Routine surveillance and surveillance in response to influenza outbreaks in avian species in Vietnam in 2009-2013 resulted in the isolation of numerous H5N1 influenza viruses of clades 1.1.2, 126.96.36.199a, 188.8.131.52b, 184.108.40.206c, and 220.127.116.11. Consistent with other studies, we found that viruses of clade 18.104.22.168c were dominant in Vietnam in 2013 and circulated in the northern, central, and southern parts of the country. Phylogenetic analysis revealed reassortment among viruses of clades 22.214.171.124a, 126.96.36.199b, and 188.8.131.52c; in contrast, no reassortment was detected between clade 184.108.40.206 viruses and viruses of clades 1.1.2 or 220.127.116.11, respectively. Deep-sequencing of 42 of the 53 isolated H5N1 viruses revealed viral subpopulations encoding variants that may affect virulence, host range, or sensitivity to antiviral compounds; virus isolates containing these subpopulations may have a higher potential to transmit and adapt to mammals. Among the viruses sequenced, a relatively high number of non-synonymous nucleotide polymorphisms was detected in a virus isolated from a barn swallow, possibly suggesting influenza virus adaption to this host.
Keywords: H5N1; Vietnam; deep-sequencing; influenza virus; surveillance.