title: Phylogeography of Influenza A(H3N2) Virus in Peru, 2010-2012.
abstract: 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.
authors.forename: Simon
authors.initials: S
authors.lastname: Pollett
authors.forename: Martha I
authors.initials: MI
authors.lastname: Nelson
authors.forename: Matthew
authors.initials: M
authors.lastname: Kasper
authors.forename: Yeny
authors.initials: Y
authors.lastname: Tinoco
authors.forename: Mark
authors.initials: M
authors.lastname: Simons
authors.forename: Candice
authors.initials: C
authors.lastname: Romero
authors.forename: Marita
authors.initials: M
authors.lastname: Silva
authors.forename: Xudong
authors.initials: X
authors.lastname: Lin
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Halpin
authors.forename: Nadia
authors.initials: N
authors.lastname: Fedorova
authors.forename: Timothy B
authors.initials: TB
authors.lastname: Stockwell
authors.forename: David
authors.initials: D
authors.lastname: Wentworth
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.forename: Daniel G
authors.initials: DG
authors.lastname: Bausch
mesh_terms: D016000:Cluster Analysis; D004196:Disease Outbreaks / Q000706:statistics & numerical data*; D004197:Disease Reservoirs / Q000706:statistics & numerical data; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006801:Humans; D053122:Influenza A Virus, H3N2 Subtype; D007251:Influenza, Human / Q000453:epidemiology*; D010568:Peru / Q000453:epidemiology; D010802:Phylogeny; D058974:Phylogeography / Q000379:methods*
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: H3N2; Peru; evolution; gene pool; human influenza; influenza; influenza A(H3N2) virus; influenza virus; interseasonal extinction; phylogeny; phylogeography; source population; source–sink dynamic; source–sink model; subtropical; surveillance; tropical; viral traffic; viruses