title: Quantifying influenza virus diversity and transmission in humans.
abstract: Influenza A virus is characterized by high genetic diversity. However, most of what is known about influenza evolution has come from consensus sequences sampled at the epidemiological scale that only represent the dominant virus lineage within each infected host. Less is known about the extent of within-host virus diversity and what proportion of this diversity is transmitted between individuals. To characterize virus variants that achieve sustainable transmission in new hosts, we examined within-host virus genetic diversity in household donor-recipient pairs from the first wave of the 2009 H1N1 pandemic when seasonal H3N2 was co-circulating. Although the same variants were found in multiple members of the community, the relative frequencies of variants fluctuated, with patterns of genetic variation more similar within than between households. We estimated the effective population size of influenza A virus across donor-recipient pairs to be approximately 100-200 contributing members, which enabled the transmission of multiple lineages, including antigenic variants.
authors.affiliation: Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China.
authors.forename: Leo L M
authors.initials: LL
authors.lastname: Poon
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.|Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.
authors.forename: Timothy
authors.initials: T
authors.lastname: Song
authors.affiliation: School of Computer Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Roni
authors.initials: R
authors.lastname: Rosenfeld
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Xudong
authors.initials: X
authors.lastname: Lin
authors.affiliation: Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
authors.forename: Matthew B
authors.initials: MB
authors.lastname: Rogers
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.
authors.forename: Bin
authors.initials: B
authors.lastname: Zhou
authors.affiliation: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Sebra
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Halpin
authors.affiliation: Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China.
authors.forename: Yi
authors.initials: Y
authors.lastname: Guan
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.
authors.forename: Alan
authors.initials: A
authors.lastname: Twaddle
authors.affiliation: Pittsburgh Supercomputer Center, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
authors.forename: Jay V
authors.initials: JV
authors.lastname: DePasse
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.affiliation: J. Craig Venter Institute, Rockville, Maryland, USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.affiliation: Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences, The University of Sydney, Sydney, New South Wales, Australia.|Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: Tisch Cancer Institute, Departments of Medicine, Hematology and Medical Oncology, and Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Greenbaum
authors.affiliation: Public Health Laboratory Sciences, School of Public Health, The University of Hong Kong, Hong Kong, China.
authors.forename: Joseph S M
authors.initials: JS
authors.lastname: Peiris
authors.affiliation: Epidemiology and Biostatistics, School of Public Health, The University of Hong Kong, Hong Kong, China.
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Cowling
authors.affiliation: Center for Genomics and Systems Biology, Department of Biology, New York University, New York, New York, USA.|College of Global Public Health, New York University, New York, New York, USA.
authors.forename: Elodie
authors.initials: E
authors.lastname: Ghedin
mesh_terms: D005814:Genes, Viral; D014644:Genetic Variation; D006801:Humans; D009980:Influenza A virus / Q000145:classification* / Q000235:genetics; D007251:Influenza, Human / Q000635:transmission* / Q000821:virology; D010802:Phylogeny