Supporting data for Genetic Pairing of the Hemagglutinin and Neuraminidase Glycoproteins of the Highly Pathogenic A(H5Nx) Avian Influenza Viruses

Viruses of the A/Goose/Guangdong/1/1996 (Gs/Gd) lineage highly pathogenic avian influenza (HPAI) virus of H5 subtype have successfully evolved to gain genetic diversity, expand the range of infected host species, and spread globally. In the context of the 2020 - 2021 clade 2.3.4.4b panzootic, This thesis aims to investigate 1) the genetic pairing relationship between surface glycoprotein hemagglutinin (HA) and neuraminidase (NA) glycoproteins, and 2) the genetic diversity of H5N6 and H5N8 detected from monthly poultry market surveillance in Guangdong, China between 2020 and 2022. For the first aim, findings reveal that HA and NA of H5N1 clade 2.3.4.4b viruses continued to pair after 2020. The HA shifted to pair from a short stalk N1 NA (NA clade NA.1) to full length N1 NA (NA clade NA.2). The dominant pairings detected after 2020 were HA clade 2.3.4.4b.1 with NA clade NA.2.2 and HA clade 2.3.4.4b.2 with NA clade NA.2.1. Geography and clade defining mutation are found to be factors differing between the pairings. For the second aim, the 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.

The dataset are divided into two chapters based on the aim. It is inclusive of scripts and necessary files to run the script (i.e. tree files and associated metadata).

• Chapter 2: Global Analysis of HA and NA genes under H5Nx HPAI Gs/Gd lineage influenza viruses. The materials include files for data curation, plot generation, phylogenetic tree generation and tanglegram generation.
• Chapter 3 "Impact of clade 2.3.4.4b reintroduction on local AIV dynamics in China. The materials include files for data curation, plot generation, and phylogenetic tree generation.