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. PereiraPedro 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. Alessandro, 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

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883 Scopus citations


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.

Original languageEnglish
Article number6544
Issue number6544
StatePublished - May 21 2021

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