The Spread and Sequence Exploration of the isolated Avian Influenza viruses H5N1from backyard ducks in Asyut-Egypt

Abstract

Avian Influenza infection is an important devastating disease among domesticated birds so our goal is to evaluate the prevalence of influenza A virus (H5N1) among backyard ducks as well as the genetic changes will be happened among the H5 gene using sequence analysis. Fifty samples of cloacal swabs were gathered from backyard ducks in Asyut Province, Egypt exposed to RNA extraction followed by H5 and N1 identification using realtime-RT-PCR and one-step RT-PCR respectively finalizing by complete sequence analysis of H5 gene for 5 isolates. 14 samples out of 50 examined samples were positive for H5N1 subtype. The deduced amino acids of the sequenced hemagglutinin (HA) genes seen that the examined isolates have two molecular characteristics of HPAIV in the polybasic amino acids of the cleavage site, including EKRRK/KR*GLF) which is a common shape for multicleavage site in Egypt since 2013. Several amino acid substitutions were observed, especially at D43N, S120D, I151T and R162K which is suggestive the examined viruses belonged to 2.2.1.2 clade. Phylogenetic analyses of the HA revealed that the examined strains were genetically belonged to 2.2.1.2 clade. Homology percentages revealed a distant of the examined strains from the vaccinal strains that commonly used in Egypt, which the lowest homology was recorded with A/chicken/Mexico/232/94 vaccinal strain. This study affirmed the potential role of backyard ducks as a reservoir for AI/H5N1 clade 2.2.1.2 in Asyut-Egypt which may help in continuation and adaptation of AI/H5N1 virus in the target area and represent a potential danger to both poultry and humans. So, a regular survey to illuminate the spread of HPAIV H5N1 among commercial poultry and backyard birds should be applied.