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20 pages, 9291 KiB  
Article
Development Using Bioluminescence Imaging of a Recombinant Anguillid Herpesvirus 1 Vaccine Candidate Associated with Normal Replication In Vitro but Abortive Infection In Vivo
by Haiyan Zhang, Arun Sridhar, Natacha Delrez, Bo He, Sophie Fourny, Yuan Gao, Owen Donohoe and Alain F. C. Vanderplasschen
Vaccines 2024, 12(12), 1423; https://doi.org/10.3390/vaccines12121423 - 17 Dec 2024
Viewed by 882
Abstract
Background/Objectives: Anguillid herpesvirus 1 (AngHV-1) (recently renamed Cyvirus anguillidallo 1) is the etiologic agent of a lethal disease that affects several eel species. It is thought to be one of the main infectious agents causing a population decline in wild eels and economic [...] Read more.
Background/Objectives: Anguillid herpesvirus 1 (AngHV-1) (recently renamed Cyvirus anguillidallo 1) is the etiologic agent of a lethal disease that affects several eel species. It is thought to be one of the main infectious agents causing a population decline in wild eels and economic loss within the eel aquaculture sector. To date, no vaccines are available against AngHV-1. Recently, we developed a safe and efficacious live attenuated recombinant vaccine against Cyprinid herpesvirus 3 (CyHV-3). This CyHV-3 recombinant vaccine encodes a deletion of ORF57. Orthologues of CyHV-3 ORF57 exist in Cyprinid herpesvirus 2 (CyHV-2, ORF57) and AngHV-1 (ORF35). Methods: In the present study, using recombinant strains and bioluminescent in vivo imaging, we investigated the effect of AngHV-1 ORF35 deletion on virus replication in vitro, virulence in vivo, and the potential of an AngHV-1 ORF35-deleted recombinant as a vaccine candidate for the mass vaccination of eels by immersion. With this goal in mind, we produced ORF35-deleted recombinants using two parental strains: a UK strain and a recombinant derived from the former strain by insertion of a Luciferase–GFP reporter cassette into a non-coding intergenic region. Results: Analyses of ORF35-deleted recombinants led to the following observations: (i) AngHV-1 ORF35 is not essential for viral growth in cell culture, and its deletion does not affect the production of extracellular virions despite reducing the size of viral plaque. (ii) In contrast to what has been observed for CyHV-3 ORF57 and CyHV-2 ORF57, in vivo bioluminescent analyses revealed that AngHV-1 ORF35 is an essential virulence factor and that its deletion led to abortive infection in vivo. (iii) Inoculation of the AngHV-1 ORF35-deleted recombinant by immersion induced a protective immune response against a wild-type challenge. This protection was shown to be dose-dependent and to rely on the infectivity of AngHV-1 ORF35-deleted virions. Conclusions: This study suggests that the AngHV-1 ORF35 protein has singular properties compared to its orthologues encoded by CyHV-2 and CyHV-3. It also supports the potential of AngHV-1 ORF35-deleted recombinants for the mass vaccination of eels by immersion. Full article
(This article belongs to the Special Issue Animal Herpesviruses)
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Graphical abstract

Graphical abstract
Full article ">Figure 1
<p>Schematic representation of the strategy used to produce AngHV-1 recombinants by homologous directed recombination (HDR). (<b>A</b>) Flowchart of the production of the UK Luc and ORF35 Del recombinant strains by HDR in eukaryotic cells. (<b>B</b>) Genotype of the UK parental strain and derived recombinant strains for the ORF32–ORF33 intergenic region and the ORF35 locus. WT, wild-type; Luc, inserted LucGFP cassette; Del, deleted. (<b>C</b>) A schematic representation of the genome structure of UK Luc. The genome of AngHV-1 flanked by two terminal repeats (LTR and RTR) and the intergenic ORF32–ORF33 genome region are shown at the top. (<b>D</b>) Schematic representation of the genome structure of the UK ORF35 Del recombinant. The genome of AngHV-1 flanked by two terminal repeats (LTR and RTR) and the ORF35 genome region are shown at the top. In panels (<b>C</b>,<b>D</b>), SacI restriction sites and predicted restriction fragments (in kb) are shown. Coordinates are those of the AngHV-1 reference strain available in GenBank (accession number: MW580855.1).</p>
Full article ">Figure 2
<p>Characterization of AngHV-1 recombinant strains. (<b>A</b>) Transcriptional analysis of genes ORF32, ORF33, ORF34, ORF35, ORF36, and ORF55 expressed by the indicated strains of AngHV-1. ORF55 (AngHV-1 DNA polymerase) expression was used as a control. Marker sizes (MSs) in base pairs (bps) are indicated on the left. The left part and the right part of the figure represent the results of the PCR performed on cDNA and RNA, respectively. (<b>B</b>) Expression of reporter genes. EK-1 cells grown in 12-well plates were infected with the indicated strains, then overlaid with a medium containing CMC. At 4 dpi, infected cells were analyzed for the expression of bioluminescence and epifluorescence. The Luc signal was detected using the IVIS system (left frame). The reporters (copGFP and mCherry) and immunofluorescent staining (anti-AngHV-1) were detected by epifluorescent microscopy. Plaques of UK and UK ORF35 Del were revealed by indirect immunofluorescent staining (anti-AngHV-1) (right frame). (<b>C</b>) The replication kinetics and (<b>D</b>) viral plaque sizes of the ORF35-deleted strains were compared with those of the parental UK and UK Luc strains. (<b>E</b>) Luc expression of AngHV-1 recombinant strains (UK Luc and UK Luc ORF35 Del). The replication kinetic data represent the mean ± SEM of triplicate measurements. The data on the plaque area are the mean ± SEM of twenty measurements. The data on Luc expression are the mean ± SEM of triplicate measurements. The horizontal dashed line in panel <b>E</b> shows the mean + 3 SD of the data obtained for control non-infected cultures. Results of statistical comparisons between ORF35 Del strains and parental strains are indicated as follows: ns, no significant differences; *, <span class="html-italic">p</span> &lt; 0.05.</p>
Full article ">Figure 3
<p>Effect of ORF35 deletion on AngHV-1 replication in vivo. (<b>A</b>) Flowchart of the experiment. At the time of inoculation, yellow eels (12.06 ± 2.72 g, mean ± SD) were mock-infected or infected with the indicated strains using different routes: IP injection of 200,000 pfu/eel or immersion in water containing 4000 pfu/mL or intradermal inoculation of 200,000 pfu/eel. At the indicated times post-infection, eels (<span class="html-italic">n</span> = 6, consisting of two eels from triplicate tanks) were imaged using an IVIS. (<b>B</b>) The effects of AngHV-1 infection routes: IP injection, immersion, and intradermal inoculation are presented in the left column, middle column, and right column, respectively. Average radiance (individual values, mean ± SEM) measured on the entire body surface of the fish, i.e., skin (individual values represent the mean values obtained for the left and right sides of each fish), gills (individual values represent the mean values obtained for the left and right gills), brain, heart, and gut-liver, were analyzed by IVIS (<span class="html-italic">n</span> = 6 per timepoint). The dashed line represents the threshold of positivity, which is the mean + 3 SD of the values obtained for the mock-infected fish (data not presented). The number of positive fish among the six analyzed fish is represented by bars (right axis). The average emitted radiances (<span class="html-italic">p</span>(<span class="html-italic">rad</span>)) of UK Luc were compared with UK Luc ORF35 Del using unpaired <span class="html-italic">t</span>-test (two-tail, Gaussian distribution) or Wilcoxon test (non-Gaussian distribution). The number of positive fish per group was compared between two strains using the Fisher–Pitman permutation test (<span class="html-italic">p</span>(<span class="html-italic">no</span>)). <span class="html-italic">p</span> values are represented as follows: ns, not significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01; ***, <span class="html-italic">p</span> &lt; 0.001. (<b>C</b>) Representative images of IVIS data (skin, gills, and brain) are presented. Eels with the closest scores to the mean of each infection route were selected for image illustration.</p>
Full article ">Figure 3 Cont.
<p>Effect of ORF35 deletion on AngHV-1 replication in vivo. (<b>A</b>) Flowchart of the experiment. At the time of inoculation, yellow eels (12.06 ± 2.72 g, mean ± SD) were mock-infected or infected with the indicated strains using different routes: IP injection of 200,000 pfu/eel or immersion in water containing 4000 pfu/mL or intradermal inoculation of 200,000 pfu/eel. At the indicated times post-infection, eels (<span class="html-italic">n</span> = 6, consisting of two eels from triplicate tanks) were imaged using an IVIS. (<b>B</b>) The effects of AngHV-1 infection routes: IP injection, immersion, and intradermal inoculation are presented in the left column, middle column, and right column, respectively. Average radiance (individual values, mean ± SEM) measured on the entire body surface of the fish, i.e., skin (individual values represent the mean values obtained for the left and right sides of each fish), gills (individual values represent the mean values obtained for the left and right gills), brain, heart, and gut-liver, were analyzed by IVIS (<span class="html-italic">n</span> = 6 per timepoint). The dashed line represents the threshold of positivity, which is the mean + 3 SD of the values obtained for the mock-infected fish (data not presented). The number of positive fish among the six analyzed fish is represented by bars (right axis). The average emitted radiances (<span class="html-italic">p</span>(<span class="html-italic">rad</span>)) of UK Luc were compared with UK Luc ORF35 Del using unpaired <span class="html-italic">t</span>-test (two-tail, Gaussian distribution) or Wilcoxon test (non-Gaussian distribution). The number of positive fish per group was compared between two strains using the Fisher–Pitman permutation test (<span class="html-italic">p</span>(<span class="html-italic">no</span>)). <span class="html-italic">p</span> values are represented as follows: ns, not significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01; ***, <span class="html-italic">p</span> &lt; 0.001. (<b>C</b>) Representative images of IVIS data (skin, gills, and brain) are presented. Eels with the closest scores to the mean of each infection route were selected for image illustration.</p>
Full article ">Figure 4
<p>Dose-protection effect conferred by UK ORF35 Del in vivo. (<b>A</b>) Flowchart of the experiment. At the time of primary inoculation, yellow eels (28.52 ± 7.30 g, mean ± SD) were mock-infected or infected for 2 h by immersion in water containing the indicated doses of UK ORF35 Del or 100,000 pfu/mL of UK ORF35 Del strain treated by psoralen/UV to inactivate virus infectivity. At 36 days post-primary inoculation, eels were infected for 2 h by immersion in water containing 4000 pfu/mL of UK Luc expressing luciferase as a reporter. At the indicated times post-secondary inoculation, eels (<span class="html-italic">n</span> = 6, consisting of two eels from triplicate tanks) were imaged using IVIS. (<b>B</b>) Average radiance (individual values, mean ± SEM) measured on the entire body surface of fish, i.e., skin (individual values represent the mean values obtained for the left and right sides of each fish), gills (individual values represent the mean values obtained for the left and right gills), brain, heart, and gut–liver, were analyzed by IVIS (<span class="html-italic">n</span> = 6 per timepoint). The average radiance (<span class="html-italic">p</span>(<span class="html-italic">rad</span>)) of each group was compared with the “primary mock-infected group” using a non-parametric Kruskal–Wallis test followed by multiple comparisons with the two-stage step-up method of Benjamini, Krieger, and Yekutieli. Throughout this panel, the data obtained for every individual eel (within each group) are represented by the same symbol to allow for a correlation of the data obtained for the different organs at a specific dpi. The dashed line represents the threshold of positivity, which was calculated by the mean + 3 SD of the values obtained for the mock fish. The number of positive fish among the six analyzed fish is represented by bars (right axis). The positive fish (<span class="html-italic">p</span>(<span class="html-italic">no</span>)) from each group was compared with the primary mock-infected group using the Fisher–Pitman permutation test. <span class="html-italic">p</span> values are represented as follows: ns, not significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01. (<b>C</b>) Representative images of IVIS data (skin, gills, and brain) are presented in the lower panel. Eels with the closest scores to the mean of each group (mock; UK ORF35 Del, 100,000 pfu/mL; psoralen/UV-inactivated UK ORF35 Del, 100,000 pfu/mL; and mock-infected with UK Luc) were selected for image illustration.</p>
Full article ">Figure 4 Cont.
<p>Dose-protection effect conferred by UK ORF35 Del in vivo. (<b>A</b>) Flowchart of the experiment. At the time of primary inoculation, yellow eels (28.52 ± 7.30 g, mean ± SD) were mock-infected or infected for 2 h by immersion in water containing the indicated doses of UK ORF35 Del or 100,000 pfu/mL of UK ORF35 Del strain treated by psoralen/UV to inactivate virus infectivity. At 36 days post-primary inoculation, eels were infected for 2 h by immersion in water containing 4000 pfu/mL of UK Luc expressing luciferase as a reporter. At the indicated times post-secondary inoculation, eels (<span class="html-italic">n</span> = 6, consisting of two eels from triplicate tanks) were imaged using IVIS. (<b>B</b>) Average radiance (individual values, mean ± SEM) measured on the entire body surface of fish, i.e., skin (individual values represent the mean values obtained for the left and right sides of each fish), gills (individual values represent the mean values obtained for the left and right gills), brain, heart, and gut–liver, were analyzed by IVIS (<span class="html-italic">n</span> = 6 per timepoint). The average radiance (<span class="html-italic">p</span>(<span class="html-italic">rad</span>)) of each group was compared with the “primary mock-infected group” using a non-parametric Kruskal–Wallis test followed by multiple comparisons with the two-stage step-up method of Benjamini, Krieger, and Yekutieli. Throughout this panel, the data obtained for every individual eel (within each group) are represented by the same symbol to allow for a correlation of the data obtained for the different organs at a specific dpi. The dashed line represents the threshold of positivity, which was calculated by the mean + 3 SD of the values obtained for the mock fish. The number of positive fish among the six analyzed fish is represented by bars (right axis). The positive fish (<span class="html-italic">p</span>(<span class="html-italic">no</span>)) from each group was compared with the primary mock-infected group using the Fisher–Pitman permutation test. <span class="html-italic">p</span> values are represented as follows: ns, not significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01. (<b>C</b>) Representative images of IVIS data (skin, gills, and brain) are presented in the lower panel. Eels with the closest scores to the mean of each group (mock; UK ORF35 Del, 100,000 pfu/mL; psoralen/UV-inactivated UK ORF35 Del, 100,000 pfu/mL; and mock-infected with UK Luc) were selected for image illustration.</p>
Full article ">Figure 4 Cont.
<p>Dose-protection effect conferred by UK ORF35 Del in vivo. (<b>A</b>) Flowchart of the experiment. At the time of primary inoculation, yellow eels (28.52 ± 7.30 g, mean ± SD) were mock-infected or infected for 2 h by immersion in water containing the indicated doses of UK ORF35 Del or 100,000 pfu/mL of UK ORF35 Del strain treated by psoralen/UV to inactivate virus infectivity. At 36 days post-primary inoculation, eels were infected for 2 h by immersion in water containing 4000 pfu/mL of UK Luc expressing luciferase as a reporter. At the indicated times post-secondary inoculation, eels (<span class="html-italic">n</span> = 6, consisting of two eels from triplicate tanks) were imaged using IVIS. (<b>B</b>) Average radiance (individual values, mean ± SEM) measured on the entire body surface of fish, i.e., skin (individual values represent the mean values obtained for the left and right sides of each fish), gills (individual values represent the mean values obtained for the left and right gills), brain, heart, and gut–liver, were analyzed by IVIS (<span class="html-italic">n</span> = 6 per timepoint). The average radiance (<span class="html-italic">p</span>(<span class="html-italic">rad</span>)) of each group was compared with the “primary mock-infected group” using a non-parametric Kruskal–Wallis test followed by multiple comparisons with the two-stage step-up method of Benjamini, Krieger, and Yekutieli. Throughout this panel, the data obtained for every individual eel (within each group) are represented by the same symbol to allow for a correlation of the data obtained for the different organs at a specific dpi. The dashed line represents the threshold of positivity, which was calculated by the mean + 3 SD of the values obtained for the mock fish. The number of positive fish among the six analyzed fish is represented by bars (right axis). The positive fish (<span class="html-italic">p</span>(<span class="html-italic">no</span>)) from each group was compared with the primary mock-infected group using the Fisher–Pitman permutation test. <span class="html-italic">p</span> values are represented as follows: ns, not significant; *, <span class="html-italic">p</span> &lt; 0.05; **, <span class="html-italic">p</span> &lt; 0.01. (<b>C</b>) Representative images of IVIS data (skin, gills, and brain) are presented in the lower panel. Eels with the closest scores to the mean of each group (mock; UK ORF35 Del, 100,000 pfu/mL; psoralen/UV-inactivated UK ORF35 Del, 100,000 pfu/mL; and mock-infected with UK Luc) were selected for image illustration.</p>
Full article ">
36 pages, 16874 KiB  
Article
Susceptibility and Permissivity of Zebrafish (Danio rerio) Larvae to Cypriniviruses
by Cindy Streiff, Bo He, Léa Morvan, Haiyan Zhang, Natacha Delrez, Mickael Fourrier, Isabelle Manfroid, Nicolás M. Suárez, Stéphane Betoulle, Andrew J. Davison, Owen Donohoe and Alain Vanderplasschen
Viruses 2023, 15(3), 768; https://doi.org/10.3390/v15030768 - 17 Mar 2023
Cited by 5 | Viewed by 3977
Abstract
The zebrafish (Danio rerio) represents an increasingly important model organism in virology. We evaluated its utility in the study of economically important viruses from the genus Cyprinivirus (anguillid herpesvirus 1, cyprinid herpesvirus 2 and cyprinid herpesvirus 3 (CyHV-3)). This revealed that [...] Read more.
The zebrafish (Danio rerio) represents an increasingly important model organism in virology. We evaluated its utility in the study of economically important viruses from the genus Cyprinivirus (anguillid herpesvirus 1, cyprinid herpesvirus 2 and cyprinid herpesvirus 3 (CyHV-3)). This revealed that zebrafish larvae were not susceptible to these viruses after immersion in contaminated water, but that infections could be established using artificial infection models in vitro (zebrafish cell lines) and in vivo (microinjection of larvae). However, infections were transient, with rapid viral clearance associated with apoptosis-like death of infected cells. Transcriptomic analysis of CyHV-3-infected larvae revealed upregulation of interferon-stimulated genes, in particular those encoding nucleic acid sensors, mediators of programmed cell death and related genes. It was notable that uncharacterized non-coding RNA genes and retrotransposons were also among those most upregulated. CRISPR/Cas9 knockout of the zebrafish gene encoding protein kinase R (PKR) and a related gene encoding a protein kinase containing Z-DNA binding domains (PKZ) had no impact on CyHV-3 clearance in larvae. Our study strongly supports the importance of innate immunity-virus interactions in the adaptation of cypriniviruses to their natural hosts. It also highlights the potential of the CyHV-3-zebrafish model, versus the CyHV-3-carp model, for study of these interactions. Full article
(This article belongs to the Special Issue Fish Virology)
Show Figures

Figure 1

Figure 1
<p>Generation and verification of CRISPR-Cas9 <span class="html-italic">eif2ak2</span> (<span class="html-italic">pkr</span>) and <span class="html-italic">pkz</span> mutations in zebrafish (<b>a</b>) Structure of zebrafish <span class="html-italic">eif2ak2</span> (<span class="html-italic">pkr</span>) and <span class="html-italic">pkz</span> genes and proteins. The protein domains including double stranded RNA-binding domains (dsRB), Z-DNA/RNA binding domains (zα) and kinase domains are aligned to the corresponding exons. The CRISPR/Cas9 gene editing targets were exon 2 in zebrafish <span class="html-italic">eif2ak2</span> gene and exon 1 in zebrafish <span class="html-italic">pkz</span> gene; sgRNA target sequences are also displayed (orange, PAM lower case). The CRISPR/Cas9-induced changes in the WT <span class="html-italic">eif2ak2</span> gene (34-base insertion) to generate PKR-KO, and WT <span class="html-italic">pkz</span> gene (14-base deletion) to generate the PKZ-KO mutant strains are displayed. After the generation of the PKZ-KO mutant strain, the WT <span class="html-italic">eif2ak2</span> gene in this strain was also mutated, resulting in the PKR-PKZ-KO mutant strain (displayed below). The mutated <span class="html-italic">eif2ak2</span> gene in the PKR-PKZ-KO strain exhibits a different mutation (7-base deletion with 1-base insertion) relative to the mutated <span class="html-italic">eif2ak2</span> gene in PKR-KO mutant. Inserted and deleted sequences are highlighted in green (deleted sequences are represented by “-“). (<b>b</b>) Results from genotyping of homozygous WT, PKR-KO, PKZ-KO and PKR-PKZ-KO zebrafish groups. This involved PCR amplification of <span class="html-italic">eif2ak2</span> (<span class="html-italic">pkr</span>) and <span class="html-italic">pkz</span> genes, in each mutant group (left and right gel images, respectively, with expected sizes of WT alleles indicated). Each gel consists of the same layout: Lane 1: 1kb Molecular Marker, Lanes 2–9 each represent a DNA extracted from single whole larva, Lanes 2–3: WT Larvae, Lanes 4–5: PKR-KO mutants, Lanes 6–7 PKZ-KO mutants, Lanes 8–9 PKR-PKZ-KO mutants. Mutant <span class="html-italic">eif2ak2</span> (<span class="html-italic">pkr</span>) alleles were detected in PKR-KO and PKR-PKZ-KO larvae exhibiting 188-bp and 148-bp amplicons, respectively (left gel). The mutant <span class="html-italic">pkz</span> allele was detected in in PKZ-KO and PKR-PKZ-KO larvae, both exhibiting 151-bp amplicons (right gel). Higher quality figures for the whole manuscript are available in the PDF version.</p>
Full article ">Figure 2
<p>Infection of ZF4 cells by cypriniviruses. ZF4 cells were infected with the AngHV-1 Luc-copGFP, CyHV-2 Luc-copGFP and CyHV-3 EGFP recombinant strains. Infection progression was imaged by epifluorescence microscopy. Infected cells were identified based on green fluorescence expression at the indicated timepoints of infection. Scale bars = 100 µm.</p>
Full article ">Figure 3
<p>Quantification of CyHV-2 and CyHV-3-infected cells in ZF4 monolayer over time. This data was acquired via time-lapse fluorescent microscopy (IncuCyte). Cells were cultured in a 24-well plate and infected with CyHV-2 Luc-copGFP or CyHV-3 EGFP recombinants (1.2 × 10<sup>6</sup> PFU/mL for each recombinant). At 24 hpi, cells were imaged every 2 h for 11 days. Data represent the mean ± standard errors from three replicates/wells. Data from each replicate at each timepoint represent the sum of fluorescent cells observed in nine separate locations of each well.</p>
Full article ">Figure 4
<p>Kinetics of appearance and death of CyHV-2 and CyHV-3-infected cells before and after infection peak. The bars relate to the temporal pattern of appearance and disappearance of CyHV-2-infected or CyHV-3-infected cells (based on fluorescent reporter expression). The quantities are based on the total amount of observations made in 9 different locations in each well/replicate. The green and red curves show the total amount of infected cells up until the peak of infection (represented by the black vertical line) and after the peak, respectively. The values on top of the curves represent the average rate of appearance of infected cells per hour (green) and the average rate of death per hour (red). Analysing the rate of appearance/hour before the peak for CyHV-2 and CyHV-3 revealed no differences between the viruses.</p>
Full article ">Figure 5
<p>Survival kinetics for CyHV-2 and CyHV-3-infected cells displayed as Kaplan-Meier plots. CyHV-2 and CyHV-3-infected cells observed at 120 hpi were monitored until the end of the experiment. Cell death events and times were identified based on the disappearance of fluorescent signals (<a href="#app1-viruses-15-00768" class="html-app">Figure S2</a>). N = Number of cells followed.</p>
Full article ">Figure 6
<p>Cell death characteristics observed in CyHV-2 and CyHV-3 infections (<b>a</b>) Representative morphological observations among populations of infected cells (those exhibiting fluorescence) in the periods leading up to cell death (disappearance of fluorescence). Top panel: Morphological features consistent with apoptosis (cell shrinkage, membrane blebbing followed by the appearance of cell debris resembling apoptotic bodies, and progressive decrease of fluorescent signal). Bottom panel: Morphological features not consistent with apoptosis (cell swelling, followed by cell shrinkage, and absence of cell debris resembling apoptotic bodies prior to disappearance of fluorescent signal). Key examples of individual cells undergoing apoptosis-like and non-apoptosis-like death in each panel are highlighted by red circle and yellow arrows, respectively, which track the progression of morphology in a single cell with respect to time. Time postinfection (in days and hours) is indicated in images. Scale bars = 100 µm. (<b>b</b>) Percentage of infected cells exhibiting features of apoptosis-like or non-apoptosis-like cell death among those that died during the observation period (<b>c</b>) Mean survival time of infected cells undergoing cell death during the observation period according to the type of death observed. Data represents mean ± standard error from 3 replicates. **** <span class="html-italic">p</span> &lt; 0.0001; *** <span class="html-italic">p</span> &lt; 0.001; * <span class="html-italic">p</span> &lt; 0.05.</p>
Full article ">Figure 7
<p>Susceptibility and permissivity of zebrafish larvae to infection with cypriniviruses after inoculation by microinjection (<b>a</b>) Epifluorescence microscopy images representative of larvae inoculated with CyHV-2 and CyHV-3 according to time postinfection (longitudinal observation of the same larvae over all timepoints) Scale bars = 200 µm. (<b>b</b>) Numbers of CyHV-2 and CyHV-3-infected larvae among groups inoculated by microinjection (n = 15). Data represents mean ± standard errors from 3 independent experiments (longitudinal observation of the same larvae over all timepoints). (<b>c</b>) Levels of AngHV-1, CyHV-2 and CyHV-3 detected in infected larvae according to time postinfection based on Luc2 signal expressed by viral recombinants. The data points represent the mean radiance per larvae according to time postinfection with mean ± standard error represented for each group at each timepoint (n = 30). The discontinuous line represents the cut-off for positivity and represents the mean + 3 × SD of the values obtained for mock-infected larvae. The number of positive larvae at each timepoint is represented by bars. * <span class="html-italic">p</span> &lt; 0.05; ** <span class="html-italic">p</span> &lt; 0.01.</p>
Full article ">Figure 8
<p>Frames from timelapse video of CyHV-3 EGFP infection in zebrafish larvae from 2–3 dpi (<a href="#app1-viruses-15-00768" class="html-app">Video S1</a>). The video represents overlay of brightfield/transmission and EGFP fluorescence (green). Time postinfection (in days, hours, and minutes) is indicated under each frame. (<b>a</b>) Entire field of view from light-sheet microscopy. For the purposes of visual orientation, identifiable anatomical features and corresponding locations within larvae body (inset image) are indicated in the first panel. Images show that the infection is primarily localized around the inoculation site (red square), and a decrease in viral levels from 2.5–3 dpi. Scale bars = 100 µm. (<b>b</b>) Enlarged images of the area within red square in (<b>a</b>), representing key examples of apoptosis-like death occurring among large numbers of infected cells (red circles) around the inoculation site, with such events primarily characterized by blebbing followed by the appearance of cell debris resembling apoptotic bodies (<b>c</b>) Key example of highly motile infected cell (highlighted with yellow circle), migrating away from the site of inoculation.</p>
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<p>Network representing the functional associations between some of the top 250 most significant DEGs at 2 dpi. Using STRING protein query function in Cytoscape, 208 of the top 250 most significant DEGs were identified and scored based on functional association with each other. These data were used to generate a network in Cytoscape, which was then arranged based on GeneMania force directed layout. Each DEG is represented by a node, with edges (connecting lines) representing functional association. The largest contiguous network resulting from this analysis (136 nodes and 696 edges) is displayed. For visualization purposes, nodes in the peripheral regions of the network (representing DEGs <span class="html-italic">LOC100006895</span>, <span class="html-italic">rnasel3</span>, <span class="html-italic">ndrg1b</span>, <span class="html-italic">pde6ha</span>, and <span class="html-italic">serpinb1l1</span>) were omitted. This resulted in one large cluster (<b>a</b>), and two smaller clusters (<b>b</b>) and (<b>c</b>). STRING functional enrichment analysis indicated that most DEGs in this network were related to the immune response to infection (<a href="#app1-viruses-15-00768" class="html-app">Table S6</a>), and genes were labelled based on the main types of gene-set categories enriched in each of their respective clusters. This revealed distinct functions associated with each gene cluster, for example (<b>a</b>) interferon and PRR signalling, (<b>b</b>) antigen processing and presentation, and (<b>c</b>) complement response. The network was also analysed by CytoHubba, which was used to identify the potentially most important hub nodes within the network, with each node scored and coloured based on maximal clique centrality within the network, according to the CytoHubba score colour scale provided; however, this is better represented in <a href="#app1-viruses-15-00768" class="html-app">Figure S5</a>, with corresponding CytoHubba scores in <a href="#app1-viruses-15-00768" class="html-app">Table S7</a>.</p>
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<p>Summary of GSEA output indicating gene-set enrichment based on gene expression in CyHV-3-infected relative to mock-infected zebrafish larvae at 2 dpi. Cytoscape Network representing functional relationships between all significantly enriched gene-sets (positive or negative) identified in GSEA output (FDR adjusted <span class="html-italic">p</span>-value &lt; 0.25). Nodes in the network represent GO (blue border) and KEGG Pathway (gold border) gene-sets. Edges (connecting lines) between nodes represent the similarity coefficient (measuring the functional/gene overlap between pairs of gene-sets). Edge thickness corresponds to magnitude of similarity coefficient (only edges with coefficient ≥2 are displayed). Each gene set exhibits either a positive or negative normalized enrichment score (NES), indicating predominant upregulation or downregulation of constituent genes, respectively. Accordingly, node colour and size both represent NES magnitude (exponentially transformed scale), with positive and negative enrichment represented by red and green, respectively, according to the colour scale provided. The node border thickness indicates the significance of enrichment (inverse of FDR adjusted <span class="html-italic">p</span>-values, thus the lower the FDR adjusted <span class="html-italic">p</span>-value, the greater the thickness). Using the MCL cluster algorithm, GO and KEGG gene-sets were clustered together based on their functional similarity as indicated by similarity coefficients (beige ovals), and numbers were assigned to each cluster. For the purposes of visual clarity, clusters were manually repositioned, and within some clusters, sub-clusters were manually grouped based on functional similarity. Clusters that are overlapping or touching in the absence of any visible edges between their respective nodes have shared edges below the 0.2 coefficient cut-off for display. Clusters that do not exhibit edges between their respective nodes and are also not touching or overlapping either have no common edges or have common edges with similarity coefficient &gt;0.1. Higher quality figures for the whole manuscript are available in the PDF version.</p>
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<p>Visualization of differential gene expression in CyHV-3-infected zebrafish larvae (2 dpi) within KEGG pathway maps. Using the R package Pathview, gene expression data from our experiment was mapped to corresponding nodes in KEGG pathways (<b>a</b>) Herpes simplex virus 1 infection (<b>b</b>) Apoptosis and (<b>c</b>) Necroptosis pathways. Nodes represent zebrafish homologs of genes known to be involved in each pathway, with colour representing the log<sub>2</sub>-fold-change in gene expression in CyHV-3-infected relative to mock infected zebrafish larvae. Upregulated and downregulated genes are represented by red and green shades respectively, according to scale in the top right of each pathway. For visual clarity (due to large differences in fold change between genes) the maximum and minimum values in the colour scale is set at –1 and 1 log<sub>2</sub>-fold-change (corresponding to a two-fold change). It should be noted that many nodes represent combined differential expression from several zebrafish paralogs, thus the generic KEGG gene symbols are used as node names, which relate to the common names used to refer to protein products at each node. Not all the paralogs represented by each node are significantly differentially regulated. The list of zebrafish orthologs/paralogs corresponding to each node in these pathways can be accessed in the KEGG database using the corresponding gene-set references (Herpes simplex virus 1 infection (DRE05168), Apoptosis (DRE04210) and Necroptosis (DRE04217)), which can then be cross-referenced with data in <a href="#app1-viruses-15-00768" class="html-app">Table S5</a> (using NCBI/Entrez/GenBank Gene IDs or Gene Symbols). Key genes involved in IFN-stimulated PKR-mediated programmed cell death, i.e., translational inhibition [<a href="#B114-viruses-15-00768" class="html-bibr">114</a>,<a href="#B116-viruses-15-00768" class="html-bibr">116</a>,<a href="#B128-viruses-15-00768" class="html-bibr">128</a>] leading to apoptosis [<a href="#B112-viruses-15-00768" class="html-bibr">112</a>] (blue), IFN-stimulated PKR-mediated apoptosis [<a href="#B129-viruses-15-00768" class="html-bibr">129</a>,<a href="#B130-viruses-15-00768" class="html-bibr">130</a>] (pink), and IFN-stimulated PKR-mediated necroptosis [<a href="#B113-viruses-15-00768" class="html-bibr">113</a>] (yellow) are highlighted. Genes with dashed line borders indicate instances where downregulation, translational inhibition or post-translational inactivation of protein products promote the processes in question (see main text and references provided within this caption for details). White nodes represent instances where zebrafish homologs have not been assigned thus far, or where gene expression from zebrafish homologs have not been detected. Higher quality figures for the whole manuscript are available in the PDF version.</p>
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<p>Replication of CyHV-3 in different zebrafish strains. (<b>a</b>) Epifluorescence microscopy images representative of larvae inoculated by microinjection with either CyHV-3 EGFP or mock-inoculated with PBS according to time postinfection (longitudinal observation of the same larvae over all timepoints). For all strains infection clearance commenced from 4–5 dpi. Scale bars = 500 µm. (<b>b</b>) Numbers of infected larvae among zebrafish strains inoculated with CyHV-3 EGFP (n = 15). Data represents mean ± standard errors from 3 independent experiments (longitudinal observation of the same larvae over all timepoints). (<b>c</b>) IVIS analysis measuring Luc2 expression in different zebrafish strains microinjected with CyHV-3 Luc (n = 30). The data points represent the mean radiance per larvae according to time postinfection with mean ± standard error represented for each group at each timepoint. The discontinuous line represents the cut-off for positivity and the mean + 3 × SD of the values obtained for mock-infected larvae. The number of positive larvae at each timepoint is represented by bars. * <span class="html-italic">p</span> &lt; 0.05; *** <span class="html-italic">p</span> &lt; 0.001; **** <span class="html-italic">p</span> &lt; 0.0001.</p>
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14 pages, 6094 KiB  
Article
Isolation and Identification of a New Isolate of Anguillid Herpesvirus 1 from Farmed American Eels (Anguilla rostrata) in China
by Rui Guo, Zheng Zhang, Tianliang He, Miaomiao Li, Yuchen Zhuo, Xiaoqiang Yang, Haiping Fan and Xinhua Chen
Viruses 2022, 14(12), 2722; https://doi.org/10.3390/v14122722 - 7 Dec 2022
Cited by 3 | Viewed by 2739
Abstract
Anguillid herpesvirus 1 (AngHV-1) is a pathogen that causes hemorrhagic disease in various farmed and wild freshwater eel species, resulting in significant economic losses. Although AngHV-1 has been detected in the American eel (Anguilla rostrata), its pathogenicity has not been well [...] Read more.
Anguillid herpesvirus 1 (AngHV-1) is a pathogen that causes hemorrhagic disease in various farmed and wild freshwater eel species, resulting in significant economic losses. Although AngHV-1 has been detected in the American eel (Anguilla rostrata), its pathogenicity has not been well characterized. In this study, an AngHV-1 isolate, tentatively named AngHV-1-FC, was isolated from diseased American eels with similar symptoms as those observed in AngHV-1-infected European eels and Japanese eels. AngHV-1-FC induced severe cytopathic effects in the European eel spleen cell line (EES), and numerous concentric circular virions were observed in the infected EES cells by transmission electron microscopy. Moreover, AngHV-1-FC caused the same symptoms as the naturally diseased European eels and Japanese eels through experimental infection, resulting in a 100% morbidity rate and 13.3% mortality rate. The whole genome sequence analyses showed that the average nucleotide identity value between AngHV-1-FC and other AngHV-1 isolates ranged from 99.28% to 99.55%. However, phylogenetic analysis revealed that there was a genetic divergence between AngHV-1-FC and other AngHV-1 isolates, suggesting that AngHV-1-FC was a new isolate of AngHV-1. Thus, our results indicated that AngHV-1-FC can infect farmed American eels, with a high pathogenicity, providing new knowledge in regard to the prevalence and prevention of AngHV-1. Full article
(This article belongs to the Special Issue Fish Antiviral Immunity)
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<p>Clinical symptoms of hemorrhagic disease in the naturally diseased American eels. (<b>A</b>) Congestion of the dorsal fin. (<b>B</b>) Congestion of the pectoral fin and anal fin, and red abdomen and swollen anus. (<b>C</b>) Ischemic gill and mandibular hyperemia. (<b>D</b>) Ischemic liver. (<b>E</b>) Enlarged and congested spleen, abdominal hemorrhage. Yellow arrows show the different tissues with clinical symptoms. Scale bar = 1 cm.</p>
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<p>AngHV-1-FC infection in EES cells. (<b>A</b>) CPE induced by AngHV-1-FC in EES cells. EES cells were infected with AngHV-1-FC at 4 dpi, and the swollen cells and syncytium were found in 400× magnification. The morphology was observed under light microscope. Black arrows represent the syncytiums, and scale bar = 200 µm. (<b>B</b>) The cells with CPE under electron microscope. Numerous concentric circular viral nucleocapsid were observed in the nuclear under electron microscope with 50,000× magnification. Black arrows represent the viral nucleocapsids, red frame represent the detail view, and scale bar = 2 µm or 500 nm.</p>
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<p>The cumulative morbidity rate and mortality rate of the American eels infected with AngHV-1-FC. (<b>A</b>) Cumulative morbidity and (<b>B</b>) cumulative mortality of the eels artificially infected AngHV-1-FC. The infection group was injected with 1.26 × 10<sup>5</sup> TCID<sub>50</sub> of AngHV-1-FC per fish. The control group was injected with PBS.</p>
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<p>Histopathological examination of tissues from the American eels infected with AngHV-1-FC. All sections were stained with H&amp;E. Black arrows represent vacuoles in cells, yellow arrows represent nuclear pyknosis, red arrows represent hemosiderin exudation, and green arrows represent syncytia. White scale bar = 100 µm.</p>
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<p>Transmission electron microscope observation of different tissues from the American eels infected with AngHV-1-FC. Virus particles were observed in the gill (<b>A</b>), liver (<b>B</b>) and spleen (<b>C</b>). Black arrows show virus particles within the cytoplasm. N, nucleus. M, mitochondrion. Scale bar = 100 nm.</p>
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<p>Map of the genome structure of AngHV-1-FC with the protein annotations. The predicated ORFs are indicated by colored arrows and the directions of arrows represent transcription initiation direction of them. ORFs are depicted as color-shaded arrows, with names (lacking the ORF prefix) between the two strands. Introns connecting spliced ORFs are shown as narrow purple bars according to the transcriptome information of the reference genome [<a href="#B15-viruses-14-02722" class="html-bibr">15</a>]. The 12 core ORFs conserved in all <span class="html-italic">Alloherpesviridae</span> isolates are presented in light green or yellow arrow. The other identical ORFs among three virus isolates FC, FJ and TW are presented in different colors with different functions and the ORFs with unknown functions are presented in grey. The name of ORFs with known functions are shown in the list below the map. The TR is shown in cyan.</p>
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<p>Phylogenetic trees of AngHV-1-FC. (<b>A</b>) The phylogenetic tree of concatenated 3 core gene amino acid sequences (DNA polymerase, DNA helicase, and terminase genes from AngHV-1, <span class="html-italic">Cyprinivirus</span> and RaHV-1 genomes). The tree was constructed by the neighbor-joining method with 1000 bootstrap replicates. (<b>B</b>) The phylogenetic tree based on whole genome sequences of AngHV-1 isolates. The tree was constructed by the UPGMA method. Only values greater than 50% are shown. The AngHV-1-FC is marked by a black triangle.</p>
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13 pages, 2064 KiB  
Article
Proteomic Profiling Skin Mucus of European Eel Anguilla anguilla Infected with Anguillid Herpesvirus
by Ying-Ying Li, Jin-Xian Yang, Xi Chen, Qiang Chen, Tie-Ying Song and Jun-Qing Ge
Int. J. Mol. Sci. 2022, 23(19), 11283; https://doi.org/10.3390/ijms231911283 - 24 Sep 2022
Cited by 6 | Viewed by 2199
Abstract
Anguillid herpesvirus 1 (AngHV) is an important viral pathogen affecting eel. This study was designed to investigate the potential molecular mechanisms and immune response elicited at the protein levels in the skin mucus of AngHV-infected Anguilla anguilla. Tandem mass tag (TMT)-labelling proteomics [...] Read more.
Anguillid herpesvirus 1 (AngHV) is an important viral pathogen affecting eel. This study was designed to investigate the potential molecular mechanisms and immune response elicited at the protein levels in the skin mucus of AngHV-infected Anguilla anguilla. Tandem mass tag (TMT)-labelling proteomics with the liquid chromatography tandem mass spectrometry (LC-MS/MS) was used for performing quantitative identification of the proteins. In addition, the quantitative protein amount was detected by parallel reaction monitoring (PRM) analysis. A total of 3486 proteins were identified, of which 2935 were quantified. When a protein fold change was greater than 1.3 or less than 0.76, it indicated a differentially expressed protein (DEP). Overall, 187 up-regulated proteins and 126 down-regulated proteins were detected, and most of the DEPs were enriched in the CAMs pathway, intestinal immune pathway, herpes simplex virus 1 infection pathway, phagosome pathway and p53 signaling pathway. The results of the DEPs detected by PRM were highly consistent with the results of the TMT-labelled quantitative proteomic analysis. The findings of this study provide an important research basis for further understanding the pathogenesis of AngHV. Full article
(This article belongs to the Special Issue Bacterial and Viral Pathogenesis: Insights from Proteomics)
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<p>The morphological and histopathological changes observed in the skin in AngHV-infected <span class="html-italic">A. anguilla</span>. The morphological image for the eel infected by AngHV (<b>a</b>) and the healthy eel (<b>b</b>) showed that the skin mucus was sloughed. The histopathological images for the AngHV group (<b>c</b>) and the control group (<b>d</b>) show that the skin had exfoliation of mucus and mucosa flat epithelial cells in the eel infected by AngHV.</p>
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<p>The volcano plot of the DEPs showing both up-regulated (red) and down-regulated (blue) proteins.</p>
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<p>GO annotation of the DEPs. (<b>a</b>) GO annotation of the up-regulated proteins; (<b>b</b>) GO annotation of the down-regulated proteins.</p>
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<p>The subcellular localization of the DEPs: (<b>a</b>) the subcellular localization of the up-regulated proteins; (<b>b</b>) the subcellular localization of the down-regulated proteins.</p>
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<p>The COG/KOG categories of the DEPs: (<b>a</b>) the COG/KOG categories of the up-regulated proteins; (<b>b</b>) the COG/KOG categories of the down-regulated proteins.</p>
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<p>GO enrichment analysis of the DEPs: (<b>a</b>) GO enrichment analysis of the up-regulated proteins; (<b>b</b>) GO enrichment analysis of the down-regulated proteins.</p>
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<p>KEGG pathway enrichment analysis of the DEPs: (<b>a</b>) KEGG enrichment analysis of the up-regulated proteins; (<b>b</b>) KEGG enrichment analysis of the down-regulated proteins.</p>
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15 pages, 3025 KiB  
Article
Complete Genome and Molecular Characterization of a New Cyprinid Herpesvirus 2 (CyHV-2) SH-01 Strain Isolated from Cultured Crucian Carp
by Jia Yang, Jinxuan Wen, Simin Xiao, Chang Wei, Fei Yu, Patarida Roengjit, Liqun Lu and Hao Wang
Viruses 2022, 14(9), 2068; https://doi.org/10.3390/v14092068 - 17 Sep 2022
Cited by 4 | Viewed by 2753
Abstract
Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during [...] Read more.
Cyprinid herpesvirus 2 (CyHV-2) is a causative factor of herpesviral hematopoietic necrosis (HVHN) in farmed crucian carp (Carassius carassius) and goldfish (Carassius auratus). In this study, we analyzed the genomic characteristics of a new strain, CyHV-2 SH-01, isolated during outbreaks in crucian carp at a local fish farm near Shanghai, China. CyHV-2 SH-01 exhibited a high sensitivity to goldfish and crucian carp in our previous research. The complete genome of SH-01 is 290,428 bp with 154 potential open reading frames (ORFs) and terminal repeat (TR) regions at both ends. Compared to the sequenced genomes of other CyHVs, Carassius auratus herpesvirus (CaHV) and Anguillid herpesvirus 1 (AngHV-1), several variations were found in SH-01, including nucleotide mutations, deletions, and insertions, as well as gene duplications, rearrangements, and horizontal transfers. Overall, the genome of SH-01 shares 99.60% of its identity with that of ST-J1. Genomic collinearity analysis showed that SH-01 has a high degree of collinearity with another three CyHV-2 isolates, and it is generally closely related to CaHV, CyHV-1, and CyHV-3, although it contains many differences in locally collinear blocks (LCBs). The lowest degree of collinearity was found with AngHV-1, despite some homologous LCBs, indicating that they are evolutionarily the most distantly related. The results provide new clues to better understand the CyHV-2 genome through sequencing and sequence mining. Full article
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<p>Genome map of CyHV-2 SH-01 and sequence lengths of proteins encoded by open reading frames (ORFs). (<b>A</b>) The SH-01 genome is 290,428 bp in length and contains 154 potential ORFs. Arrows indicate the size, location, and orientation of the 154 ORFs, with nomenclature lacking the ORF prefix given below. The number of arrows in an ORF indicates the number of exon-formed coding sequences (CDS) it contains due to the presence of introns. Two terminal repeat (TR) regions are marked with grey boxes. Seven core ORFs are indicated by yellow arrows (Core ORFs). Three ORFs with a RING-finger domain are indicated by orange arrows (RING family). One ORF belonging to the TNFR family is indicated by a pink arrow (TNFR family). The 143 unclassified ORFs are indicated by white arrows (Other ORFs). Five immediate-early (IE), 34 early (E), and 39 late (L) genes are marked in red, green, and blue, respectively, and unidentified genes are marked in black. (<b>B</b>) The graph of the sequence lengths of the proteins encoded by 154 ORFs (X-axis) vs. the number of proteins per length was calculated by Geneious Prime v2022.2.1 (Y-axis).</p>
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<p>Comparison of genome structures between SH-01 and the other seven strains. Long frames and grey frames indicate the sizes of genomes and terminal repeat (TR) regions, respectively. Long yellow triangles show that the positions of <span class="html-italic">ORF28</span> and <span class="html-italic">ORF28A</span> in SY-C1 are opposite to each other relative to SH-01 and other isolates of CyHV-2. White triangles in SY-C1, CyHV-1, and CyHV-3 indicate deletions relative to SH-01. Black triangles in CyHV-1 and CyHV-3 indicate insertions relative to SH-01. <span class="html-italic">ORF140</span>, with a large translocation in CyHV-1, and <span class="html-italic">ORF4</span>, located at the TR in CyHV-3, distinct from SH-01, are marked as red triangles. The dashed frame at the upstream end of the CaHV genome indicates the nucleotides deleted relative to SH-01. The long, green, diagonal dashed lines between SH-01 and CaHV indicate that the 5′-terminal <span class="html-italic">ORF1</span>–<span class="html-italic">13</span> of CaHV (blue shaded frame) corresponds to the 3′-terminal <span class="html-italic">ORF153B</span>–<span class="html-italic">ORF8</span> (<span class="html-italic">ORF144</span>, with long blue triangles at the downstream end, of CaHV corresponds to <span class="html-italic">ORF4</span> of SH-01) of SH-01 (blue shaded frame), similar to ST-J1, SY, and SY-C1 (absence of <span class="html-italic">ORF7</span>) marked in blue-shaded frames. The short vertical lines in AngHV-1 indicate the ORFs homologous to SH-01.</p>
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<p>Genomic evolutionary relationships and phylogenetic analysis of SH-01 and the other seven strains. (<b>A</b>) Evolutionary patterns among the homologous or heterologous regions of the genomes of eight isolates, including SH-01, were analyzed by Mauve alignment in DNASTAR Lasergene v17.3. Different locally collinear blocks (LCBs) are marked with regions in different colors. Each genome was aligned by the LCB1 of SH-01, and homologous LCBs are connected by corresponding lines. Compared to SH-01, the large “jump” of <span class="html-italic">ORF140</span> in CyHV-1 is marked in red. (<b>B</b>) Comparison of LCBs among SH-01, CyHV-1, and CyHV-3 using the progressive Mauve algorithm in Geneious Prime v2022.2.1. Different LCBs are marked with regions in different colors, and homologous LCBs are connected by corresponding lines. (<b>C</b>) Phylogenetic tree was constructed based on the amino acid sequences of helicase (ORF71) using the neighbor-joining method in MEGA v11 (<a href="https://megasoftware.net" target="_blank">https://megasoftware.net</a> accessed on 10 July 2022). Bootstrap values of 1000 replications are shown at nodes.</p>
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26 pages, 5168 KiB  
Article
Genomes of Anguillid Herpesvirus 1 Strains Reveal Evolutionary Disparities and Low Genetic Diversity in the Genus Cyprinivirus
by Owen Donohoe, Haiyan Zhang, Natacha Delrez, Yuan Gao, Nicolás M. Suárez, Andrew J. Davison and Alain Vanderplasschen
Microorganisms 2021, 9(5), 998; https://doi.org/10.3390/microorganisms9050998 - 5 May 2021
Cited by 11 | Viewed by 3277
Abstract
Anguillid herpesvirus 1 (AngHV-1) is a pathogen of eels and a member of the genus Cyprinivirus in the family Alloherpesviridae. We have compared the biological and genomic features of different AngHV-1 strains, focusing on their growth kinetics in vitro and genetic content, [...] Read more.
Anguillid herpesvirus 1 (AngHV-1) is a pathogen of eels and a member of the genus Cyprinivirus in the family Alloherpesviridae. We have compared the biological and genomic features of different AngHV-1 strains, focusing on their growth kinetics in vitro and genetic content, diversity, and recombination. Comparisons based on three core genes conserved among alloherpesviruses revealed that AngHV-1 exhibits a slower rate of change and less positive selection than other cypriniviruses. We propose that this may be linked to major differences in host species and corresponding epidemiological circumstances. Efforts to derive evolutionary rate estimates for cypriniviruses under various theoretical models were ultimately unrewarding. We highlight the potential value of future collaborative efforts towards generating short-term evolutionary rate estimates based on known sequence sampling dates. Finally, we revealed that there is significantly less genetic diversity in core gene sequences within cyprinivirus species clades compared to species in the family Herpesviridae. This suggests that cyprinivirus species may have undergone much more vigorous purifying selection post species clade divergence. We discuss whether this may be linked to biological and anthropogenic factors or to sampling bias, and we propose that the comparison of short-term evolutionary rates between species may provide further insights into these differences. Full article
(This article belongs to the Special Issue Herpesvirus Diversity and Evolution)
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<p>Analysis of AngHV-1 genome sequences. (<b>a</b>) Phylogenetic analysis (UPGMA). Bootstrap values (1000 replicates) are indicated at the right of each node. These values are also illustrated by the colors of the branches leading to each node. Numbers above each branch represent substitutions per nucleotide observed along the branch. The geographical origin of each strain is indicated in brackets. (<b>b</b>) Recombination analysis. Five potential recombination events were identified using nine sequenced isolates as input. For each event, the left column illustrates the results of RDP analyses, including locations of recombination events and <span class="html-italic">p</span>-values. The middle and the right columns show phylogenetic analyses based on the genome excluding the region of recombination and the same tree based on the recombination region only, respectively. Numbers on internal branches indicate bootstrap values (1000 replicates); only values &gt;50% are shown. The scales illustrate the number of substitutions per nucleotide. The color code used is described at the top.</p>
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<p>Comparisons of the growth of AngHV-1 strains in vitro. (<b>a</b>) Viral growth assay. EK-1 cells were infected with the strains indicated (see top for symbol codes) and the log<sub>10</sub> value of the titer (pfu/mL) in the cell supernatant was determined at the indicated dpi. Data are presented in <a href="#microorganisms-09-00998-t001" class="html-table">Table 1</a>. Cells were infected with the strains indicated, and plaque areas were measured over time. Data presented are the mean ± SEM for measurements of 20 randomly selected plaques. (<b>c</b>) Correlation between plaque area measured at 8 dpi (panel (<b>a</b>)) and viral titers measured at 4 dpi (panel (<b>b</b>)). Data presented are the mean ± SEM.</p>
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<p>Phylogenetic analysis of concatenated cyprinivirus core gene sequences. Cladogram of bootstrap consensus tree (UPGMA) from phylogenetic analysis of concatenated AA sequences of three core genes (DNA polymerase, helicase and terminase) derived from sequenced cyprinivirus genomes. Bootstrap values (1000 replicates) are indicated at the right of each node. These values are also illustrated through the colors of the branches leading to each node, according to the scale on the top left. Branch lengths are arbitrary.</p>
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<p>Relative rates of cyprinivirus evolution. ML trees were produced based on the same data used to generate the cladograms in <a href="#microorganisms-09-00998-f003" class="html-fig">Figure 3</a>. (<b>a</b>) ML tree based on concatenated core gene AA sequences. (<b>b</b>) ML tree based on concatenated core gene DNA sequences excluding the third codon position. In these trees, branch lengths represent the number of substitutions per site. The results of Tajima’s relative rate tests for pairwise comparison between species clades are presented in each panel. <span class="html-italic">p</span>-values highlighted in red indicate significant differences in the rate of evolution between species. The results for Tajima’s relative rate tests presented in panel (<b>b</b>) were obtained by considering transversions only. Equivalent tests, considering transitions only, are presented in <a href="#app1-microorganisms-09-00998" class="html-app">Table S4</a>.</p>
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<p>AA changes in cyprinivirus core genes driven by positive selection. CodeML analysis was performed to identify AA changes between cyprinivirus species that were driven by positive selection. Positive selection was identified in the (<b>a</b>) DNA polymerase and (<b>b</b>) helicase genes. The ML trees based on DNA polymerase and helicase codon alignments are displayed. A summary of results and <span class="html-italic">p</span>-values are indicated above each branch of interest. Only changes supported by PP &gt; 0.95 are shown. Codon and AA changes are displayed to the right of each tree, with position in alignments and color-coded descriptions of codon changes indicated on top of each column. Boxes around codons in each column are colored corresponding to the color-coded codon changes on top of each column, with codons representing the changes driven by positive selection indicated by thicker lines. PP values and species-specific positions of AA sites are summarized in <a href="#microorganisms-09-00998-t003" class="html-table">Table 3</a>.</p>
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<p>Comparison of species-specific nucleotide substitution rate estimates between HHV-1 and cypriniviruses. HHV-1 substitution rates were reported in the studies described in <a href="#app1-microorganisms-09-00998" class="html-app">Table S9</a>. Rate estimates for cypriniviruses were estimated based on two different calibration hypotheses. Corresponding time trees are available in <a href="#app1-microorganisms-09-00998" class="html-app">Figure S3</a>.</p>
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<p>Comparison of nucleotide diversity in core genes between cypriniviruses and members of the family <span class="html-italic">Herpesviridae</span>. Comparisons were based on species-level nucleotide alignments and trees generated using DNA polymerase, helicase, and terminase sequences from each species. Sequences from a fourth core gene, uracil-DNA glycosylase, were also added, facilitating the comparison of diversity between highly conserved and less well conserved core genes. All species name acronyms are defined in <a href="#app1-microorganisms-09-00998" class="html-app">Table S1</a>. The comparison consisted of 492 sequences from 123 sequenced strains. The 48 phylogenetic trees corresponding to each species-level gene alignment are provided in <a href="#app1-microorganisms-09-00998" class="html-app">Figures S4 and S5</a>. (<b>a</b>) Diversity (π) from each species-level nucleotide sequence alignment. (<b>b</b>) Mean branch length for each species-level tree. Pairwise comparison: * = <span class="html-italic">p</span> &lt; 0.05, ** = <span class="html-italic">p</span> &lt; 0.01.</p>
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