Emerging GI-23 infectious bronchitis virus in vaccinated broiler chickens: detection and molecular characterization...

Infectious Bronchitis Virus (IBV) is an avian coronavirus that significantly impacts poultry production worldwide. Analysis of the complete S1 gene has classified IBV into genotypes GI to GIX and more than 40 lineages to date. This study aimed to investigate whether a new IBV variant was involved in respiratory disease outbreaks observed in 2021 in vaccinated commercial broiler flocks in Paraná State, Brazil. Day-old chicks in all affected flocks had received mass IBV vaccination at the hatchery with a combination of two live-attenuated vaccines, specifically the predominant lineages GI-1 (Mass-type) and GI-11 (BR-I). Organ samples (air sac, trachea, lung, cecal tonsils, and kidney) were collected from twelve commercial broiler flocks across four poultry companies. Semi-nested RT-PCR targeting the HVR3 region detected IBV in all flocks, with 80.4% (37/46) of samples testing positive. IBV was detected in all types of organs studied, with a 100% detection rate in kidneys and trachea, and 90.9% in cecal tonsils. Eighteen amplicons, representing samples from all flocks, and one derived from the commercial vaccine containing IBV Var-2 strain were sequenced. The nucleotide identities ranged from 99.2 to 100% among them and demonstrated high homology with IBV Var-2 strain sequences (GI-23 lineage), prevalent in the Middle East and Europe. Phylogenetic analysis based on HVR3 clustered the Brazilian field strains within subclade GI-23.1. A second phylogenetic reconstruction using full-length S1 sequences showed the same topology, indicating that HVR3-based classification provided satisfactory resolution for lineage identification in the context of initial molecular surveillance efforts. The detection of the exotic GI-23 lineage underscores the importance of continued surveillance of circulating IBV strains to refine disease control strategies.