Complete Genome Sequencing and Phylogenetic Analysis of Avian Infectious Bronchitis Viruses from Indonesia During 2021-22.

Abstract

Infectious bronchitis is an acute, highly contagious avian disease affecting chickens worldwide and is associated with respiratory signs, nephritis, and egg production disorders, causing major economic problems in the poultry industry. Limited information is available on the infectious bronchitis virus (IBV) strains circulating in Indonesia. This study sequenced the whole genome of six IBVs isolated from various regions in Indonesia during 2021-22. Phylogenetic analysis of the S1 subunit (S1) of the spike glycoprotein (S) coding sequences classified these strains within the GI-19 lineage, with no evidence of recombination in the S1 coding sequences. Full-genome analysis revealed evidence of recombination, but potential progenitors could not be identified due to the lack of closely related sequences in public databases. The closest genetic relatives to these Indonesian strains are IBVs from Malaysia and Thailand, likely due to geographic proximity. To our knowledge, this is the first report of whole-genome sequences of IBV strains isolated in Indonesia. These findings contribute to a deeper understanding of the epidemiology of current IBV strains circulating in Southeast Asia.