title: Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans.
abstract: The Chinese rufous horseshoe bat (Rhinolophus sinicus) has been suggested to carry the direct ancestor of severe acute respiratory syndrome (SARS) coronavirus (SCoV), and the diversity of SARS-like CoVs (SLCoV) within this Rhinolophus species is therefore worth investigating. Here, we demonstrate the remarkable diversity of SLCoVs in R. sinicus and identify a strain with the same pattern of phylogenetic incongruence (i.e. an indication of recombination) as reported previously in another SLCoV strain. Moreover, this strain possesses a distinctive 579 nt deletion in the nsp3 region that was also found in a human SCoV from the late-phase epidemic. Phylogenetic analysis of the Orf1 region suggested that the human SCoVs are phylogenetically closer to SLCoVs in R. sinicus than to SLCoVs in other Rhinolophus species. These findings reveal a closer evolutionary linkage between SCoV in humans and SLCoVs in R. sinicus, defining the scope of surveillance to search for the direct ancestor of human SCoVs.
authors.affiliation: State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences (CAS), Wuhan, PR China.
authors.forename: Junfa
authors.initials: J
authors.lastname: Yuan
authors.forename: Chung-Chau
authors.initials: CC
authors.lastname: Hon
authors.forename: Yan
authors.initials: Y
authors.lastname: Li
authors.forename: Dingming
authors.initials: D
authors.lastname: Wang
authors.forename: Gelin
authors.initials: G
authors.lastname: Xu
authors.forename: Huajun
authors.initials: H
authors.lastname: Zhang
authors.forename: Peng
authors.initials: P
authors.lastname: Zhou
authors.forename: Leo L M
authors.initials: LL
authors.lastname: Poon
authors.forename: Tommy Tsan-Yuk
authors.initials: TT
authors.lastname: Lam
authors.forename: Frederick Chi-Ching
authors.initials: FC
authors.lastname: Leung
authors.forename: Zhengli
authors.initials: Z
authors.lastname: Shi
mesh_terms: D000818:Animals; D001483:Base Sequence; D002685:Chiroptera / Q000821:virology*; D045303:Cytochromes b / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics; D011995:Recombination, Genetic; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification* / Q000235:genetics; D017361:Viral Nonstructural Proteins / Q000235:genetics
chemical_list: D017361:Viral Nonstructural Proteins; D045303:Cytochromes b; C510959:Nsp3 protein, SARS-CoV; D012324:RNA-Dependent RNA Polymerase