Key Laboratory of Jilin Province for Zoonosis Prevention and Control, Institute of Military Veterinary, Academy of Military Medical Sciences, Changchun, Jilin Province, China Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu Province, China.
Yunnan Institute of Endemic Diseases Control and Prevention, Dali, Yunnan Province, China.
J Virol. 2014 Jun;88(12):7070-82. doi: 10.1128/JVI.00631-14. Epub 2014 Apr 9.
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 CoVs. 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 nucleotides (nt) in length with 13 open reading frames (ORFs), sharing 91% nucleotide identity with human/civet SARS CoVs and the most recently reported SARS-like CoV Rs3367, while sharing 89% with other bat SARS-like CoVs. Notably, it showed the 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.
Although many severe acute respiratory syndrome-like coronaviruses (SARS-like CoVs) have been discovered in bats worldwide, there are significant different genic structures, particularly in the S1 domain, which are 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 sequencing 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.
虽然在中国、欧洲和非洲的蝙蝠中已经发现了许多严重急性呼吸系统综合征样冠状病毒（SARS 样 CoV），但大多数在受体结合域（RBD）中的遗传结构与人类/大花白鼻长尾猴 SARS CoV 有很大的不同，该区域介导受体结合并决定宿主范围，导致它们不能引起人类感染，也不太可能成为人类/大花白鼻长尾猴 SARS CoV 的前体。在此，对来自云南省四个县的 268 份蝙蝠直肠拭子进行的病毒宏基因组分析鉴定了数百种与甲型和乙型冠状病毒有关的序列。基于 RNA 依赖性 RNA 聚合酶基因保守区的系统发育分析显示，甲型冠状病毒的多样性与以前报道的有明显差异。来自保山（LYRa11）的新型 SARS 样 CoV 的全基因组分析表明，其长度为 29805 个核苷酸（nt），有 13 个开放阅读框（ORF），与人类/大花白鼻长尾猴 SARS CoV 和最近报道的 SARS 样 CoV Rs3367 的核苷酸同一性为 91%，而与其他蝙蝠 SARS 样 CoV 的核苷酸同一性为 89%。值得注意的是，它与 SARS CoV 和 Rs3367 的 S 基因显示出最高的序列同一性，特别是在 RBD 区域。抗原分析表明，LYRa11 的 S1 结构域可被 SARS 恢复期人类血清有效识别，表明 LYRa11 是一种新型病毒，与 SARS CoV 具有高度抗原性。重组分析表明，LYRa11 可能是由进化成多种蝙蝠 SARS 样 CoV 的亲代谱系衍生而来的重组病毒。
虽然在全球范围内的蝙蝠中已经发现了许多严重急性呼吸系统综合征样冠状病毒（SARS 样 CoV），但蝙蝠 SARS 样 CoV 和人类 SARS CoV 之间存在显著不同的基因结构，特别是在决定宿主趋向性的 S1 结构域，表明大多数报道的蝙蝠 SARS 样 CoV 不是人类 SARS CoV 的前体。我们在中国云南采集的蝙蝠中发现了多种甲型冠状病毒和 SARS CoV 的近亲（LYRa11）。进一步分析表明，α-和乙型冠状病毒在蝙蝠种群中有不同的循环和传播动态。值得注意的是，全基因组测序和抗原研究表明，LYRa11 在系统发育和抗原性上与 SARS CoV 密切相关。重组分析表明，LYRa11 是云南省流行的某些蝙蝠 SARS 样 CoV 的重组病毒。
