Extensive geographical mixing of 2009 human H1N1 influenza a virus in a single university community

Edward C. Holmes, Elodie Ghedin, Rebecca A. Halpin, Timothy B. Stockwell, Xing Quan Zhang, Regina Fleming, Richard Davey, Constance A. Benson, Sanjay Mehta, Randy Taplitz, Yu Tseung Liu, Kimberly C. Brouwer, David E. Wentworth, Xudong Lin, Robert T. Schooley

Research output: Contribution to journalArticlepeer-review


Despite growing interest in the molecular epidemiology of influenza virus, the pattern of viral spread within individual communities remains poorly understood. To determine the phylogeography of influenza virus in a single population, we examined the spatial diffusion of H1N1/09 influenza A virus within the student body of the University of California, San Diego (UCSD), sampling for a 1-month period between October and November 2009. Despite the highly focused nature of our study, an analysis of complete viral genome sequences revealed between 24 and 33 independent introductions of H1N1/09 into the UCSD community, comprising much of the global genetic diversity in this virus. These data were also characterized by a relatively low level of on-campus transmission as well as extensive spatial mixing, such that there was little geographical clustering by either student residence or city ZIP code. Most notably, students experiencing illness on the same day and residing in the same dorm possessed phylogenetically distinct lineages. H1N1/09 influenza A virus is therefore characterized by a remarkable spatial fluidity, which is likely to impede community-based methods for its control, including class cancellations, quarantine, and chemoprophylaxis.

Original languageEnglish (US)
Pages (from-to)6923-6929
Number of pages7
JournalJournal of virology
Issue number14
StatePublished - Jul 2011

ASJC Scopus subject areas

  • Microbiology
  • Immunology
  • Insect Science
  • Virology


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