title: Comparative analysis of complete genome sequences of three avian coronaviruses reveals a novel group 3c coronavirus.
abstract: In this territory-wide molecular epidemiology study of coronaviruses (CoVs) in Hong Kong involving 1,541 dead wild birds, three novel CoVs were identified in three different bird families (bulbul CoV HKU11 [BuCoV HKU11], thrush CoV HKU12 [ThCoV HKU12], and munia CoV HKU13 [MuCoV HKU13]). Four complete genomes of the three novel CoVs were sequenced. Their genomes (26,396 to 26,552 bases) represent the smallest known CoV genomes. In phylogenetic trees constructed using chymotrypsin-like protease (3CL(pro)), RNA-dependent RNA polymerase (Pol), helicase, spike, and nucleocapsid proteins, BuCoV HKU11, ThCoV HKU12, and MuCoV HKU13 formed a cluster distantly related to infectious bronchitis virus and turkey CoV (group 3a CoVs). For helicase, spike, and nucleocapsid, they were also clustered with a CoV recently discovered in Asian leopard cats, for which the complete genome sequence was not available. The 3CL(pro), Pol, helicase, and nucleocapsid of the three CoVs possessed higher amino acid identities to those of group 3a CoVs than to those of group 1 and group 2 CoVs. Unique genomic features distinguishing them from other group 3 CoVs include a distinct transcription regulatory sequence and coding potential for small open reading frames. Based on these results, we propose a novel CoV subgroup, group 3c, to describe this distinct subgroup of CoVs under the group 3 CoVs. Avian CoVs are genetically more diverse than previously thought and may be closely related to some newly identified mammalian CoVs. Further studies would be important to delineate whether the Asian leopard cat CoV was a result of interspecies jumping from birds, a situation analogous to that of bat and civet severe acute respiratory syndrome CoVs.
authors.affiliation: Department of Microbiology, State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Queen Mary Hospital, Hong Kong.
authors.forename: Patrick C Y
authors.initials: PC
authors.lastname: Woo
authors.forename: Susanna K P
authors.initials: SK
authors.lastname: Lau
authors.forename: Carol S F
authors.initials: CS
authors.lastname: Lam
authors.forename: Kenneth K Y
authors.initials: KK
authors.lastname: Lai
authors.forename: Yi
authors.initials: Y
authors.lastname: Huang
authors.forename: Paul
authors.initials: P
authors.lastname: Lee
authors.forename: Geraldine S M
authors.initials: GS
authors.lastname: Luk
authors.forename: Kitman C
authors.initials: KC
authors.lastname: Dyrting
authors.forename: Kwok-Hung
authors.initials: KH
authors.lastname: Chan
authors.forename: Kwok-Yung
authors.initials: KY
authors.lastname: Yuen
mesh_terms: D000818:Animals; D001483:Base Sequence; D001715:Bird Diseases / Q000453:epidemiology / Q000821:virology*; D001717:Birds; D016000:Cluster Analysis; D017934:Coronavirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D018352:Coronavirus Infections / Q000453:epidemiology / Q000662:veterinary* / Q000821:virology; D016679:Genome, Viral; D006723:Hong Kong / Q000453:epidemiology; D017720:Molecular Epidemiology; D008969:Molecular Sequence Data; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D026801:Synteny; D014764:Viral Proteins / Q000235:genetics
chemical_list: D012367:RNA, Viral; D014764:Viral Proteins