Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.
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DOI：
10.1126/science.abh2644
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发表时间：
2021-05-21
期刊：
影响因子：
--
通讯作者：
Sabino EC
中科院分区：
文献类型：
--
作者：
Faria NR;Mellan TA;Whittaker C;Claro IM;Candido DDS;Mishra S;Crispim MAE;Sales FCS;Hawryluk I;McCrone JT;Hulswit RJG;Franco LAM;Ramundo MS;de Jesus JG;Andrade PS;Coletti TM;Ferreira GM;Silva CAM;Manuli ER;Pereira RHM;Peixoto PS;Kraemer MUG;Gaburo N Jr;Camilo CDC;Hoeltgebaum H;Souza WM;Rocha EC;de Souza LM;de Pinho MC;Araujo LJT;Malta FSV;de Lima AB;Silva JDP;Zauli DAG;Ferreira ACS;Schnekenberg RP;Laydon DJ;Walker PGT;Schlüter HM;Dos Santos ALP;Vidal MS;Del Caro VS;Filho RMF;Dos Santos HM;Aguiar RS;Proença-Modena JL;Nelson B;Hay JA;Monod M;Miscouridou X;Coupland H;Sonabend R;Vollmer M;Gandy A;Prete CA Jr;Nascimento VH;Suchard MA;Bowden TA;Pond SLK;Wu CH;Ratmann O;Ferguson NM;Dye C;Loman NJ;Lemey P;Rambaut A;Fraiji NA;Carvalho MDPSS;Pybus OG;Flaxman S;Bhatt S;Sabino EC
尽管巴西拥有广泛的初级保健网络，但在严重急性呼吸系统综合征冠状病毒2型（SARS-CoV-2）大流行期间，巴西遭受了严重影响。卡斯特罗等人利用各州卫生办公室的每日数据，分析了2020年2月至10月该国COVID-19病例和死亡病例的传播模式。在病例变得明显之前的死亡集群表明了未缓解的传播。SARS-CoV-2在巴西传播了一个多月而未被发现，因为它从圣保罗向北传播。在马瑙斯，传播在2020年年中短暂缓解后达到前所未有的水平。Faria等人追踪了一种新的、更具侵略性的谱系P.1的进化，它有17个突变，包括刺突蛋白中的三个（K417 T、E484 K和N501 Y）。经过一段时间的加速演变，该变种于2020年11月在巴西出现。随着P.1的出现，当地严重的不平等和政治动荡加速了疾病的传播，这损害了联邦的迅速反应。《科学》，abh 1558和abh 2644，本期p.和p. 815一个与巴西马瑙斯快速传播相关的SARS-CoV-2变异谱系，于2020年11月进化出具有免疫逃逸特征。巴西马瑙斯的严重急性呼吸系统综合征冠状病毒2型（SARS-CoV-2）感染病例于二零二零年底再度出现，尽管先前的感染水平较高。2020年11月至2021年1月期间在马瑙斯采样的病毒基因组测序显示，一种令人担忧的新型SARS-CoV-2变体的出现和传播。谱系P.1获得了17个突变，包括刺突蛋白中的三个突变（K417 T、E484 K和N501 Y），这些突变与人ACE 2（血管紧张素转换酶2）受体结合增加有关。分子钟分析显示，P.1的出现发生在2020年11月中旬左右，之前有一段更快的分子进化期。使用一个两类动态模型，整合基因组和死亡率数据，我们估计，P.1可能是1.7- 2.4倍以上的传染性和以前（非P.1）感染提供了54%至79%的保护，防止感染P.1，它提供了对非P.1谱系。加强对可能表现出更高的传播性和/或免疫逃避的受关注变异的全球基因组监测，对于加速大流行反应至关重要。
Despite an extensive network of primary care availability, Brazil has suffered profoundly during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Using daily data from state health offices, Castro et al. analyzed the pattern of spread of COVID-19 cases and deaths in the country from February to October 2020. Clusters of deaths before cases became apparent indicated unmitigated spread. SARS-CoV-2 circulated undetected in Brazil for more than a month as it spread north from S o Paulo. In Manaus, transmission reached unprecedented levels after a momentary respite in mid-2020. Faria et al. tracked the evolution of a new, more aggressive lineage called P.1, which has 17 mutations, including three (K417T, E484K, and N501Y) in the spike protein. After a period of accelerated evolution, this variant emerged in Brazil during November 2020. Coupled with the emergence of P.1, disease spread was accelerated by stark local inequalities and political upheaval, which compromised a prompt federal response. Science, abh1558 and abh2644, this issue p. and p. 815 A variant lineage of SARS-CoV-2 associated with rapid transmission in Manaus, Brazil, evolved in November 2020 with immune escape characteristics. Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
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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
DOI：
10.1007/s10096-020-03930-8
发表时间：
2020-10
期刊：
European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology
影响因子：
--
作者：
Farfour E;Lesprit P;Visseaux B;Pascreau T;Jolly E;Houhou N;Mazaux L;Asso-Bonnet M;Vasse M;SARS-CoV-2 Foch Hospital study group
通讯作者：
SARS-CoV-2 Foch Hospital study group
DOI：
10.1126/science.abf2946
发表时间：
2021-02-12
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
du Plessis L;McCrone JT;Zarebski AE;Hill V;Ruis C;Gutierrez B;Raghwani J;Ashworth J;Colquhoun R;Connor TR;Faria NR;Jackson B;Loman NJ;O'Toole Á;Nicholls SM;Parag KV;Scher E;Vasylyeva TI;Volz EM;Watts A;Bogoch II;Khan K;COVID-19 Genomics UK (COG-UK) Consortium;Aanensen DM;Kraemer MUG;Rambaut A;Pybus OG
通讯作者：
Pybus OG
影响因子：
56.9
作者：
Candido, Darlan S.;Claro, Ingra M.;Faria, Nuno Rodrigues
通讯作者：
Faria, Nuno Rodrigues
影响因子：
5.3
作者：
Bletsa, Magda;Suchard, Marc A.;Lemey, Philippe
通讯作者：
Lemey, Philippe