An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.
An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic.
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COVID-19大流行中祖先SARS-CoV-2及其优势分支的进化肖像
DOI：
10.1093/molbev/msab118
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发表时间：
2021-07-29
影响因子：
10.7
通讯作者：
Miura S
中科院分区：
文献类型：
--
作者：
Kumar S;Tao Q;Weaver S;Sanderford M;Caraballo-Ortiz MA;Sharma S;Pond SLK;Miura S
对严重急性呼吸综合征冠状病毒2 （SARS-CoV-2）基因组的全球测序继续揭示新的遗传变异，这些变异是揭示其早期进化史和追踪其全球传播的关键。在这里，我们通过对数千个高质量基因组的分析，介绍了SARS-CoV-2迄今为止的隐变变史和时空动态。我们报告了SARS-CoV-2可能最近的共同祖先，通过最初用于推断患者肿瘤细胞突变史的计算方法的新应用和进步重建了SARS-CoV-2。该祖基因组与中国首批冠状病毒样本的基因组有三个变体不同，这意味着最早的患者中没有一个是指示病例，也没有引起所有人类感染。然而，在2020年1月及之后，中国和美国的多起冠状病毒感染都带有祖病毒的遗传指纹，这表明在中国首次报告COVID-19病例之前和之后的几个月里，祖病毒已经在全球传播。祖病毒及其分支的突变产生了许多主导的冠状病毒株，这些株随着时间的推移会间歇性地传播。基于常见突变的指纹识别显示，在2020年大流行的大部分时间里，同一种冠状病毒谱系在北美占主导地位。在欧洲和亚洲，主要的冠状病毒毒株出现了多种替代，在亚洲和北美，多种高频毒株持续存在。我们开发了一个不断更新的SARS-CoV-2全球演变和时空趋势仪表板（http://sars2evo.datamonkey.org/）。
Global sequencing of genomes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continued to reveal new genetic variants that are the key to unraveling its early evolutionary history and tracking its global spread over time. Here we present the heretofore cryptic mutational history and spatiotemporal dynamics of SARS-CoV-2 from an analysis of thousands of high-quality genomes. We report the likely most recent common ancestor of SARS-CoV-2, reconstructed through a novel application and advancement of computational methods initially developed to infer the mutational history of tumor cells in a patient. This progenitor genome differs from genomes of the first coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the United States harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide months before and after the first reported cases of COVID-19 in China. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains that have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic in 2020. There have been multiple replacements of predominant coronavirus strains in Europe and Asia as well as continued presence of multiple high-frequency strains in Asia and North America. We have developed a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).
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影响因子：
64.5
作者：
Fauver, Joseph R.;Petrone, Mary E.;Grubaugh, Nathan D.
通讯作者：
Grubaugh, Nathan D.
单细胞数据的树推断。
影响因子：
12.3
作者：
Jahn K;Kuipers J;Beerenwinkel N
通讯作者：
Beerenwinkel N
SARS-COV-2血统的估计可传播和影响B.1.1.7在英国。
DOI：
10.1126/science.abg3055
发表时间：
2021-04-09
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Davies NG;Abbott S;Barnard RC;Jarvis CI;Kucharski AJ;Munday JD;Pearson CAB;Russell TW;Tully DC;Washburne AD;Wenseleers T;Gimma A;Waites W;Wong KLM;van Zandvoort K;Silverman JD;CMMID COVID-19 Working Group;COVID-19 Genomics UK (COG-UK) Consortium;Diaz-Ordaz K;Keogh R;Eggo RM;Funk S;Jit M;Atkins KE;Edmunds WJ
通讯作者：
Edmunds WJ
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
影响因子：
13.6
作者：
Di Giorgio, Salvatore;Martignano, Filippo;Conticello, Silvestro G.
通讯作者：
Conticello, Silvestro G.