Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses
Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses
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DOI：
10.1111/j.1096-0031.2008.00199.x
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发表时间：
2008-04-01
期刊：
影响因子：
3.6
通讯作者：
Pol, Diego
中科院分区：
文献类型：
--
作者：
Janies, Daniel;Habib, Farhat;Pol, Diego
严重急性呼吸综合征（SARS）是由一种以前未被认识的冠状病毒（SARS-CoV）引起的一种新型人类疾病。关于SARS-CoV的动物宿主有相互矛盾的报道。许多认为食肉动物是SARS冠状病毒的原始宿主的团体使用一个遗传学来支持他们的论点。然而，在这些研究中的同源性往往缺乏确定SARS冠状病毒起源所必需的外群和根源标准。最近，SARS-CoV已经从来自中国的各种翼手目物种中分离出来（例如，中华菊头蝠），从而导致重新考虑SARS冠状病毒的原始水库。我们通过从包括翼手目、食肉动物、偶蹄动物、啮齿动物、鸟类和人类在内的不同宿主中采集SARS-CoV和非SARS-CoV样本，评估了从翼手目分离的SARS-CoV是SARS-CoV原始人畜共患来源的假设。无论比对参数、最优性标准或分离样本如何，所得到的遗传学结果清楚地表明，SARS冠状病毒在2002年底开始在人类中流行之后很久就传播给了小型食肉动物。从深圳市场的小型食肉动物中分离的SARS-CoV形成了一个最近从人类SARS-CoV辐射中出现的终端分支。有证据表明，SARS冠状病毒随后在人类和食肉动物之间交换。此外，SARS-CoV是独立从人类传播到养殖猪（Sus scrofa）的。从翼手目分离的SARS-CoV的位置是从人类和食肉动物分离的SARS-CoV分支的基础。虽然序列数据表明，翼手目是一个很好的候选人的原始水库的SARS冠状病毒，刺突蛋白的结构生物学从翼手目分离的SARS冠状病毒表明，这些病毒不能与人类变异的SARS冠状病毒的受体，血管紧张素转换酶2（ACE 2）。在SARS-CoV中，我们研究了不稳定的基因组片段和可能与宿主转移相关的刺突蛋白的推定关键突变。我们在描绘SARS-CoV传播的虚拟球体中投影的树上显示宿主转移和候选突变。这些结果表明，需要从不同宿主，特别是翼手目，食肉动物和灵长类动物中采集更多的冠状病毒样本，以了解包括SARS-CoV在内的冠状病毒的基因组和生化进化。(c)2008年，威利·亨尼格协会。
Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, as well as carnivores, artiodactyls, rodents, birds and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV we study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV. (c) The Willi Hennig Society 2008.