Moreover, we revealed the circulation of 2.3.2.1a (new) clade among the chicken and duck population without occurring outbreak which might be due to vaccination.
The findings indicate that H5 and H9 subtypes of AIV are circulating in the backyard poultry with or without clinical symptoms. The phylogenetic analysis of M, HA, NA, and PB1 genes revealed intra-genomic similarity, and they are closely related to previously reported AIV strains in Bangladesh and Southeast Asia.
The prevalence of subtypes H5 and H9 in backyard poultry was 2.7% and 3.3%, respectively. Prevalence varied with season, ranging from 3.1% in the summer to 8.2% in the winter. We found that the prevalence of AIV RNA at the household level was 6.2% ( n = 18 N = 292), whereas duck and chicken prevalence was 3.6% and 3.2%, respectively. All AIV-positive samples were subjected to four-gene segment sequencing (M, PB1, HA, and NA gene). We tested cloacal samples from birds for the matrix gene (M gene) followed by H5 and H9 subtypes using real-time reverse transcriptase-polymerase chain reaction (rRT-PCR). We administered structured pre-tested questionnaires to farmers through direct interviews. We randomly selected a total of 292 households' poultry (having both chicken and duck) for sampling. The present cross-sectional study was carried out to reveal the genomic epidemiology of AIV of backyard poultry in coastal (Anowara) and plain land (Rangunia) areas of Bangladesh. In Bangladesh, earlier research was mainly focused on AIV in commercial poultry and live bird markets, where there is scanty literature reported on AIV in apparently healthy backyard poultry at the household level. Ducks, the natural reservoir of avian influenza virus (AIV), act as reassortment vessels for HPAI and low pathogenic avian influenza (LPAI) virus for domestic and wild bird species.
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