title: Prevalence and diversity of H9N2 avian influenza in chickens of Northern Vietnam, 2014.
abstract: Despite their classification as low pathogenicity avian influenza viruses (LPAIV), A/H9N2 viruses cause significant losses in poultry in many countries throughout Asia, the Middle East and North Africa. To date, poultry surveillance in Vietnam has focused on detection of influenza H5 viruses, and there is limited understanding of influenza H9 epidemiology and transmission dynamics. We determined prevalence and diversity of influenza A viruses in chickens from live bird markets (LBM) of 7 northern Vietnamese provinces, using pooled oropharyngeal swabs collected from October to December 2014. Screening by real time RT-PCR revealed 1207/4900 (24.6%) of pooled swabs to be influenza A virus positive; overall prevalence estimates after accounting for pooling (5 swabs/pools) were 5.8% (CI 5.4-6.0). Subtyping was performed on 468 pooled swabs with M gene Ct<26. No influenza H7 was detected; 422 (90.1%) were H9 positive; and 22 (4.7%) were H5 positive. There was no evidence was of interaction between H9 and H5 virus detection rates. We sequenced 17 whole genomes of A/H9N2, 2 of A/H5N6, and 11 partial genomes. All H9N2 viruses had internal genes that clustered with genotype 57 and were closely related to Chinese human isolates of A/H7N9 and A/H10N8. Using a nucleotide divergence cutoff of 98%, we identified 9 distinct H9 genotypes. Phylogenetic analysis suggested multiple introductions of H9 viruses to northern Vietnam rather than in-situ transmission. Further investigations of H9 prevalence and diversity in other regions of Vietnam are warranted to assess H9 endemicity elsewhere in the country.
authors.affiliation: National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors.forename: Duong Mai
authors.initials: DM
authors.lastname: Thuy
authors.affiliation: Avian Viral Diseases programme, The Pirbright Institute, Woking, UK; St Mary's Campus, Imperial College London, London, UK.
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Peacock
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam.
authors.forename: Vu Thi Ngoc
authors.initials: VTN
authors.lastname: Bich
authors.affiliation: St Jude's Center for Excellence in Influenza Research and Surveillance, Memphis, TN, USA.
authors.forename: Thomas
authors.initials: T
authors.lastname: Fabrizio
authors.affiliation: Division of Epidemiology, Department of Animal Health, Hanoi, Vietnam.
authors.forename: Dang Nguyen
authors.initials: DN
authors.lastname: Hoang
authors.affiliation: MIVEGEC (UM1-UM2-CNRS 5290-IRD 224), Centre de Recherche IRD, Montpellier, France.
authors.forename: Nguyen Dang
authors.initials: ND
authors.lastname: Tho
authors.affiliation: Division of Epidemiology, Department of Animal Health, Hanoi, Vietnam.
authors.forename: Nguyen Thi
authors.initials: NT
authors.lastname: Diep
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam.
authors.forename: Minh
authors.initials: M
authors.lastname: Nguyen
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam.
authors.forename: Le Nguyen Minh
authors.initials: LNM
authors.lastname: Hoa
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam.
authors.forename: Hau Thi Thu
authors.initials: HTT
authors.lastname: Trang
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; MIVEGEC (UM1-UM2-CNRS 5290-IRD 224), Centre de Recherche IRD, Montpellier, France.
authors.forename: Marc
authors.initials: M
authors.lastname: Choisy
authors.affiliation: Food and Agriculture Organization of the United Nations, Hanoi, Vietnam.
authors.forename: Ken
authors.initials: K
authors.lastname: Inui
authors.affiliation: Food and Agriculture Organization of the United Nations, Hanoi, Vietnam.
authors.forename: Scott
authors.initials: S
authors.lastname: Newman
authors.affiliation: National Hospital Tropical Diseases, Hanoi, Vietnam.
authors.forename: Nguyen Vu
authors.initials: NV
authors.lastname: Trung
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK.
authors.forename: Rogier
authors.initials: R
authors.lastname: van Doorn
authors.affiliation: National Center for Veterinary Diagnostics, Department of Animal Health, Hanoi, Vietnam.
authors.forename: Thanh Long
authors.initials: TL
authors.lastname: To
authors.affiliation: Avian Viral Diseases programme, The Pirbright Institute, Woking, UK.
authors.forename: Munir
authors.initials: M
authors.lastname: Iqbal
authors.affiliation: Oxford University Clinical Research Unit and Wellcome Trust Major Overseas Programme, Hanoi, Vietnam; Center for Tropical Medicine, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK. Electronic address: jbryant@oucru.org.
authors.forename: Juliet E
authors.initials: JE
authors.lastname: Bryant
mesh_terms: D000818:Animals; D002645:Chickens / Q000821:virology*; D016679:Genome, Viral; D005838:Genotype; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000737:chemistry / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D053127:Influenza A Virus, H9N2 Subtype / Q000145:classification* / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology* / Q000821:virology*; D008958:Models, Molecular; D009154:Mutation; D010802:Phylogeny; D058974:Phylogeography; D015995:Prevalence; D011487:Protein Conformation; D062486:Public Health Surveillance; D014744:Vietnam / Q000453:epidemiology
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus
keywords: Avian influenza; Chicken; H5; H9N2; Poultry; Vietnam; Zoonotic