After accumulating data through a nationwide survey, we characterized the recent prevalences and geographic distributions of various genotypes of infectious bronchitis virus (IBV) on layer farms in Japan. RT-PCR analysis of fecal samples revealed the presence of the IBV nucleoprotein (N) gene on approximately 30% of the farms surveyed. N-gene detection rates were higher in Chugoku and Kyushu than in the remaining surveyed regions. Phylogenetic analysis of S1 gene sequences revealed that genotypes JP-I, JP-II, JP-III, and Mass were particularly prevalent, with JP-I isolated throughout the country. In addition, JP-II was the genotype detected most frequently in Chugoku, and JP-III was the most frequent in Kyushu. Unlike in the previous results obtained in 1998 through 2003, the European-prevalent 4/91 genotype was no longer circulating in Japan. In addition, the number of prefectures where multiple genotypes were detected simultaneously had increased since 1998 through 2003.

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