Data for "Genetic diversity of highly pathogenic avian influenza H5N6 and H5N8 viruses in poultry markets in Guangdong, China, 2020-2022"
This study investigates the genetic diversity of H5N6 and H5N8 detected from monthly poultry market surveillance in Guangdong, China between 2020 and 2022 in the context of the clade 2.3.4.4b panzootic that has been occurring since 2020. Our findings reveal that H5N6 viruses were of clades 2.3.4.4b and 2.3.4.4h, while H5N8 viruses were of clade 2.3.4.4b. The N6 genes were divided into two clusters: full-length and with stalk deletion, while the N8 genes clustered with clade 2.3.4.4 H5N8 viruses circulating among wild birds. 10 genotypes were identified among the 22 isolates. Specifically, H5N6 isolates contained genes derived from HPAI H5Nx viruses and low pathogenic avian influenza in China, while the H5N8 isolates contained genes derived from HPAI A(H5N8) 2.3.4.4b and A(H5N1) 2.3.2.1c. No positive selection on amino acid residues associated with mammalian adaptation was found.
These are 3 main datasets included from a surveillance study conducted in live poultry markets in Guangdong. It is inclusive of scripts and necessary files to run the script (i.e. tree files and associated metadata).
- Genetic analysis of the HA genes of H5Nx isolates.
- Genetic analysis of the N6 and N8 genes of the H5Nx isolates
- Genetic analysis on the internal gene segments of H5Nx viruses.