Published ahead of print 9 April 2014, doi: 10.1128/JVI.00631-14 JVI.00631-14

Identification of diverse alphacoronaviruses and genomic characterization of a novel SARS-like coronavirus from bats in China

Biao He1,4,
Yuzhen Zhang2,
Lin Xu1,4,
Weihong Yang2,
Fanli Yang1,
Yun Feng2,
Lele Xia1,
Jihua Zhou2,
Weibin Zhen3,
Ye Feng1,4,
Huancheng Guo1,4,
Hailin Zhang2* and
Changchun Tu1,4*

1Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin province, China
2Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan province, China
3Baoshan Prefecture Center for Diseases Control and Prevention, Baoshan, Yunnan province, China
4Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu province, China


Although many severe acute respiratory syndrome-like coronaviruses (SARS-like CoVs) have been identified in bats in China, Europe and Africa, most have a genetic organization significantly distinct from human/civet SARS CoVs in the receptor-binding domain (RBD), which mediates receptor binding and determines the host spectrum, resulting in their failure to cause human infections and making them unlikely progenitors of human/civet SARS CoV. Here, a viral metagenomic analysis of 268 bat rectal swabs collected from four counties in Yunnan province has identified hundreds of sequences relating to alpha- and betacoronaviruses. Phylogenetic analysis based on a conserved region of the RNA-dependent RNA polymerase gene revealed that alphacoronaviruses had diversities with some obvious differences from those reported previously. Full genomic analysis of a new SARS-like CoV from Baoshan (LYRa11) showed that it was 29,805 nt in length with 13 open reading frames (ORFs), sharing 91% nt identity with human/civet SARS CoVs and the most recently reported SARS-like CoV Rs3367, while 89% with other bat SARS-like CoVs. Notably it showed highest sequence identity with the S gene of SARS CoVs and Rs3367, especially in the RBD region. Antigenic analysis showed that the S1 domain of LYRa11 could be efficiently recognized by SARS-convalescent human serum indicating that LYRa11 is a novel virus antigenically close to SARS CoV. Recombination analyses indicate that LYRa11 is likely a recombinant descended from parental lineages that had evolved into a number of bat SARS-like CoVs.

IMPORTANCE Although many SARS-like coronaviruses (CoV) have been discovered in bats worldwide, there are significant different genic structure, particularly in S1 domain, which is responsible for host tropism determination, between bat SARS-like CoVs and human SARS CoVs, indicating that most reported bat SARS-like CoVs are not the progenitors of human SARS CoV. We have identified diverse alphacoronaviruses and a close relative (LYRa11) to SARS CoV in bats collected in Yunnan, China. Further analysis showed that alpha- and betacoronaviruses have different circulation and transmission dynamics in bat populations. Notably full genomic sequence and antigenic study demonstrated that LYRa11 is phylogenetically and antigenically closely related to SARS CoV. Recombination analyses indicate that LYRa11 is a recombinant from certain bat SARS-like CoVs circulating in Yunnan province.