title: Emergence of multiple clade 2.3.2.1 influenza A (H5N1) virus subgroups in Vietnam and detection of novel reassortants.
abstract: Phylogenetic analyses of 169 influenza A(H5N1) virus genomes were conducted for samples collected through active surveillance and outbreak responses in Vietnam between September 2010 and September 2012. While clade 1.1 viruses persisted in southern regions, three genetically distinct subgroups of clade 2.3.2.1 were found in northern and central Vietnam. The identification of each subgroup corresponded with detection of novel reassortants, likely due to their overlapping circulation throughout the country. While the previously identified clade 1.1 and A/Hubei/1/2010-like 2.3.2.1 genotypes remained the predominant viruses detected, four viruses were found to be reassortants between A/Hubei/1/2010-like (HA, NA, PB2, PB1, PA, NP) and A/duck/Vietnam/NCVD-885/2010-like (M, NS) viruses and one virus was identified as having A/duck/Vietnam/NCVD-885/2010-like HA, NA, PB1, and NP with A/Hubei/1/2010-like PB2 and PA genes. Additionally, clade 2.3.2.1 A/Hong Kong/6841/2010-like viruses, first detected in mid-2012, were identified as reassortants comprised of A/Hubei/1/2010-like PB2 and PA and A/duck/Vietnam/NCVD-885/2010-like PB1, NP, NA, M, NS genes.
authors.affiliation: Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA 30333 USA.
authors.forename: Adrian
authors.initials: A
authors.lastname: Creanga
authors.forename: Diep
authors.initials: D
authors.lastname: Thi Nguyen
authors.forename: Nancy
authors.initials: N
authors.lastname: Gerloff
authors.forename: Hoa
authors.initials: H
authors.lastname: Thi Do
authors.forename: Amanda
authors.initials: A
authors.lastname: Balish
authors.forename: Hoang
authors.initials: H
authors.lastname: Dang Nguyen
authors.forename: Yunho
authors.initials: Y
authors.lastname: Jang
authors.forename: Vui
authors.initials: V
authors.lastname: Thi Dam
authors.forename: Sharmi
authors.initials: S
authors.lastname: Thor
authors.forename: Joyce
authors.initials: J
authors.lastname: Jones
authors.forename: Natosha
authors.initials: N
authors.lastname: Simpson
authors.forename: Bo
authors.initials: B
authors.lastname: Shu
authors.forename: Shannon
authors.initials: S
authors.lastname: Emery
authors.forename: LaShondra
authors.initials: L
authors.lastname: Berman
authors.forename: Ha T
authors.initials: HT
authors.lastname: Nguyen
authors.forename: Juliet E
authors.initials: JE
authors.lastname: Bryant
authors.forename: Steve
authors.initials: S
authors.lastname: Lindstrom
authors.forename: Alexander
authors.initials: A
authors.lastname: Klimov
authors.forename: Ruben O
authors.initials: RO
authors.lastname: Donis
authors.forename: C Todd
authors.initials: CT
authors.lastname: Davis
authors.forename: Tung
authors.initials: T
authors.lastname: Nguyen
mesh_terms: D000818:Animals; D016000:Cluster Analysis; D005838:Genotype; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D005585:Influenza in Birds / Q000821:virology*; D008969:Molecular Sequence Data; D058974:Phylogeography; D011200:Poultry; D012367:RNA, Viral / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D016865:Reassortant Viruses / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014744:Vietnam
chemical_list: D012367:RNA, Viral
keywords: Evolution; Geographic distribution; H5N1; Highly pathogenic avian influenza virus; Orthomyxovirus; Phylogenetics; Reassortment