title: Comparative genomics of QX-like infectious bronchitis viruses in Korea.
abstract: To minimize the spread of infectious bronchitis virus (IBV), domestic fowl have been extensively vaccinated with the KM91 strain. However, various IBV QX-like virus strains have become increasingly prevalent in Korea. We conducted comparative genomic analyses of seven QX-like viruses: early viruses (n = 2), new cluster 1 (NC1; recombinants of KM91 and the early QX-like viruses, n = 3) and recurrent viruses (n = 2), to understand their genomic backgrounds. The early and NC1 viruses had KM91-like backgrounds, but the recurrent viruses had QX-like genomic backgrounds. The absence of pure QX-like viruses before the appearance of the early viruses suggests that the viruses were introduced from other countries after recombination, but the NC1 viruses originated in Korea. The recent prevalence of recurrent viruses with different genomic backgrounds and spike genes from the early and the NC1 viruses may indicate the repeated introduction of different infectious bronchitis viruses from other countries and their successful evasion of vaccine immunity in the field. Furthermore, a 1ab gene-based phylogenetic analysis revealed three distinct lineages: North America-Europe, China/Taiwan, and China. KM91 and the early and NC1 viruses were included in the North America-Europe lineage, and the recurrent QX-like viruses were included in the China lineage. The phylogenetic positions of KM91-like 1ab and QX-like spike suggest frequent recombination between the North America-Europe and China lineages. Additional studies on the patterns of recombination, including donor-acceptor relationships, geographical sites, and non-poultry hosts, may be valuable for understanding the evolution of IBVs.
authors.affiliation: Laboratory of Avian Diseases, College of Veterinary Medicine, BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
authors.forename: Seung-Min
authors.initials: SM
authors.lastname: Hong
authors.affiliation: Laboratory of Poultry Production Medicine, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. kwonhj01@snu.ac.kr.|Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. kwonhj01@snu.ac.kr.
authors.forename: Hyuk-Joon
authors.initials: HJ
authors.lastname: Kwon
authors.affiliation: Avian Disease Division, Animal and Plant Quarantine Agency, Gimcheon, 39660, Gyeongsangbuk-Do, Republic of Korea.
authors.forename: Kang-Seuk
authors.initials: KS
authors.lastname: Choi
authors.affiliation: Laboratory of Avian Diseases, College of Veterinary Medicine, BK21 Plus Program for Veterinary Science and Research Institute for Veterinary Science, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. kimhong@snu.ac.kr.|Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. kimhong@snu.ac.kr.
authors.forename: Jae-Hong
authors.initials: JH
authors.lastname: Kim
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition / Q000235:genetics; D001483:Base Sequence; D002642:Chick Embryo; D002645:Chickens / Q000821:virology*; D018352:Coronavirus Infections / Q000821:virology*; D016679:Genome, Viral / Q000235:genetics*; D001351:Infectious bronchitis virus / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011201:Poultry Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics*; D011995:Recombination, Genetic; D056910:Republic of Korea; D017423:Sequence Analysis, RNA
chemical_list: D012367:RNA, Viral