{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T01:07:01Z","timestamp":1790125621080,"version":"4.0.1"},"reference-count":31,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T00:00:00Z","timestamp":1753228800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"abstract":"<jats:p>The continuous emergence of avian infectious bronchitis virus (IBV) variants poses a critical threat to poultry health and productivity in China. In this study, we conducted comprehensive genetic and antigenic analyses of IBV strains isolated in our laboratory between 2020 and 2024. A total of 94 IBV isolates were sequenced for the S1 gene, revealing widespread nucleotide insertions, deletions, and mutations. Phylogenetic analysis indicated that GI-19 was the predominant genotype (70.21%), followed by GI-13 (21.28%). Recombination analysis using RDP 5.42 identified 14 recombinant strains, primarily GI-13\/GI-22 (50%), GI-19\/GI-7 (28.6%), and GI-19\/GI-22 (21.4%), which were further confirmed using Simplot. Glycosylation analysis revealed that all isolates possessed 14 to18 N-glycosylation sites, whereas only the SDJN3\/23 strain contained an O-glycosylation site (position 416). Novel cleavage site motifs (HRRKR, HRHRR, RRFRR) were identified in GI-19 strains, diverging from the canonical HRRRR. The evolutionary rate calculated via BEAST software, was 1.98 \u00d7 10<jats:sup>-4<\/jats:sup> substitutions\/site\/year. Serum neutralization assays demonstrated that GI-19 recombinants exhibited partial one-way cross-protection against GI-1, GI-13, and GI-22 genotypes (titer \u2265 1:32), but reciprocal neutralization was limited. Overall, we systematically characterized the genetic diversity and antigenic evolution of the currently circulating IBV strains in China, emphasizing the critical demand for genotype-specific vaccine development and dynamic surveillance systems to counteract viral immune escape.<\/jats:p>","DOI":"10.3389\/fcimb.2025.1640152","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T05:35:24Z","timestamp":1753248924000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":8,"title":["Dominance of the GI-19 genotype and genomic characterization of the S1 gene in avian infectious bronchitis virus from 2020 to 2024"],"prefix":"10.3389","volume":"15","author":[{"given":"Xiaozhen","family":"Guo","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cunxia","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liping","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tong","family":"Zhu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuehua","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongyin","family":"Lin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaiying","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bing","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuoming","family":"Qin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiuli","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,7,23]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"57","DOI":"10.3390\/v11010057","article-title":"Genetic diversity and phylodynamics of avian coronaviruses in Egyptian wild birds","volume":"11","author":"AR","year":"2019","journal-title":"Viruses."},{"key":"B2","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1093\/molbev\/mss243","article-title":"Accurate model selection of relaxed molecular clocks in bayesian phylogenetics","volume":"30","author":"Baele","year":"2013","journal-title":"Mol. 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