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.

Poultry trading behaviours in Vietnamese live bird markets as risk factors for avian influenza infection in chickens

“…Next‐generation sequencing (NGS) of M gene‐positive samples yielded whole‐genome sequence data for 12 H9N2 viruses and partial genomes for 19 H9N2 and 2 H5N6 viruses. H9N2 viruses sequenced in this study were most closely related to previously sequenced H9N2 viruses from Vietnam (Thuy et al, ) (Figure and Figure S1). For example, BLASTn analysis of the PB1 gene of A/chicken/Vietnam/1DO10/2017 from this study was most closely related to A/chicken/Vietnam/H7F‐BG4‐383 with nucleotide homology of 98%.…”

“…Vietnam has enzootic H5N1 and H9N2 and is at risk of incursion by H7N9 due to a shared border with China (Thuy et al, ). Poultry traders are an integral component of poultry production in Vietnam.…”

Insight into live bird markets of Bangladesh: an overview of the dynamics of transmission of H5N1 and H9N2 avian influenza viruses

“…16 Despite the fact that many studies have been conducted in countries such as China on the effect LBMs have on the dissemination of AIVs, 17 , 18 , 19 , 20 to date, there are no studies that provide in-depth analyses on the dynamics of transmission of avian influenza H5N1 and H9N2 viruses within live poultry markets in Bangladesh. The data presented here indicate that the drinking water serves as a reservoir of AIVs within LBMs.…”

Co‐circulation and characterization of HPAI‐H5N1 and LPAI‐H9N2 recovered from a duck farm, Yogyakarta, Indonesia

“…Our result showed that the HA gene of LPAI‐H9N2 was grouped together with the H9N2 viruses of China–Vietnam–Indonesia (CVI) lineage. It has been reported that Vietnam H9N2 viruses (H7F‐LC4‐51/14, H7F‐LC4‐26/14 and H7F 14 BN4 423/14) have been previously identified as Y280‐like group (Thuy et al, ). Recent study revealed that the HA gene of Indonesia H9 formed a distinct cluster with some H9 from China and Vietnam.…”

“…Our results were in agreement with previous report that all internal genes of Vietnam H9N2 viruses were closely related to H7N9‐like viruses. For example, all internal genes of H9N2 isolated from chicken in live bird market in Vietnam in 2016 were clustered with human H7N9 viruses from China (Thuy et al, ).…”