Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging.
Molecular Epidemiology Surveillance of SARS-CoV-2: Mutations and Genetic Diversity One Year after Emerging.
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DOI：
10.3390/pathogens10020184
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发表时间：
2021-02-09
期刊：
影响因子：
--
通讯作者：
Morales-Espinosa R
中科院分区：
文献类型：
--
作者：
Flores-Alanis A;Cruz-Rangel A;Rodríguez-Gómez F;González J;Torres-Guerrero CA;Delgado G;Cravioto A;Morales-Espinosa R
2019年12月，中国武汉市发现了首例新型严重急性呼吸综合征冠状病毒2型（SARS-CoV-2）病例。从那时起，它已经在世界范围内传播，并报告了新的突变。本研究的目的是监测遗传多样性的变化，并跟踪可能与SARS-CoV-2的适应性及其在2019年12月至2020年11月期间在不同地区的传播有关的非同义替换（dN）。我们分析了来自全球6个地理区域的2213个完整的基因组，这些基因组从GenBank和GISAID数据库下载。尽管SARS-CoV-2的遗传多样性较低，但随着时间的推移，随着整个基因组中存在几个热点突变，遗传多样性有所增加。我们确定了七个常见的突变，导致dN取代。其中两个，C14408 T> P323 L和A23403 G> D 614 G，分别位于nsp 12和Spike蛋白中，在大流行早期出现，并且随着时间的推移频率显着增加。另外两个突变，nsp 2中的A1163 T> I120 F和Spike蛋白中的G22992 A> S477 N，最近出现并在大洋洲和欧洲传播。P323 L、D 614 G、R203 K和G204 R置换与疾病严重程度相关。对SARS-CoV-2的持续分子监测将是必要的，以检测和描述具有临床相关性的病毒新变体的传播动力学。这些信息对于改进控制病毒的程序很重要。
In December 2019, the first cases of the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were identified in the city of Wuhan, China. Since then, it has spread worldwide with new mutations being reported. The aim of the present study was to monitor the changes in genetic diversity and track non-synonymous substitutions (dN) that could be implicated in the fitness of SARS-CoV-2 and its spread in different regions between December 2019 and November 2020. We analyzed 2213 complete genomes from six geographical regions worldwide, which were downloaded from GenBank and GISAID databases. Although SARS-CoV-2 presented low genetic diversity, there has been an increase over time, with the presence of several hotspot mutations throughout its genome. We identified seven frequent mutations that resulted in dN substitutions. Two of them, C14408T>P323L and A23403G>D614G, located in the nsp12 and Spike protein, respectively, emerged early in the pandemic and showed a considerable increase in frequency over time. Two other mutations, A1163T>I120F in nsp2 and G22992A>S477N in the Spike protein, emerged recently and have spread in Oceania and Europe. There were associations of P323L, D614G, R203K and G204R substitutions with disease severity. Continuous molecular surveillance of SARS-CoV-2 will be necessary to detect and describe the transmission dynamics of new variants of the virus with clinical relevance. This information is important to improve programs to control the virus.
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DOI：
10.1093/bioinformatics/btq224
发表时间：
2010-08-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Katoh K;Toh H
通讯作者：
Toh H
影响因子：
64.8
作者：
Barnes CO;Jette CA;Abernathy ME;Dam KA;Esswein SR;Gristick HB;Malyutin AG;Sharaf NG;Huey-Tubman KE;Lee YE;Robbiani DF;Nussenzweig MC;West AP Jr;Bjorkman PJ
通讯作者：
Bjorkman PJ
DOI：
10.1126/science.abc4730
发表时间：
2020-09-25
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Gu H;Chen Q;Yang G;He L;Fan H;Deng YQ;Wang Y;Teng Y;Zhao Z;Cui Y;Li Y;Li XF;Li J;Zhang NN;Yang X;Chen S;Guo Y;Zhao G;Wang X;Luo DY;Wang H;Yang X;Li Y;Han G;He Y;Zhou X;Geng S;Sheng X;Jiang S;Sun S;Qin CF;Zhou Y
通讯作者：
Zhou Y
DOI：
10.1126/science.abe8499
发表时间：
2020-12-18
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Hou YJ;Chiba S;Halfmann P;Ehre C;Kuroda M;Dinnon KH 3rd;Leist SR;Schäfer A;Nakajima N;Takahashi K;Lee RE;Mascenik TM;Graham R;Edwards CE;Tse LV;Okuda K;Markmann AJ;Bartelt L;de Silva A;Margolis DM;Boucher RC;Randell SH;Suzuki T;Gralinski LE;Kawaoka Y;Baric RS
通讯作者：
Baric RS
影响因子：
28.3
作者：
Gorbalenya, Alexander E.;Baker, Susan C.;Ziebuhr, John
通讯作者：
Ziebuhr, John