title: Comparative analysis of four Massachusetts type infectious bronchitis coronavirus genomes reveals a novel Massachusetts type strain and evidence of natural recombination in the genome.
abstract: Four Massachusetts-type (Mass-type) strains of infectious bronchitis coronavirus (IBV) were compared genetically with the pathogenic M41 and H120 vaccine strains using the complete genomic sequences. The results revealed that strains ck/CH/LNM/091017 and ck/CH/LDL/101212 were closely related to the H120 vaccine, which suggests that they might represent re-isolations of vaccine strains or variants of vaccine strains that have resulted from the accumulated point mutations after several passages in chickens. In contrast, strains ck/CH/LHLJ/07VII and ck/CH/LHLJ/100902 had a close genetic relationship with the pathogenic M41 strain. In addition, molecular markers have been identified that distinguish between field and vaccine (or vaccine-like) Mass-type viruses, which may be able to differentiate between field and vaccine strains for diagnostic purposes. Phylogenetic analysis, and pairwise comparison of full-length genomes and the nine genes, identified the occurrence of recombination events in the genome of strain CK/VH/LHLJ/07VII, which suggests that this virus originated from recombination events between M41- and H120-like strains at the switch site located at the 3' end of the nucleocapsid (N) genes. To our knowledge, this is the first time that evidence for the evolution and natural recombination under field conditions between Mass-type pathogenic and vaccinal IBV strains has been documented. These findings provide insights into the emergence and evolution of the Mass-type IB coronaviruses and may help to explain the emergence of Mass-type IBV in chicken flocks all over the world.
authors.affiliation: Division of Avian Infectious Diseases, National Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, The Chinese Academy of Agricultural Sciences, Harbin 150001, People's Republic of China.
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Liu
authors.forename: Yuhao
authors.initials: Y
authors.lastname: Shao
authors.forename: Huijie
authors.initials: H
authors.lastname: Ma
authors.forename: Chuyang
authors.initials: C
authors.lastname: Sun
authors.forename: Xiaonan
authors.initials: X
authors.lastname: Zhang
authors.forename: Chengren
authors.initials: C
authors.lastname: Li
authors.forename: Zongxi
authors.initials: Z
authors.lastname: Han
authors.forename: Baolong
authors.initials: B
authors.lastname: Yan
authors.forename: Xiangang
authors.initials: X
authors.lastname: Kong
authors.forename: Shengwang
authors.initials: S
authors.lastname: Liu
mesh_terms: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions; D000818:Animals; D002645:Chickens; D023061:Gene Order; D016679:Genome, Viral; D001351:Infectious bronchitis virus / Q000145:classification* / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D011995:Recombination, Genetic
chemical_list: D020413:3' Untranslated Regions; D020121:5' Untranslated Regions