@article{fdi:010068169,
  title = {{P}revalence and diversity of {H}9{N}2 avian influenza in chickens of {N}orthern {V}ietnam, 2014},
  author = {{D}uong {M}ai {T}huy and {P}eacock, {T}.{P}. and {V}u {T}hi {N}goc {B}ich and {F}abrizio, {T}. and {D}ang {N}guyen {H}oang and {N}guyen {D}ang {T}ho and {N}guyen {T}hi {D}iep and {M}inh {N}guyen and {L}e {N}guyen {M}inh {H}oa and {H}au {T}hi {T}hu {T}rang and {C}hoisy, {M}arc and {I}nui, {K}. and {N}ewman, {S}. and {N}guyen vu {T}rung and van {D}oorn, {R}. and {T}hanh {L}ong {T}o and {I}qbal, {M}. and {B}ryant, {J}.{E}.},
  editor = {},
  language = {{ENG}},
  abstract = {{D}espite their classification as low pathogenicity avian influenza viruses ({LPAIV}), {A}/{H}9{N}2 viruses cause significant losses in poultry in many countries throughout {A}sia, the {M}iddle {E}ast and {N}orth {A}frica. {T}o date, poultry surveillance in {V}ietnam has focused on detection of influenza {H}5 viruses, and there is limited understanding of influenza {H}9 epidemiology and transmission dynamics. {W}e determined prevalence and diversity of influenza {A} viruses in chickens from live bird markets ({LBM}) of 7 northern {V}ietnamese provinces, using pooled oropharyngeal swabs collected from {O}ctober to {D}ecember 2014. {S}creening 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). {S}ubtyping was performed on 468 pooled swabs with {M}gene {C}t < 26. {N}o influenza {H}7 was detected; 422 (90.1%) were {H}9 positive; and 22 (4.7%) were {H}5 positive. {T}here was no evidence was of interaction between {H}9 and {H}5 virus detection rates. {W}e sequenced 17 whole genomes of {A}/{H}9{N}2, 2 of {A}/{H}5{N}6, and 11 partial genomes. {A}ll {H}9{N}2 viruses had internal genes that clustered with genotype 57 and were closely related to {C}hinese human isolates of {A}/{H}7{N}9 and {A}/{H}10{N}8. {U}sing a nucleotide divergence cutoff of 98%, we identified 9 distinct {H}9 genotypes. {P}hylogenetic analysis suggested multiple introductions of {H}9 viruses to northern {V}ietnam rather than in-situ transmission. {F}urther investigations of {H}9 prevalence and diversity in other regions of {V}ietnam are warranted to assess {H}9 endemicity elsewhere in the country.},
  keywords = {{A}vian influenza ; {V}ietnam ; {H}9{N}2 ; {P}oultry ; {C}hicken ; {H}5 ; {Z}oonotic ; {VIET} {NAM}},
  booktitle = {},
  journal = {{I}nfection {G}enetics and {E}volution},
  volume = {44},
  numero = {},
  pages = {530--540},
  ISSN = {1567-1348},
  year = {2016},
  DOI = {10.1016/j.meegid.2016.06.038},
  URL = {https://www.documentation.ird.fr/hor/fdi:010068169},
}