Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination.
Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination.
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DOI：
10.1093/gbe/evac018
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发表时间：
2022-02-04
影响因子：
3.3
通讯作者：
Robertson DL
中科院分区：
文献类型：
--
作者：
Lytras S;Hughes J;Martin D;Swanepoel P;de Klerk A;Lourens R;Kosakovsky Pond SL;Xia W;Jiang X;Robertson DL
由于缺乏可识别的SARS-CoV-2近端动物祖先的中间宿主物种，以及武汉与在马蹄蝠（sarbecvirus亚属成员）中传播的进化上最接近的冠状病毒之间的地理距离较远，这加剧了人们对SARS-CoV-2自然起源的猜测。我们对SARS-CoV-2和迄今为止采集的所有相关蝙蝠和穿山甲sarbecovirus进行了全面的系统发育研究。确定可能的重组事件揭示了这组冠状病毒内部高度网状的进化史。推断的重组事件的分布是非随机的，有证据表明，体液免疫的主要靶点Spike位于重组热点附近，可能驱动蝙蝠sarbecovirus祖先的抗原转移事件。再加上其宿主的地理范围和采样地点，在中国南部和东南亚，我们确认马蹄铁蝙蝠，犀牛，可能是SARS-CoV-2祖先的储存库物种。通过追踪重组序列模式，我们得出结论，在过去的100年里，这些病毒的祖先在中国和东南亚的蝙蝠宿主范围内进行了相对较近的地理运动和共循环。我们确认，尚未对SARS-CoV-2的直接近端祖先进行采样，因为在云南收集的已知最接近的亲属大约40年前与SARS-CoV-2有共同的祖先。我们的分析强调需要大量的野生动物样本：1)查明SARS-CoV-2的动物祖先的确切起源，2)促进从蝙蝠传播给人类的中间物种（如果有的话），以及3)调查相关sarbecovirus系统发育的多样性程度，这些系统发育对未来的溢出风险很高。
The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses’ ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses’ phylogeny that present high risk for future spillovers.
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影响因子：
28.3
作者：
Gorbalenya, Alexander E.;Baker, Susan C.;Ziebuhr, John
通讯作者：
Ziebuhr, John
影响因子：
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作者：
Holmes, EC;Worobey, M;Rambaut, A
通讯作者：
Rambaut, A
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
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作者：
Katoh K;Standley DM
通讯作者：
Standley DM
影响因子：
64.5
作者：
Holmes EC;Goldstein SA;Rasmussen AL;Robertson DL;Crits-Christoph A;Wertheim JO;Anthony SJ;Barclay WS;Boni MF;Doherty PC;Farrar J;Geoghegan JL;Jiang X;Leibowitz JL;Neil SJD;Skern T;Weiss SR;Worobey M;Andersen KG;Garry RF;Rambaut A
通讯作者：
Rambaut A