molecule producing (iii) or (iv); and

(vi) an RNA particle comprising or producing any one of (i) - (v);

e) producing a vaccine comprising said protective molecule, wherein said vaccine does not comprise said microorganism or a replicable or living pathogenic microorganism; and f) providing said protective molecule in said vaccine in an amount that when administered to an animal protects said animal from said biotype of said microorganism.

2. The method of claim 1, wherein said vaccine is produced in one month or less from the time of obtaining said sample.

3. The method of claim 1, wherein said vaccine is produced in seven days or less from the time of obtaining said sample.

4. The method of claim 1, further comprising introducing an alphavirus replicon vector comprising said NOI into a host cell, expressing a polypeptide or fragment thereof from said NOI, and extracting said polypeptide or fragment from said host, wherein said extracted polypeptide or fragment thereof comprises said protective molecule.

5. The method of claim 4, wherein said vector comprises a Venezuelan Equine Encephalitis (VEE) vector, said host comprises Vero cells and said polypeptide or fragment thereof is extracted by lysing said Vero cells.

6. The method of claim 1, wherein said protective molecule comprises an RNA particle, and said RNA particle comprises said NOI or a fragment thereof.

7. The method of claim 1, wherein said protective molecule comprises an RNA particle, and said RNA particle produces a dsRNA molecule.

8. The method of claim 1, further comprising determining the amount of protective molecule by determining the amount of RNA Particle (RP) titer and providing said protective molecule at a RP titer that when administered protects said animal.

9. The method of claim 8 further comprising determining the genome equivalent of the protective molecule, determining the genome equivalent:RNA Particle titer (GE:RP) ratio and providing said protective molecule at a GE:RP ratio that when administered protects said animal.

10. The method of claim 1, wherein said NOI is obtained by a process selected from the group consisting of polymerase chain reaction of said NOI in said sample, and synthesis of said NOI.

11. The method of claim 1, further comprising determine the biotype of said microorganism and producing said vaccine if said microorganism is a biotype different from biotypes of microorganisms for which vaccines exist.

12. The method of claim 1, wherein said at least one animal from which a biological sample is obtained is a first animal in a first plurality of animals exposed to a first microorganism for which a first protective molecule is produced, which first plurality of animals has or will have sufficient exposure to at least one animal or biological sample of a second plurality of animals exposed to a second microorganism, such that said first and second plurality of animals are at risk of exposure to microorganisms present in the other plurality of animals, said method further comprising,

a) obtaining a biological sample from at least one animal in said second plurality of animals; b) producing a second protective molecule from a NOI obtained from said biological sample of at least one animal of said second plurality of without the need to isolate said second

microorganism; and

c) providing said second protective molecule in said vaccine in an amount that when

administered to an animal protects said animal from said biotype of said second microorganism.

13. The method of claim 1, further comprising obtaining biological samples over a period of time, obtaining a NOI from said samples and comparing a later obtained NOI with an earlier obtained NOI and producing said vaccine when said later obtained NOI is different from said earlier obtained NOI.

14. The method of claim 1, wherein said animal is selected from the group consisting of swine, cattle, canines, felines, equines and aquatic invertebrates.

15. A method of protecting an animal from a biotype of a microorganism, the method comprising,

a) identifying a nucleic acid molecule of interest or fragment thereof (NOI) of a

microorganism, said NOI known to be capable of producing a protective molecule; b) obtaining a biological sample from at least one animal where said animal has been

exposed to said microorganism;

c) obtaining from said sample said NOI of said microorganism without the need to isolate said microorganism;

d) producing a protective molecule from said NOI, said protective molecule, selected from the group consisting of:

(i) a nucleic acid molecule comprising the sequence of said NOI or a fragment thereof;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a nucleic acid molecule producing (iii) or (iv); and

(vi) a RNA particle comprising or producing any one of (i) - (v);

e) producing a vaccine comprising said protective molecule and wherein said vaccine does not comprise said microorganism or a replicable or living pathogenic microorganism; f) providing said protective molecule in an amount that when administered to an animal protects said animal from said biotype of said microorganism;

g) administering said protective molecule to at least one animal ; and

h) producing a protective response to said biotype of said microorganism in said animal.

16. The method of claim 15, further comprising administering said protective molecule to an animal selected from the group consisting of (i) said animal from which said biological sample was obtained, (ii) an animal living with said animal from which said biological sample was obtained, and (iii) an animal having or which will have sufficient exposure to said animal or a biological sample of (i) or (ii) so as to be at risk of exposure to said biotype of said

microorganism.

17. The method of claim 15, further comprising introducing a alpha virus RNA vector comprising said NOI into a host cell, expressing a polypeptide or fragment thereof from said NOI, and extracting said polypeptide or fragment from said host, wherein said extracted polypeptide or fragment thereof comprises said protective molecule and is administered to said animal.

18. The method of claim 17, wherein said vector comprises a Venezuelan Equine Encephalitis (VEE) vector, said host comprises Vero cells and said polypeptide or fragment thereof is extracted by lysing said Vero cells.

19. The method of claim 15, wherein said protective molecule comprises an RNA particle, and said RNA particle comprises said NOI or a fragment thereof.

20. The method of claim 15, wherein said protective molecule comprises an RNA particle, and said RNA particle produces a dsRNA molecule.

21. The method of claim 15, further comprising determining the amount of protective molecule by determining the amount of RNA Particle (RP) titer and providing said protective molecule at a RP titer that when administered protects said animal.

22. The method of claim 21 further comprising determining the genome equivalent of the protective molecule, determining the genome equivalent:RNA Particle titer (GE:RP) ratio and providing said protective molecule at a GE:RP ratio that when administered in a vaccine protects said animal.

21. The method of claim 15, wherein said NOI is obtained by a process selected from the group consisting of polymerase chain reaction of said NOI in said sample, and synthesis of said NOI.

22. The method of claim 15, further comprising, determine the biotype of said microorganism and producing and administering said protective molecule if said microorganism is a biotype different from biotypes of microorganisms for which vaccines exist.

23. The method of claim 15, wherein said protective molecule is administered to a plurality of animals living with said animal from which said biological sample was obtained.

24. The method of claim 15, wherein said protective molecule is administered to a single animal, and wherein said single animal is the animal from which said biological sample was obtained.

25. The method of claim 15, wherein said animal from which said biological sample is obtained is an animal in a first plurality of animals exposed to a first microorganism for which a first protective molecule is produced, which first plurality of animals has or will have sufficient exposure to at least one animal or biological sample of a second plurality of animals exposed to a second microorganism, such that said first and second plurality of animals are at risk of exposure to microorganisms present in the other plurality of animals, said method further comprising, a) obtaining a biological sample from at least one animal in said second plurality of animals; b) producing a second protective molecule from a NOI obtained from said biological sample of said at least one animal of said second plurality of without the need to isolate said second microorganism;

c) providing said second protective molecule in an amount that when administered to an animal protects said animal from the biotype of said second microorganism; and

d) administering said first and second protective molecules to said first and second plurality of animals.

27. The method of claim 15, further comprising obtaining biological samples over a period of time, obtaining a NOI from said samples and comparing a later obtained NOI with an earlier obtained NOI and producing said vaccine when said later obtained NOI is different from said earlier obtained NOI.

28. The method of claim 15, wherein said animal is selected from the group consisting of swine, cattle, canines, felines, equines and aquatic invertebrates.

29. A vaccine to protect an animal from a biotype of a microorganism, said vaccine comprising, a) a protective molecule selected from the group consisting of: (i) a nucleic acid molecule comprising the sequence of a nucleic acid molecule of interest or a fragment thereof (NOI) known to be capable of producing a protective molecule, said NOI obtained from a sample from an animal which has been exposed to said microorganism;

(ii) a polypeptide or fragment thereof expressed by said NOI;

(iii) at least one RNA molecule comprising a sequence that corresponds to all or a portion of said NOI and forms a dsRNA;

(iv) at least one RNA molecule that is antisense to all or a portion of said NOI;

(v) a nucleic acid molecule producing (iii) or (iv); and

(vi) a RNA particle comprising or producing any one of (i) - (v);

b) said vaccine does not comprise said microorganism or a replicable or living pathogenic microorganism

c) wherein said microorganism is a biotype for which available vaccines when administered to an animal provide no response or a reduced protective response compared to the protective response obtained when administering said protective molecule; and

d) said protective molecule is provided in an amount that when administered protects said animal from said biotype of said microorganism.

30. The vaccine of claim 29 further comprising an adjuvant comprising a non-mutated E. coli heat labile entero toxin.