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Research Article

Whole-Genome Analysis of Human Influenza A Virus Reveals Multiple Persistent Lineages and Reassortment among Recent H3N2 Viruses

  • Edward C Holmes,

    Affiliation: Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America

    X
  • Elodie Ghedin,

    Affiliation: Institute for Genomic Research, Rockville, Maryland, United States of America

    X
  • Naomi Miller,

    Affiliation: Institute for Genomic Research, Rockville, Maryland, United States of America

    X
  • Jill Taylor,

    Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, United States of America

    X
  • Yiming Bao,

    Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America

    X
  • Kirsten St George,

    Affiliation: Wadsworth Center, New York State Department of Health, Albany, New York, United States of America

    X
  • Bryan T Grenfell,

    Affiliation: Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America

    X
  • Steven L Salzberg,

    Affiliation: Institute for Genomic Research, Rockville, Maryland, United States of America

    X
  • Claire M Fraser,

    Affiliation: Institute for Genomic Research, Rockville, Maryland, United States of America

    X
  • David J Lipman mail,

    To whom correspondence should be addressed. E-mail: lipman@ncbi.nlm.nih.gov

    Affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America

    X
  • Jeffery K Taubenberger

    Affiliation: Department of Molecular Pathology, Armed Forces Institute of Pathology, Rockville, Maryland, United States of America

    X
  • Published: July 26, 2005
  • DOI: 10.1371/journal.pbio.0030300

About the Authors

Edward C Holmes, Bryan T Grenfell
Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, Pennsylvania, United States of America
Elodie Ghedin, Naomi Miller, Steven L Salzberg, Claire M Fraser
Institute for Genomic Research, Rockville, Maryland, United States of America
Jill Taylor, Kirsten St George
Wadsworth Center, New York State Department of Health, Albany, New York, United States of America
Yiming Bao, David J Lipman
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland, United States of America
Jeffery K Taubenberger
Department of Molecular Pathology, Armed Forces Institute of Pathology, Rockville, Maryland, United States of America

Corresponding Author

Email: lipman@ncbi.nlm.nih.gov

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

ECH conducted the phylogenetic analyses. EG and NM developed the laboratory protocols and sequenced the genomes for the influenza sequencing project. JT and KS collected the clinical isolates, selected the subset for sequencing, and prepared the viral RNA. YB performed quality assurance and annotated the sequences. SLS managed development of bioinformatics software for assembly and data management for the influenza sequencing project. CMF contributed to overall project management. DJL and JKT analyzed the data. ECH, BTG, DJL, and JKT wrote the paper.