Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

doi:10.1126/science.abh2644

GSTDTAP > 气候变化

DOI	10.1126/science.abh2644
	Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
	Nuno R. Faria; Thomas A. Mellan; Charles Whittaker; Ingra M. Claro; Darlan da S. Candido; Swapnil Mishra; Myuki A. E. Crispim; Flavia C. S. Sales; Iwona Hawryluk; John T. McCrone; Ruben J. G. Hulswit; Lucas A. M. Franco; Mariana S. Ramundo; Jaqueline G. de Jesus; Pamela S. Andrade; Thais M. Coletti; Giulia M. Ferreira; Camila A. M. Silva; Erika R. Manuli; Rafael H. M. Pereira; Pedro S. Peixoto; Moritz U. G. Kraemer; Nelson Gaburo; Cecilia da C. Camilo; Henrique Hoeltgebaum; William M. Souza; Esmenia C. Rocha; Leandro M. de Souza; Mariana C. de Pinho; Leonardo J. T. Araujo; Frederico S. V. Malta; Aline B. de Lima; Joice do P. Silva; Danielle A. G. Zauli; Alessandro C. de S. Ferreira; Ricardo P. Schnekenberg; Daniel J. Laydon; Patrick G. T. Walker; Hannah M. Schlüter; Ana L. P. dos Santos; Maria S. Vidal; Valentina S. Del Caro; Rosinaldo M. F. Filho; Helem M. dos Santos; Renato S. Aguiar; José L. Proença-Modena; Bruce Nelson; James A. Hay; Mélodie Monod; Xenia Miscouridou; Helen Coupland; Raphael Sonabend; Michaela Vollmer; Axel Gandy; Carlos A. Prete; Vitor H. Nascimento; Marc A. Suchard; Thomas A. Bowden; Sergei L. K. Pond; Chieh-Hsi Wu; Oliver Ratmann; Neil M. Ferguson; Christopher Dye; Nick J. Loman; Philippe Lemey; Andrew Rambaut; Nelson A. Fraiji; Maria do P. S. S. Carvalho; Oliver G. Pybus; Seth Flaxman; Samir Bhatt; Ester C. Sabino
	2021-05-21
发表期刊	Science
出版年	2021
英文摘要	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 Sã 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. [821][1] and p. [815][2] 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. [1]: /lookup/doi/10.1126/science.abh1558 [2]: /lookup/doi/10.1126/science.abh2644
领域	气候变化 ; 资源环境
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文献类型	期刊论文
条目标识符	http://119.78.100.173/C666/handle/2XK7JSWQ/328821
专题	气候变化资源环境科学
推荐引用方式 GB/T 7714	Nuno R. Faria,Thomas A. Mellan,Charles Whittaker,et al. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil[J]. Science,2021.
APA	Nuno R. Faria.,Thomas A. Mellan.,Charles Whittaker.,Ingra M. Claro.,Darlan da S. Candido.,...&Ester C. Sabino.(2021).Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil.Science.
MLA	Nuno R. Faria,et al."Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil".Science (2021).