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.
Highlights
Vietnam has a well-developed system for the active surveillance of highly pathogenic avian influenza (HPAI) strains within live bird markets (LBMs)
Our results confirm the hyperendemicity of avian influenza viruses in chickens sampled in LBM of northern Vietnam, where influenza H9N2 viruses are by far the dominant subtype in circulation
Our detection rates are comparable to those reported from China, where overall prevalence of AIV in chickens has ranged from 21 to 36% in Hubei, 34– 46% in Zhejiang province (Chen et al, 2016), and 15.7% in Hunan (Huang et al, 2015a), and where H9N2 is the dominant AIV subtype detected throughout all provinces (Shi et al, 2014)
Summary
Vietnam has a well-developed system for the active surveillance of highly pathogenic avian influenza (HPAI) strains within live bird markets (LBMs). From 2010 to 2015, surveillance focused primarily on Abbreviations: LPAI, low pathogenicity avian influenza; HPAI, highly pathogenic avian influenza; FAO, Food and Agriculture Organization of the United Nations; LBM, live bird market. Starting in 2013, additional surveillance activity was initiated in provinces along the Chinese border to promote early detection of H7N9 viruses, and was focused largely on collections from chickens and environmental samples. To date, this second surveillance activity has screened N33,480 pooled chicken oropharyngeal swabs and environmental samples, no A/H7N9 viruses have been identified in Vietnam (FAO, 2014). Thuy et al / Infection, Genetics and Evolution 44 (2016) 530–540
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