Phylogenetic Analyses of HA and NA Genes of Algerian H5N1 and H5N8 Strains Reveal Putative NA Recombination Hotspots

Highly pathogenic Avian influenza H5Nx became an uncontrolled threat, causing iterative outbreaks in avian and jumping the species barriers to other vertebrates. Two AIV outbreaks caused by H5N8 in 2020-2021 (mortality of 70%) and by H5N1 in 2022-2023 (mortality of 40%) targeted the Algerian poultry flocks from December 2020 to July 2023. Hemagglutinin (HA) and neuraminidase (NA) coding sequences of isolated strains were genetically analyzed by RT-PCR, sequencing, and phylogeny to determine their pathotypes and origins. Analyses of sequencing data confirmed the highest homology of the strains to the described H5N8 and H5N1 strains, respectively, and the presence of a multi-basic cleavage site in the HA aa-sequences confirmed the highly pathogenic property of both subtypes. Closer phylogenetic analysis of all sequences showed genetic proximity with African, European, and Asian strains. While all genes seem to be of Eurasian lineage, the N1 gene consensus was closer to both. Recombination events and stalk deletion were revealed in N1 genes. These findings have encouraged us to explore the two proteins for a better understanding of their antigenic interactions.