Molecular characterization and complete genome analysis of highly pathogenic avian influenza virus H5N1 isolated from live bird markets of East Java Indonesia

<strong>Background</strong> The highly pathogenic H5N1 avian influenza virus continues to be dangerous to both animal and human health because it can infect a wide range of animals. H5N1 virus comes in a variety of genotypes, but only a small number of them are known to infect mammals. The molecular characterization of viral subtypes in animal populations is indispensable for comprehending the distribution of different viral subtypes in a variety of hosts. <strong>Materials and Methods</strong> The influenza isolate was obtained from a tracheal sample of healthy poultry from live bird markets of East Java Province from March 2021 to April 2022. HA and HI were used for screening and qRT-PCR were used for amplification. Sequencing was done and a genomic sequence was obtained from the GISAID database. MEGA-11 software was used to understand the transformations in the isolate. <strong>Results</strong> A/chicken/East Java/Av1955/2022 contain multiple basic amino acids (PQRE RRRKR /GLF) at the cleavage site in the HA gene that showed the characteristics of HPAIV. All the segments (PB2, PB1, PA, HA, NP, NA, NP, and M) of the study isolate revealed mutations in nucleotides and amino acid sequence and depicted a phylogenetically close relationship to isolates of A/ turkey/East Java/Av154, Malaysia, Thailand, and Japan. Study isolate showed reassortment from the reference virus in all gene segments which was the indication of newly emerging strains of H5N1 in the study area. <strong>Conclusion</strong> The findings of the current study depicted that the mutations in nucleotides and amino acid sequence might be the cause of newly emerging subtypes in the study area. These mutations could potentially make the virus more pathogenic in chickens and ducks.