title: Discovery, diversity and evolution of novel coronaviruses sampled from rodents in China.
abstract: Although rodents are important reservoirs for RNA viruses, to date only one species of rodent coronavirus (CoV) has been identified. Herein, we describe a new CoV, denoted Lucheng Rn rat coronavirus (LRNV), and novel variants of two Betacoronavirus species termed Longquan Aa mouse coronavirus (LAMV) and Longquan Rl rat coronavirus (LRLV), that were identified in a survey of 1465 rodents sampled in China during 2011-2013. Phylogenetic analysis revealed that LAMV and LRLV fell into lineage A of the genus Betacoronavirus, which included CoVs discovered in humans and domestic and wild animals. In contrast, LRNV harbored by Rattus norvegicus formed a distinct lineage within the genus Alphacoronavirus in the 3CL(pro), RdRp, and Hel gene trees, but formed a more divergent lineage in the N and S gene trees, indicative of a recombinant origin. Additional recombination events were identified in LRLV. Together, these data suggest that rodents may carry additional unrecognized CoVs.
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
authors.forename: Wen
authors.initials: W
authors.lastname: Wang
authors.affiliation: Wenzhou Center for Disease Control and Prevention, Wenzhou, Zhejiang Province, China.
authors.forename: Xian-Dan
authors.initials: XD
authors.lastname: Lin
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
authors.forename: Wen-Ping
authors.initials: WP
authors.lastname: Guo
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
authors.forename: Run-Hong
authors.initials: RH
authors.lastname: Zhou
authors.affiliation: Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China.
authors.forename: Miao-Ruo
authors.initials: MR
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
authors.forename: Cai-Qiao
authors.initials: CQ
authors.lastname: Wang
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
authors.forename: Shuang
authors.initials: S
authors.lastname: Ge
authors.affiliation: Longquan Center for Disease Control and Prevention, Longquan, Zhejiang Province, China.
authors.forename: Sheng-Hua
authors.initials: SH
authors.lastname: Mei
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
authors.forename: Ming-Hui
authors.initials: MH
authors.lastname: Li
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Mang
authors.initials: M
authors.lastname: Shi
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia.
authors.forename: Edward C
authors.initials: EC
authors.lastname: Holmes
authors.affiliation: State Key Laboratory for Infectious Disease Prevention and Control, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China. Electronic address: zhangyongzhen@icdc.cn.
authors.forename: Yong-Zhen
authors.initials: YZ
authors.lastname: Zhang
mesh_terms: D000818:Animals; D002681:China; D017934:Coronavirus / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification*; D017941:Coronavirus, Rat / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D004197:Disease Reservoirs / Q000821:virology; D019143:Evolution, Molecular; D014644:Genetic Variation; D016679:Genome, Viral; D006801:Humans; D051379:Mice; D008969:Molecular Sequence Data; D010802:Phylogeny; D051381:Rats; D012377:Rodentia / Q000821:virology*; D064370:Spike Glycoprotein, Coronavirus / Q000737:chemistry / Q000235:genetics
chemical_list: D064370:Spike Glycoprotein, Coronavirus
keywords: Coronavirus; Evolution; Phylogeny; Recombination; Rodents