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 isolatesGenetic analysis on the internal gene segments of H5Nx viruses.本研究针对2020至2022年中国广东省活禽市场月度监测中检出的H5N6与H5N8亚型禽流感病毒的遗传多样性展开调查，研究背景为2020年以来暴发的2.3.4.4b进化枝全球禽流感动物大流行。研究结果显示，H5N6病毒分属2.3.4.4b与2.3.4.4h两个进化枝，而H5N8病毒均隶属于2.3.4.4b进化枝。N6神经氨酸酶（neuraminidase）基因可划分为两个簇：全长型及茎部缺失型；N8基因则与野生鸟类中流行的2.3.4.4分支H5N8病毒聚类。在22株病毒分离株中共鉴定出10种基因型。具体而言，H5N6分离株的基因片段来源于中国境内的高致病性禽流感（Highly Pathogenic Avian Influenza, HPAI）H5Nx毒株与低致病性禽流感病毒；而H5N8分离株的基因片段则来源于高致病性禽流感A(H5N8) 2.3.4.4b毒株及A(H5N1) 2.3.2.1c毒株。未发现与哺乳动物适应相关的氨基酸残基存在正选择现象。 本数据集包含该项广东省活禽市场监测研究的三类核心数据，同时附带运行脚本所需的全部文件（即进化树文件及相关元数据（metadata）），具体包括：H5Nx分离株血凝素（hemagglutinin, HA）基因的遗传分析数据、H5Nx分离株N6与N8基因的遗传分析数据，以及H5Nx病毒内部基因片段的遗传分析数据。