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CAPS Genomic Subtyping on Orthomyxoviridae

  • Conference paper
Emerging Intelligent Computing Technology and Applications (ICIC 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5754))

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Abstract

The Orthomyxoviridae is a family of single strained RNA viruses including five genera: Influenza virus A, Influenza virus B, Influenza virus C, Thogotovirus, and Isavirus. Usually, Influenza viruses are identified by antigenic differences in their nucleoprotein and matrix protein. In this paper, we propose an algorithm to determine a set of suitable restriction enzymes for producing recognizable restriction maps on Orthomyxoviridae. Our method is applied to viral strains of highly pathogenic avian influenza (HPAI), containing potentially homozygous, heterozygous, and various genetic variations. In the analysis of CAPS (Cleaved Amplified Polymorphic Sequence) subtyping, our method outperforms the RNA coding of representative and epidemiologically significant human wild-type viruses, including H3N8, H5N1, H5N9, H7N1, H7N7, and H9N2. These isolates are analyzed by CAPS with enzymes AgeI, EciI, KpnI, and XbaI. The HPAI strains show a different RFLP (Restriction Fragment Length Polymorphism) profile by comparing with other low pathogenic avian influenza (LPAI) strains. We provide a rapid, specific, and reproducible identification of the genotypes on Orthomyxoviridae. It permits us to quickly confirm subtypes of Orthomyxoviridae.

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Authors and Affiliations

  1. Department of Computer Science and Information Engineering, National Dong Hwa University, Hualien, 974, Taiwan

    Sheng-Lung Peng & Yu-Wei Tsay

  2. Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan

    Chich-Sheng Lin

  3. Department of Computer Science, National Tsing Hua University, Hsinchu, 300, Taiwan

    Chuan Yi Tang

Authors
  1. Sheng-Lung Peng
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  2. Yu-Wei Tsay
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  3. Chich-Sheng Lin
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  4. Chuan Yi Tang
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Editor information

Editors and Affiliations

  1. Institute of Intelligent Machines, Chinese Academy of Sciences, China

    De-Shuang Huang

  2. Graduate School of Electrical Engineering, University of Ulsan, Korea, San 29, Mugeo-Dong, Nam-Ku, 680 - 749, Ulsan, Korea

    Kang-Hyun Jo

  3. School of Electrical Engineering, University of Ulsan, Ulsan, South Korea

    Hong-Hee Lee

  4. School of Electrical Engineering, University of Ulsan, South Korea

    Hee-Jun Kang

  5. e.B.I.S. s.r.l. (electronic Business in Security), Spin-Off of Polytechnic of Bari, Str. Prov. per Casamassima Km., 3-70010, Valenzano, (BA), Italy

    Vitoantonio Bevilacqua

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© 2009 Springer-Verlag Berlin Heidelberg

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Peng, SL., Tsay, YW., Lin, CS., Tang, C.Y. (2009). CAPS Genomic Subtyping on Orthomyxoviridae . In: Huang, DS., Jo, KH., Lee, HH., Kang, HJ., Bevilacqua, V. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2009. Lecture Notes in Computer Science, vol 5754. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04070-2_15

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  • DOI: https://doi.org/10.1007/978-3-642-04070-2_15

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04069-6

  • Online ISBN: 978-3-642-04070-2

  • eBook Packages: Computer ScienceComputer Science (R0)

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