Genetics of natural recombinant infectious bronchitis viruses isolated in Kagoshima Prefecture of Japan

Avian infectious bronchitis (IB), caused by IB virus (IBV; family Coronaviridae, genus Gammacoronavirus, species Gammacoronavirus galli), is a highly contagious and acute upper respiratory tract disease in chickens (Gallus gallus) that has a serious economic impact worldwide. Genomic mutations and recombination of IBV strains result in novel pathogenicity phenotypes. This study focused on three IBV strains isolated from a farm in Kagoshima Prefecture in Japan (KS2-4) and two from the surrounding area (KS and KS1). These strains were evaluated using whole-genome sequencing, followed by detection of genomic recombination events and phylogenetic analyses. Genomic recombination analysis using nearly complete genome sequences revealed that the candidate donor strains, defined as those contributing recombinant segments to the detected isolates, for KS2, KS3, and KS4 were identical except in some regions. Furthermore, KS and KS1 were predicted to have different donor strains across their genomic regions despite being classified as belonging to the same genotype based on the S1 gene. Phylogenetic analysis revealed that KS and KS1 are a variant of a vaccine strain and a previously unreported recombinant strain, respectively. KS2-4 were found to be multi-recombinant strains that may have experienced several different recombination events with unknown strains, including recombinant strains with complex genetic backgrounds. These results suggest that unidentified IBV strains with various genetic backgrounds may have circulated in Japan and that multiple genetic recombination events may have occurred among these strains.