Sporadic Outbreaks of Avian Infectious Bronchitis Viruses Highly Similar to the S95 Live Attenuated Vaccine Strain in Japan: A Comparative Study of Ten Field Isolates and S95.

BACKGROUND: As infectious bronchitis virus (IBV) strains similar to the IBV S95 live attenuated vaccine strain have been occasionally detected in poultry farms in Japan, we investigated the suspicion that outbreaks of the disease were related to the S95 vaccine. METHODS: We isolated ten S95 vaccine-like strains, classified in the JP-I genotype of S1, the VIb (Y-4) genogroup of S2, and the GI-18 lineage, from IBV-affected chickens in Japan between 2020 and 2024. The whole-genome sequence and adaptation to embryonated chicken eggs were investigated. We developed a method for distinguishing the S95 vaccine strain from S95-like wild-type strains using specific primer sets having either the S95 vaccine or S95 parent-specific nucleotide at the 3' termini of primers on the ORF2 gene. RESULTS: Nine of ten S95 vaccine-like strains lacked identical mutations to the ORF1ab, ORF2, and ORF5a genes that the S95 vaccine strain acquired during attenuation. The remaining S95-like strain, B3389, had identical mutations to the S95 vaccine strain in the ORF1ab and ORF5a genes. The B3389 strain, however, had strain-specific nucleotides that were not found in the S95 vaccine or S95 parent strains, and produced fewer embryonated egg-adapted phenotypes than the S95 vaccine strain. CONCLUSIONS: The ten S95-like strains appear not to have emerged from the S95 vaccine strain. Instead, sporadic outbreaks of S95 vaccine-like IBV strains in Japan were indicated. A method for distinguishing and excluding the S95-like wild-type strains as suspected revertants of the S95 vaccine may be utilized for comprehensive IBV surveillance to facilitate development of a vaccination strategy.