Circulation and genetic variation of type A/H5N6 avian influenza virus in poultry in Tra Vinh, Dong Thap and Kien Giang provinces

Abstract

The study was conducted to determine the circulation and genetic variation of type A/H5N6 avian influenza virus in Tra Vinh, Dong Thap, and Kien Giang provinces. A total of 432 oropharyngeal swab samples were collected from chickens and ducks in 12 poultry markets of 12 districts in 3 studied
provinces, average of 36 samples per district. By realtime RT-PCR method, the positive samples of type A were tested for subtypes H5 and N6. These positive samples of type A H5N6 avian influenza virus were selected for sequencing H5 gene, and was built a phylogenic tree of type A/H5N6 virus for comparison with the reference strains in GenBank. The studied results showed that the circulation of type A/H5N6 avian influenza virus in chicken and duck populations in Tra Vinh and Kien Giang provineces appeared at
low rate (1.39%). The circulation rate of type A/H5N6 avian influenza virus in chickens was 1.54% and in ducks was 1.16%. The result of nucleotide genetic variation analysis showed that the nucleotide similarity among type A/H5N6 avian influenza virus circulating in chicken and duck strains in Tra Vinh province was 95.32% and the amino acid difference between other reported strains in Viet Nam and in the world was 1.9 - 12.2%. The type A/H5N6 avian influenza virus strains circulating in Tra Vinh province belonged to the clade 2.3.4.4c and in the same phylogenetic branch with A/H5N6 influenza virus strains isolated in
Viet Nam in 2017-2019 and isolated in China in 2016