Kim Ji-Ye, Le Hoang Duc, Thai Tuyet Ngan, Kim Jae-Kyeom, Song Hye-Soon, Her Moon, Kim Hye-Ryoung
Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea.
Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon 39660, Gyeongsangbuk-do, Republic of Korea; Institute of Biotechnology, Vietnam Academy of Science and Technology, Cau Giay 11300, Hanoi, Vietnam.
Infect Genet Evol. 2025 Mar;128:105717. doi: 10.1016/j.meegid.2025.105717. Epub 2025 Jan 16.
Infectious bronchitis (IB), caused by the infectious bronchitis virus (IBV), is a highly contagious chicken disease, causing economic losses worldwide. New IBV strains and variants continue to emerge despite using inactivated and live-attenuated vaccines to prevent or control IB. In this study, the S1 genes of 46 IBV strains, isolated from commercial chicken flocks between 2003 and 2024 in Korea were sequenced and genetically characterized. The IBV isolates belonged to Korean group II (K-II), which was included in the GI-19 lineage. The K-II was divided into five sub-genogroups (a-e) based on phylogenetic tree analysis results and nucleotide identification of the S1 gene. Of these, K-IId was the most common genotype in Korea; however, eight novel isolates belonging to the K-IIe sub-genotype were discovered. The nucleotide and amino acid identities of the other four K-II sub-genotypes and the eight isolates were 84.42-95.89 % and 84.02-95.86 %, respectively. The complete genomes of the eight K-IIe isolates were obtained using next-generation sequencing. Various recombination patterns were observed despite the high homology of the S1 gene among the eight IBV strains. Among the eight K-IIe isolates, six were recombinants, exhibiting recombinations between K-IIe and K-IIc, K-IIe and K-IIa, and with the live vaccine strain. Most recombination breakpoints were detected in the nsp2 region of the ORF1a, S2, and M genes. The present study proposed new classification criteria for the K-II belonged to the GI-19 lineage prevalent in South Korea and revealed the recombination patterns of recently identified novel isolates, providing important information on novel viral sub-genotype strains and IBV evolution.
传染性支气管炎(IB)由传染性支气管炎病毒(IBV)引起,是一种高度传染性的鸡病,在全球范围内造成经济损失。尽管使用灭活疫苗和减毒活疫苗来预防或控制IB,但新的IBV毒株和变种仍不断出现。在本研究中,对2003年至2024年期间从韩国商业鸡群中分离出的46株IBV毒株的S1基因进行了测序和基因特征分析。这些IBV分离株属于韩国II组(K-II),该组包含在GI-19谱系中。根据系统发育树分析结果和S1基因的核苷酸鉴定,K-II被分为五个亚基因组(a-e)。其中,K-IId是韩国最常见的基因型;然而,发现了八株属于K-IIe亚基因型的新型分离株。其他四个K-II亚基因型和这八株分离株的核苷酸和氨基酸同一性分别为84.42%-95.89%和84.02%-95.86%。使用下一代测序技术获得了八株K-IIe分离株的完整基因组。尽管八株IBV毒株的S1基因具有高度同源性,但仍观察到各种重组模式。在八株K-IIe分离株中,有六株是重组体,表现出K-IIe与K-IIc、K-IIe与K-IIa之间以及与活疫苗株之间的重组。大多数重组断点在ORF1a的nsp2区域、S2和M基因中被检测到。本研究提出了针对韩国流行的GI-19谱系中K-II的新分类标准,并揭示了最近鉴定的新型分离株的重组模式,为新型病毒亚基因型毒株和IBV进化提供了重要信息。