title: Genomic Analysis and Surveillance of the Coronavirus Dominant in Ducks in China.
abstract: The genetic diversity, evolution, distribution, and taxonomy of some coronaviruses dominant in birds other than chickens remain enigmatic. In this study we sequenced the genome of a newly identified coronavirus dominant in ducks (DdCoV), and performed a large-scale surveillance of coronaviruses in chickens and ducks using a conserved RT-PCR assay. The viral genome harbors a tandem repeat which is rare in vertebrate RNA viruses. The repeat is homologous to some proteins of various cellular organisms, but its origin remains unknown. Many substitutions, insertions, deletions, and some frameshifts and recombination events have occurred in the genome of the DdCoV, as compared with the coronavirus dominant in chickens (CdCoV). The distances between DdCoV and CdCoV are large enough to separate them into different species within the genus Gammacoronavirus. Our surveillance demonstrated that DdCoVs and CdCoVs belong to different lineages and occupy different ecological niches, further supporting that they should be classified into different species. Our surveillance also demonstrated that DdCoVs and CdCoVs are prevalent in live poultry markets in some regions of China. In conclusion, this study shed novel insight into the genetic diversity, evolution, distribution, and taxonomy of the coronaviruses circulating in chickens and ducks.
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Qing-Ye
authors.initials: QY
authors.lastname: Zhuang
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Kai-Cheng
authors.initials: KC
authors.lastname: Wang
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Shuo
authors.initials: S
authors.lastname: Liu
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Guang-Yu
authors.initials: GY
authors.lastname: Hou
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Wen-Ming
authors.initials: WM
authors.lastname: Jiang
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Su-Chun
authors.initials: SC
authors.lastname: Wang
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Jin-Ping
authors.initials: JP
authors.lastname: Li
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Jian-Min
authors.initials: JM
authors.lastname: Yu
authors.affiliation: China Animal Health and Epidemiology Center, Qingdao, 266032, China.
authors.forename: Ji-Ming
authors.initials: JM
authors.lastname: Chen
mesh_terms: D000818:Animals; D002645:Chickens; D002681:China / Q000453:epidemiology; D017124:Conserved Sequence; D017934:Coronavirus / Q000145:classification / Q000235:genetics*; D018352:Coronavirus Infections / Q000662:veterinary*; D004372:Ducks; D023061:Gene Order; D016679:Genome, Viral; D023281:Genomics; D010802:Phylogeny; D011201:Poultry Diseases / Q000453:epidemiology* / Q000821:virology*; D062486:Public Health Surveillance; D011995:Recombination, Genetic; D020080:Tandem Repeat Sequences