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

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  • Samuel S Shepard
  • C Todd Davis
  • Justin Bahl
  • Pierre Rivailler
  • Ian A York
  • Ruben O Donis

Abstract

The evolutionary classification of influenza genes into lineages is a first step in understanding their molecular epidemiology and can inform the subsequent implementation of control measures. We introduce a novel approach called Lineage Assignment By Extended Learning (LABEL) to rapidly determine cladistic information for any number of genes without the need for time-consuming sequence alignment, phylogenetic tree construction, or manual annotation. Instead, LABEL relies on hidden Markov model profiles and support vector machine training to hierarchically classify gene sequences by their similarity to pre-defined lineages. We assessed LABEL by analyzing the annotated hemagglutinin genes of highly pathogenic (H5N1) and low pathogenicity (H9N2) avian influenza A viruses. Using the WHO/FAO/OIE H5N1 evolution working group nomenclature, the LABEL pipeline quickly and accurately identified the H5 lineages of uncharacterized sequences. Moreover, we developed an updated clade nomenclature for the H9 hemagglutinin gene and show a similarly fast and reliable phylogenetic assessment with LABEL. While this study was focused on hemagglutinin sequences, LABEL could be applied to the analysis of any gene and shows great potential to guide molecular epidemiology activities, accelerate database annotation, and provide a data sorting tool for other large-scale bioinformatic studies.

Suggested Citation

  • Samuel S Shepard & C Todd Davis & Justin Bahl & Pierre Rivailler & Ian A York & Ruben O Donis, 2014. "LABEL: Fast and Accurate Lineage Assignment with Assessment of H5N1 and H9N2 Influenza A Hemagglutinins," PLOS ONE, Public Library of Science, vol. 9(1), pages 1-12, January.
  • Handle: RePEc:plo:pone00:0086921
    DOI: 10.1371/journal.pone.0086921
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    References listed on IDEAS

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    1. H. Chen & G. J. D. Smith & S. Y. Zhang & K. Qin & J. Wang & K. S. Li & R. G. Webster & J. S. M. Peiris & Y. Guan, 2005. "H5N1 virus outbreak in migratory waterfowl," Nature, Nature, vol. 436(7048), pages 191-192, July.
    2. Dhanasekaran Vijaykrishna & Gavin J. D. Smith & Oliver G. Pybus & Huachen Zhu & Samir Bhatt & Leo L. M. Poon & Steven Riley & Justin Bahl & Siu K. Ma & Chung L. Cheung & Ranawaka A. P. M. Perera & Hon, 2011. "Long-term evolution and transmission dynamics of swine influenza A virus," Nature, Nature, vol. 473(7348), pages 519-522, May.
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