Emergence of the GI-23 lineage of infectious bronchitis virus in Brazilian backyard poultry

Infectious bronchitis virus (IBV) remains a major threat to poultry production worldwide, with the GI-23 lineage emerging as one of the most epidemiologically relevant variants in recent years. Although GI-23 has been reported in Brazilian commercial poultry, its occurrence and genomic characteristics in backyard poultry remain poorly understood. This study investigated the molecular epidemiology and evolutionary features of IBV circulating in backyard poultry from São Paulo State, Brazil. Samples from 893 backyard birds were screened for IBV using RT-qPCR targeting the 5' untranslated region (5'UTR). Positive samples were further characterized by lineage-specific RT-PCR assays, S1 gene sequencing, virus isolation, and whole-genome sequencing, followed by phylogenetic, phylogenomic, and recombination analyses. IBV was detected exclusively in chickens, with an overall prevalence of 13.8% (42/304 swab pools; 95% CI: 10.1-18.2). Among RT-qPCR-positive samples, 23.9% were identified as belonging to the GI-23 lineage, while GI-1 and GI-11 lineages were not detected. Phylogenetic analysis of partial S1 gene sequences revealed multiple GI-23 sublineages circulating in Brazil, indicating different viral introductions. Whole-genome sequencing of a Brazilian GI-23 isolate showed high identity to a virus identified in Mexico and revealed recombination events involving European and Middle Eastern IBV lineages. These findings provide the molecular and genomic evidence of IBV GI-23 circulation in Brazilian backyard poultry and highlight the importance of monitoring viral evolution and supporting effective disease control strategies.