Phylogeography of influenza A(H3N2) virus in Peru, 2010–2012

Simon Pollett*, Martha I. Nelson, Matthew Kasper, Yeny Tinoco, Mark Simons, Candice Romero, Marita Silva, Xudong Lin, Rebecca A. Halpin, Nadia Fedorova, Timothy B. Stockwell, David Wentworth, Edward C. Holmes, Daniel G. Bausch

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


It remains unclear whether lineages of influenza A(H3N2) virus can persist in the tropics and seed temperate areas. We used viral gene sequence data sampled from Peru to test this source–sink model for a Latin American country. Viruses were obtained during 2010–2012 from influenza surveillance cohorts in Cusco, Tumbes, Puerto Maldonado, and Lima. Specimens positive for influenza A(H3N2) virus were randomly selected and underwent hemagglutinin sequencing and phylogeographic analyses. Analysis of 389 hemagglutinin sequences from Peru and 2,192 global sequences demonstrated interseasonal extinction of Peruvian lineages. Extensive mixing occurred with global clades, but some spatial structure was observed at all sites; this structure was weakest in Lima and Puerto Maldonado, indicating that these locations may experience greater viral traffic. The broad diversity and co-circulation of many simultaneous lineages of H3N2 virus in Peru suggests that this country should not be overlooked as a potential source for novel pandemic strains.

Original languageEnglish
Pages (from-to)1330-1338
Number of pages9
JournalEmerging Infectious Diseases
Issue number8
StatePublished - 23 Jul 2015


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