ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

Van der Auwera, Sandra; Bulla, Ingo; Ziller, Mario; Pohlmann, Anne; Harder, Timm; Stanke, Mario

doi:10.1371/journal.pone.0084558

ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

Journal Article · Fri Jan 03 00:00:00 EST 2014 · PLoS ONE

DOI:https://doi.org/10.1371/journal.pone.0084558· OSTI ID:1627669

Van der Auwera, Sandra ^[1]; Bulla, Ingo ^[2]; Ziller, Mario ^[3]; Pohlmann, Anne ^[3]; Harder, Timm ^[3]; Stanke, Mario ^[4]

Ernst-Moritz-Arndt Universitat Greifswald (Germany); DOE/OSTI
Ernst-Moritz-Arndt Universitat Greifswald (Germany); Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Federal Research Institute for Animal Health, Island of Riems, Greifswald (Germany)
Ernst-Moritz-Arndt Universitat Greifswald (Germany)

Accurate and rapid characterization of influenza A virus (IAV) hemagglutinin (HA) and neuraminidase (NA) sequences with respect to subtype and clade is at the basis of extended diagnostic services and implicit to molecular epidemiologic studies. ClassyFlu is a new tool and web service for the classification of IAV sequences of the HA and NA gene into subtypes and phylogenetic clades using discriminatively trained profile hidden Markov models (HMMs), one for each subtype or clade. ClassyFlu merely requires as input unaligned, full-length or partial HA or NA DNA sequences. It enables rapid and highly accurate assignment of HA sequences to subtypes H1–H17 but particularly focusses on the finer grained assignment of sequences of highly pathogenic avian influenza viruses of subtype H5N1 according to the cladistics proposed by the H5N1 Evolution Working Group. NA sequences are classified into subtypes N1–N10. ClassyFlu was compared to semiautomatic classification approaches using BLAST and phylogenetics and additionally for H5 sequences to the new ‘‘Highly Pathogenic H5N1 Clade Classification Tool’’ (IRD-CT) proposed by the Influenza Research Database. Our results show that both web tools (ClassyFlu and IRD-CT), although based on different methods, are nearly equivalent in performance and both are more accurate and faster than semiautomatic classification. A retraining of ClassyFlu to altered cladistics as well as an extension of ClassyFlu to other IAV genome segments or fragments thereof is undemanding. This is exemplified by unambiguous assignment to a distinct cluster within subtype H7 of sequences of H7N9 viruses which emerged in China early in 2013 and caused more than 130 human infections.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: German Science Foundation (DFG); USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1627669

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 1 Vol. 9; ISSN 1932-6203

Publisher:: Public Library of ScienceCopyright Statement

Country of Publication:: United States

Language:: English

References (17)

The emergence of pandemic influenza viruses Guan, Yi; Vijaykrishna, Dhanasekaran; Bahl, Justin Protein & Cell, Vol. 1, Issue 1 https://doi.org/10.1007/s13238-010-0008-z	journal	January 2010
Rapid haemagglutinin subtyping and pathotyping of avian influenza viruses by a DNA microarray Gall, Astrid; Hoffmann, Bernd; Harder, Timm Journal of Virological Methods, Vol. 160, Issue 1-2 https://doi.org/10.1016/j.jviromet.2009.05.004	journal	September 2009
Avian influenza: our current understanding Suarez, David L. Animal Health Research Reviews, Vol. 11, Issue 1 https://doi.org/10.1017/s1466252310000095	journal	June 2010
The neuraminidase of bat influenza viruses is not a neuraminidase García-Sastre, Adolfo Proceedings of the National Academy of Sciences, Vol. 109, Issue 46 https://doi.org/10.1073/pnas.1215857109	journal	October 2012
Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative Anisimova, Maria; Gascuel, Olivier Systematic Biology, Vol. 55, Issue 4 https://doi.org/10.1080/10635150600755453	journal	August 2006
Jalview Version 2--a multiple sequence alignment editor and analysis workbench Waterhouse, A. M.; Procter, J. B.; Martin, D. M. A. Bioinformatics, Vol. 25, Issue 9 https://doi.org/10.1093/bioinformatics/btp033	journal	January 2009
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
Influenza Research Database: an integrated bioinformatics resource for influenza research and surveillance: Influenza Research Database Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria Influenza and Other Respiratory Viruses, Vol. 6, Issue 6 https://doi.org/10.1111/j.1750-2659.2011.00331.x	journal	January 2012
The Evolving Threat of Influenza Viruses of Animal Origin and the Challenges in Developing Appropriate Diagnostics Mak, Polly WY; Jayawardena, Shanthi; Poon, Leo LM Clinical Chemistry, Vol. 58, Issue 11 https://doi.org/10.1373/clinchem.2012.182626	journal	November 2012
Basic local alignment search tool Altschul, Stephen F.; Gish, Warren; Miller, Webb Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2	journal	October 1990
Avian influenza: our current understanding Suarez, David L. Animal Health Research Reviews, Vol. 11, Issue 1 https://doi.org/10.1017/S1466252310000095	journal	June 2010
The genesis and source of the H7N9 influenza viruses causing human infections in China Lam, Tommy Tsan-Yuk; Wang, Jia; Shen, Yongyi Nature, Vol. 502, Issue 7470 https://doi.org/10.1038/nature12515	journal	August 2013
Crystal structures of two subtype N10 neuraminidase-like proteins from bat influenza A viruses reveal a diverged putative active site Zhu, Xueyong; Yang, Hua; Guo, Zhu Proceedings of the National Academy of Sciences, Vol. 109, Issue 46 https://doi.org/10.1073/pnas.1212579109	journal	September 2012
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0 Guindon, Stéphane; Dufayard, Jean-François; Lefort, Vincent Systematic Biology, Vol. 59, Issue 3 https://doi.org/10.1093/sysbio/syq010	journal	March 2010
Cross-species comparison of site-specific evolutionary-rate variation in influenza haemagglutinin Meyer, Austin G.; Dawson, Eric T.; Wilke, Claus O. Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 368, Issue 1614 https://doi.org/10.1098/rstb.2012.0334	journal	March 2013
Accelerated Profile HMM Searches Eddy, Sean R. PLoS Computational Biology, Vol. 7, Issue 10 https://doi.org/10.1371/journal.pcbi.1002195	journal	October 2011

Cited By (3)

Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains Phan, My V. T.; Ngo Tri, Tue; Hong Anh, Pham Virus Evolution, Vol. 4, Issue 2 https://doi.org/10.1093/ve/vey035	journal	July 2018
Overview of Virus Metagenomic Classification Methods and Their Biological Applications Nooij, Sam; Schmitz, Dennis; Vennema, Harry Frontiers in Microbiology, Vol. 9 https://doi.org/10.3389/fmicb.2018.00749	journal	April 2018
Identification and characterization of Coronaviridae genomes from Vietnamese bats and rats based on conserved protein domains. Phan, My VT; Ngo Tri, Tue; Hong Anh, Pham Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.69918	text	January 2018

Similar Records

LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins

Journal Article · Wed Jan 22 19:00:00 EST 2014 · PLoS ONE · OSTI ID:1904881

Genetically Diverse Low Pathogenicity Avian Influenza A Virus Subtypes Co-Circulate among Poultry in Bangladesh

Journal Article · Wed Mar 23 20:00:00 EDT 2016 · PLoS ONE · OSTI ID:1377073

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
BLAST algorithm
H5N1
animal phylogenetics
hidden Markov models
influenza A virus
phylogenetic analysis
sequence databases
viral pathogens

ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

Citation Formats

References (17)

Cited By (3)

Similar Records

Related Subjects