Tanikawa Taichiro, Mase Masaji, Hiramatsu Kanae, Watanabe Satoko, Iseki Hiroshi
National Institute of Animal Health, National Agriculture and Food Research Organization (NARO), 3-1-5 Kannondai, Tsukuba, Ibaraki, 305-0856, Japan.
Arch Virol. 2025 Aug 27;170(9):203. doi: 10.1007/s00705-025-06389-0.
Avian infectious bronchitis (IB), caused by IB virus (IBV; family Coronaviridae, genus Gammacoronavirus, species Gammacoronavirus galli), is a highly contagious and acute upper respiratory tract disease in chickens (Gallus gallus) that has a serious economic impact worldwide. Genomic mutations and recombination of IBV strains result in novel pathogenicity phenotypes. This study focused on three IBV strains isolated from a farm in Kagoshima Prefecture in Japan (KS2-4) and two from the surrounding area (KS and KS1). These strains were evaluated using whole-genome sequencing, followed by detection of genomic recombination events and phylogenetic analyses. Genomic recombination analysis using nearly complete genome sequences revealed that the candidate donor strains, defined as those contributing recombinant segments to the detected isolates, for KS2, KS3, and KS4 were identical except in some regions. Furthermore, KS and KS1 were predicted to have different donor strains across their genomic regions despite being classified as belonging to the same genotype based on the S1 gene. Phylogenetic analysis revealed that KS and KS1 are a variant of a vaccine strain and a previously unreported recombinant strain, respectively. KS2-4 were found to be multi-recombinant strains that may have experienced several different recombination events with unknown strains, including recombinant strains with complex genetic backgrounds. These results suggest that unidentified IBV strains with various genetic backgrounds may have circulated in Japan and that multiple genetic recombination events may have occurred among these strains.
禽传染性支气管炎（IB）由禽传染性支气管炎病毒（IBV；冠状病毒科，γ冠状病毒属，禽γ冠状病毒种）引起，是鸡（家鸡）的一种高度传染性急性上呼吸道疾病，在全球范围内造成严重经济影响。IBV毒株的基因组突变和重组会导致新的致病表型。本研究聚焦于从日本鹿儿岛县一个农场分离出的3株IBV毒株（KS2 - 4）以及从周边地区分离出的2株（KS和KS1）。对这些毒株进行全基因组测序评估，随后检测基因组重组事件并进行系统发育分析。使用近乎完整的基因组序列进行基因组重组分析表明，KS2、KS3和KS4的候选供体毒株（定义为对检测到的分离株贡献重组片段的毒株）除某些区域外是相同的。此外，尽管根据S1基因KS和KS1被归类为同一基因型，但预计它们在整个基因组区域具有不同的供体毒株。系统发育分析表明，KS和KS1分别是疫苗株的一个变体和一种先前未报道的重组毒株。发现KS2 - 4是多重组毒株，可能与包括具有复杂遗传背景的重组毒株在内的未知毒株经历了几种不同的重组事件。这些结果表明，具有各种遗传背景的未鉴定IBV毒株可能在日本传播，并且这些毒株之间可能发生了多次基因重组事件。
