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

2021; American Association for the Advancement of Science; Volume: 372; Issue: 6544 Linguagem: Inglês

10.1126/science.abh2644

1095-9203

Nuno R. Faria, Thomas A. Mellan, Charles Whittaker, Ingra Morales Claro, Darlan da Silva Cândido, Swapnil Mishra, Myuki Alfaia Esashika Crispim, Flavia Cristina da Silva Sales, Iwona Hawryluk, John T. McCrone, Ruben J. G. Hulswit, Lucas Augusto Moysés Franco, Mariana Severo Ramundo, Jaqueline Góes de Jesus, Pâmela dos Santos Andrade, Thaís M. Coletti, Giulia Magalhães Ferreira, Camila Alves Maia da Silva, Erika R. Manuli, Rafael H. M. Pereira, Pedro S. Peixoto, Moritz U. G. Kraemer, Nelson Gaburo, Cecilia da C. Camilo, Henrique Hoeltgebaum, William Marciel de Souza, E Rocha, L. M. de S. e Souza, Mariana C. Pinho, Leonardo José Tadeu de Araújo, Frederico Scott Varella Malta, Aline Brito de Lima, Joice do Prado Silva, Danielle Alves Gomes Zauli, Alessandro Clayton de Souza Ferreira, Ricardo P. Schnekenberg, Daniel J. Laydon, Patrick Walker, Hannah M. Schlüter, Ana L. P. dos Santos, Maria S. Vidal, Valentina S. Del, Rosinaldo M. F. Filho, Helem M. dos Santos, Renato Santana Aguiar, José Luiz Proença-Módena, Bruce Nelson, James A. Hay, Mélodie Monod, Xenia Miscouridou, Helen Coupland, Raphael Sonabend, Michaela Vollmer, Axel Gandy, Carlos A. Prete, Vítor H. Nascimento, Marc A. Suchard, Thomas A. Bowden, Sergei L. Kosakovsky Pond, Chieh‐Hsi Wu, Oliver Ratmann, Neil M. Ferguson, Christopher Dye, Nicholas J. Loman, Philippe Lemey, Andrew Rambaut, Nelson Abrahim Fraiji, Maria do P. S. S. Carvalho, Oliver G. Pybus, Seth Flaxman, Samir Bhatt, Éster Cerdeira Sabino,

COVID-19 Clinical Research Studies

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.