title: Migration and persistence of human influenza A viruses, Vietnam, 2001-2008.
abstract: Understanding global influenza migration and persistence is crucial for vaccine strain selection. Using 240 new human influenza A virus whole genomes collected in Vietnam during 2001-2008, we looked for persistence patterns and migratory connections between Vietnam and other countries. We found that viruses in Vietnam migrate to and from China, Hong Kong, Taiwan, Cambodia, Japan, South Korea, and the United States. We attempted to reduce geographic bias by generating phylogenies subsampled at the year and country levels. However, migration events in these phylogenies were still driven by the presence or absence of sequence data, indicating that an epidemiologic study design that controls for prevalence is required for robust migration analysis. With whole-genome data, most migration events are not detectable from the phylogeny of the hemagglutinin segment alone, although general migratory relationships between Vietnam and other countries are visible in the hemagglutinin phylogeny. It is possible that virus lineages in Vietnam persisted for >1 year.
authors.forename: Mai Quynh
authors.initials: MQ
authors.lastname: Le
authors.forename: Ha Minh
authors.initials: HM
authors.lastname: Lam
authors.forename: Vuong Duc
authors.initials: VD
authors.lastname: Cuong
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.forename: Rebecca A
authors.initials: RA
authors.lastname: Halpin
authors.forename: David E
authors.initials: DE
authors.lastname: Wentworth
authors.forename: Nguyen Tran
authors.initials: NT
authors.lastname: Hien
authors.forename: Le Thi
authors.initials: le T
authors.lastname: Thanh
authors.forename: Hoang Vu Mai
authors.initials: HV
authors.lastname: Phuong
authors.forename: Peter
authors.initials: P
authors.lastname: Horby
authors.forename: Maciej F
authors.initials: MF
authors.lastname: Boni
mesh_terms: D016679:Genome, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D006801:Humans; D053118:Influenza A Virus, H1N1 Subtype; D053122:Influenza A Virus, H3N2 Subtype; D009980:Influenza A virus / Q000145:classification* / Q000235:genetics*; D007251:Influenza, Human / Q000453:epidemiology* / Q000635:transmission*; D008969:Molecular Sequence Data; D010802:Phylogeny; D058974:Phylogeography; D062486:Public Health Surveillance; D014744:Vietnam / Q000453:epidemiology
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: Vietnam; influenza; migration; persistence; phylogeography; tropics; viruses