Revealing a novel GI-19 lineage infectious bronchitis virus sub-genotype with multiple Recombinations in South Korea using whole-genome sequencing

Infectious bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a highly contagious chicken disease, causing economic losses worldwide. New IBV strains and variants continue to emerge despite using inactivated and live-attenuated vaccines to prevent or control IB. In this study, the S1 genes of 46 IBV strains, isolated from commercial chicken flocks between 2003 and 2024 in Korea were sequenced and genetically characterized. The IBV isolates belonged to Korean group II (K-II), which was included in the GI-19 lineage. The K-II was divided into five sub-genogroups (a-e) based on phylogenetic tree analysis results and nucleotide identification of the S1 gene. Of these, K-IId was the most common genotype in Korea; however, eight novel isolates belonging to the K-IIe sub-genotype were discovered. The nucleotide and amino acid identities of the other four K-II sub-genotypes and the eight isolates were 84.42-95.89 % and 84.02-95.86 %, respectively. The complete genomes of the eight K-IIe isolates were obtained using next-generation sequencing. Various recombination patterns were observed despite the high homology of the S1 gene among the eight IBV strains. Among the eight K-IIe isolates, six were recombinants, exhibiting recombinations between K-IIe and K-IIc, K-IIe and K-IIa, and with the live vaccine strain. Most recombination breakpoints were detected in the nsp2 region of the ORF1a, S2, and M genes. The present study proposed new classification criteria for the K-II belonged to the GI-19 lineage prevalent in South Korea and revealed the recombination patterns of recently identified novel isolates, providing important information on novel viral sub-genotype strains and IBV evolution.