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Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis

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Hemorrhagic Fever Viruses

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1604))

Abstract

During the last decade, genome sequence-based classification of viruses has become increasingly prominent. Viruses can be even classified based on coding-complete genome sequence data alone. Nevertheless, classification remains arduous as experts are required to establish phylogenetic trees to depict the evolutionary relationships of such sequences for preliminary taxonomic placement. Pairwise sequence comparison (PASC) of genomes is one of several novel methods for establishing relationships among viruses. This method, provided by the US National Center for Biotechnology Information as an open-access tool, circumvents phylogenetics, and yet PASC results are often in agreement with those of phylogenetic analyses. Computationally inexpensive, PASC can be easily performed by non-taxonomists. Here we describe how to use the PASC tool for the preliminary classification of novel viral hemorrhagic fever-causing viruses.

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References

  1. International Committee on Taxonomy of Viruses (ICTV) (2016) International Committee on Taxonomy of Viruses. http://www.ictvonline.org/

  2. National Center for Biotechnology Information (NCBI) (2016) GenBank. http://www.ncbi.nlm.nih.gov/genbank/

  3. Brister JR, Ako-Adjei D, Bao Y, Blinkova O (2015) NCBI viral genomes resource. Nucleic Acids Res 43(Database issue):D571–D577. doi:10.1093/nar/gku1207

    Article  CAS  PubMed  Google Scholar 

  4. Bao Y, Chetvernin V, Tatusova T (2014) Improvements to pairwise sequence comparison (PASC): a genome-based web tool for virus classification. Arch Virol 159(12):3293–3304. doi:10.1007/s00705-014-2197-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Bao Y, Kapustin Y, Tatusova T (2008) Virus classification by PAirwise Sequence Comparison (PASC). In: Mahy BWJ, van Regenmortel MHV (eds) Encyclopedia of virology, vol 5, 3rd edn. Elsevier, Oxford, UK, pp 342–348

    Google Scholar 

  6. Lauber C, Gorbalenya AE (2012) Partitioning the genetic diversity of a virus family: approach and evaluation through a case study of picornaviruses. J Virol 86(7):3890–3904. doi:10.1128/JVI.07173-11

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9(9):e108277. doi:10.1371/journal.pone.0108277

    Article  PubMed  PubMed Central  Google Scholar 

  8. National Center for Biotechnology Information (NCBI) (2016) PASC. http://www.ncbi.nlm.nih.gov/sutils/pasc/viridty.cgi?textpage=overview

  9. International Committee on Taxonomy of Viruses (ICTV) (2016) Taxonomy Proposal Templates. https://talk.ictvonline.org/files/taxonomy-proposal-templates/

  10. National Center for Biotechnology Information (NCBI) (2016) Viral Genomes. http://www.ncbi.nlm.nih.gov/genome/viruses/

  11. National Center for Biotechnology Information (NCBI) (2016) Taxonomy. http://www.ncbi.nlm.nih.gov/taxonomy

  12. Pearson WR (2014) BLAST and FASTA similarity searching for multiple sequence alignment. Methods Mol Biol 1079:75–101. doi:10.1007/978-1-62703-646-7_5

    Article  PubMed  Google Scholar 

  13. Pearson WR (2016) Finding protein and nucleotide similarities with FASTA. Curr Protoc Bioinformatics 53:3.9.1–3.9.25. doi:10.1002/0471250953.bi0309s53

    Article  Google Scholar 

  14. Ladner JT, Beitzel B, Chain PS, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O’Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu GY, The Threat Characterization Consortium, Sozhamannan S, Bradburne C, Palacios G (2014) Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio 5(3):e01360–e01314. doi:10.1128/mBio.01360-14

    Article  PubMed  PubMed Central  Google Scholar 

  15. Ladner JT, Kuhn JH, Palacios G (2016) Standard finishing categories for high-throughput sequencing of viral genomes. Rev Sci Tech 35(1):43–52. doi:10.20506/rst.35.1.2416

    Article  CAS  PubMed  Google Scholar 

  16. Radoshitzky SR, Bào Y, Buchmeier MJ, Charrel RN, Clawson AN, Clegg CS, DeRisi JL, Emonet S, Gonzalez J-P, Kuhn JH, Lukashevich IS, Peters CJ, Romanowski V, Salvato MS, Stenglein MD, de la Torre JC (2015) Past, present, and future of arenavirus taxonomy. Arch Virol 160(7):1851–1874. doi:10.1007/s00705-015-2418-y

    Article  CAS  PubMed  Google Scholar 

  17. Bao Y, Chetvernin V, Tatusova T (2012) PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses. Viruses 4(8):1318–1327. doi:10.3390/v4081318

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kuhn JH, Becker S, Ebihara H, Geisbert TW, Johnson KM, Kawaoka Y, Lipkin WI, Negredo AI, Netesov SV, Nichol ST, Palacios G, Peters CJ, Tenorio A, Volchkov VE, Jahrling PB (2010) Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviations. Arch Virol 155(12):2083–2103. doi:10.1007/s00705-010-0814-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Grard G, Fair JN, Lee D, Slikas E, Steffen I, Muyembe J-J, Sittler T, Veeraraghavan N, Ruby JG, Wang C, Makuwa M, Mulembakani P, Tesh RB, Mazet J, Rimoin AW, Taylor T, Schneider BS, Simmons G, Delwart E, Wolfe ND, Chiu CY, Leroy EM (2012) A novel rhabdovirus associated with acute hemorrhagic fever in Central Africa. PLoS Pathog 8(9):e1002924. doi:10.1371/journal.ppat.1002924

    Article  PubMed  PubMed Central  Google Scholar 

  20. Mansfield KL, Morales AB, Johnson N, Ayllón N, Höfle U, Alberdi P, Fernández de Mera IG, García Marín JF, Gortázar C, de la Fuente J, Fooks AR (2015) Identification and characterization of a novel tick-borne flavivirus subtype in goats (Capra hircus) in Spain. J Gen Virol 96(Pt 7):1676–1681. doi:10.1099/vir.0.000096

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

We thank Vyacheslav Chetvernin for developing and maintaining the PASC tool. We also thank Laura Bollinger of the IRF-Frederick for critically editing this manuscript.

This work was funded in part through Battelle Memorial Institute’s prime contract with the US National Institute of Allergy and Infectious Diseases (NIAID) under Contract No. HHSN272200700016I. A subcontractor to Battelle Memorial Institute who performed this work is J.H.K., an employee of Tunnell Government Services, Inc. This research was also supported in part by the Intramural Research Program of the National Institutes of Health, National Library of Medicine (Y.B.). Opinions expressed here are our own and do not reflect the view of the NIH, the Department of Health and Human Services, or the US government.

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Authors and Affiliations

  1. Information Engineering Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bldg. 45, Room 6AS.47D-45, 45 Center Drive, MSC-6510, Bethesda, MD, 20894, USA

    Yīmíng Bào

  2. Integrated Research Facility at Fort Detrick (IRF-Frederick), Division of Clinical Research (DCR), National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), 8200 Research Plaza, Fort Detrick, Frederick, MD, 21702, USA

    Jens H. Kuhn

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  1. Yīmíng Bào
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  2. Jens H. Kuhn
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Correspondence to Yīmíng Bào .

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Editors and Affiliations

  1. School of Medicine, University of Maryland, Baltimore, Maryland, USA

    Maria S. Salvato

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Bào, Y., Kuhn, J.H. (2018). Preliminary Classification of Novel Hemorrhagic Fever-Causing Viruses Using Sequence-Based PAirwise Sequence Comparison (PASC) Analysis. In: Salvato, M. (eds) Hemorrhagic Fever Viruses. Methods in Molecular Biology, vol 1604. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6981-4_3

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  • DOI: https://doi.org/10.1007/978-1-4939-6981-4_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6980-7

  • Online ISBN: 978-1-4939-6981-4

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