AUTHOR=Zhong Gongxun , Fan Shufang , Lopes Tiago J. S. , Le Mai Quynh , van Bakel Harm , Dutta Jayeeta , Smith Gavin J. D. , Jayakumar Jayanthi , Nguyen Hang Le Khanh , Hoang Phuong Vu Mai , Halfmann Peter , Hatta Masato , Su Yvonne C. F. , Neumann Gabriele , Kawaoka Yoshihiro TITLE=Isolation of Highly Pathogenic H5N1 Influenza Viruses in 2009–2013 in Vietnam JOURNAL=Frontiers in Microbiology VOLUME=10 YEAR=2019 URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01411 DOI=10.3389/fmicb.2019.01411 ISSN=1664-302X ABSTRACT=

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, 2.3.2.1a, 2.3.2.1b, 2.3.2.1c, and 2.3.4.1. Consistent with other studies, we found that viruses of clade 2.3.2.1c 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 2.3.2.1a, 2.3.2.1b, and 2.3.2.1c; in contrast, no reassortment was detected between clade 2.3.2.1 viruses and viruses of clades 1.1.2 or 2.3.4.1, 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.