Cited by 1,461SARS-CoV-2 and COVID-19 ResearchCOVID-19 epidemiological studiesEvolution and Genetic Dynamics

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

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Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C. S., Hawryluk, Iwona, McCrone, John T., Hulswit, Ruben J. G., Franco, Lucas A. M., Ramundo, Mariana S., de Jesus, Jaqueline G., Andrade, Pamela S., Coletti, Thais M., Ferreira, Giulia M., Silva, Camila A. M., Manuli, Erika R., Pereira, Rafael H. M., Peixoto, Pedro S., Kraemer, Moritz U. G., Gaburo, Nelson, Camilo, Cecilia da C., Hoeltgebaum, Henrique, Souza, William M., Rocha, Esmenia C., de Souza, Leandro M., de Pinho, Mariana C., Araujo, Leonardo J. T., Malta, Frederico S. V., de Lima, Aline B., Silva, Joice do P., Zauli, Danielle A. G., Ferreira, Alessandro C. de S., Schnekenberg, Ricardo P., Laydon, Daniel J., Walker, Patrick G. T., Schlüter, Hannah M., dos Santos, Ana L. P., Vidal, Maria S., Del Caro, Valentina S., Filho, Rosinaldo M. F., dos Santos, Helem M., Aguiar, Renato S., Proença-Modena, José L., Nelson, Bruce, Hay, James A., Monod, Mélodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A., Nascimento, Vitor H., Suchard, Marc A., Bowden, Thomas A., Pond, Sergei L. K., Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M., Dye, Christopher, Loman, Nick J., Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A., Carvalho, Maria do P. S. S., Pybus, Oliver G., Flaxman, Seth, Bhatt, Samir, Sabino, Ester C.·2021·Science

DOI 10.1126/science.abh2644PMC PMC8139423

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Abstract

Unmitigated spread in Brazil: 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 and p. 815

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Authors: Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C. S., Hawryluk, I., McCrone, J. T., Hulswit, R. J. G., Franco, L. A. M., Ramundo, M. S., de Jesus, J. G., Andrade, P. S., Coletti, T. M., Ferreira, G. M., Silva, C. A. M., Manuli, E. R., Pereira, R. H. M., Peixoto, P. S., Kraemer, M. U. G., Gaburo, N., Camilo, C. D. C., Hoeltgebaum, H., Souza, W. M., Rocha, E. C., de Souza, L. M., de Pinho, M. C., Araujo, L. J. T., Malta, F. S. V., de Lima, A. B., Silva, J. D. P., Zauli, D. A. G., Ferreira, A. C. D. S., Schnekenberg, R. P., Laydon, D. J., Walker, P. G. T., Schlüter, H. M., dos Santos, A. L. P., Vidal, M. S., Del Caro, V. S., Filho, R. M. F., dos Santos, H. M., Aguiar, R. S., Proença-Modena, J. L., Nelson, B., Hay, J. A., Monod, M., Miscouridou, X., Coupland, H., Sonabend, R., Vollmer, M., Gandy, A., Prete, C. A., Nascimento, V. H., Suchard, M. A., Bowden, T. A., Pond, S. L. K., Wu, C.-H., Ratmann, O., Ferguson, N. M., Dye, C., Loman, N. J., Lemey, P., Rambaut, A., Fraiji, N. A., Carvalho, M. D. P. S. S., Pybus, O. G., Flaxman, S., Bhatt, S., & Sabino, E. C.
Affiliations: Universidade de São Paulo (BR)
Imperial College London (GB)
Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas (BR)
University of Edinburgh (GB)
Centre for Human Genetics (GB)
Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil.
Universidade Federal de Uberlândia (BR)
Institute of Applied Economic Research (BR)
University of Oxford (GB)
DB Diagnósticos do Brasil, São Paulo, Brazil.
Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil.
Instituto Hermes Pardini, Belo Horizonte, Brazil.
CDL Laboratório Santos e Vidal, Manaus, Brazil.
Universidade Federal de Minas Gerais (BR)
Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil.
Instituto Nacional de Pesquisas da Amazônia (BR)
Harvard University (US)
Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil.
University of California, Los Angeles (US)
Temple University (US)
University of Southampton (GB)
Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
Rega Institute for Medical Research (BE)
Royal Veterinary College (GB)
University of Copenhagen (DK)
Corresponding author: Faria, Nuno R.
Mellan, Thomas A.
Whittaker, Charles
Claro, Ingra M.
Mishra, Swapnil
Pybus, Oliver G.
Flaxman, Seth
Bhatt, Samir
ORCID: Faria, Nuno R.
Mellan, Thomas A.
Whittaker, Charles
Claro, Ingra M.
Candido, Darlan da S.
Mishra, Swapnil
Crispim, Myuki A. E.
Sales, Flavia C. S.
Hawryluk, Iwona
McCrone, John T.
Hulswit, Ruben J. G.
Franco, Lucas A. M.
Ramundo, Mariana S.
de Jesus, Jaqueline G.
Andrade, Pamela S.
Coletti, Thais M.
Ferreira, Giulia M.
Silva, Camila A. M.
Manuli, Erika R.
Pereira, Rafael H. M.
Peixoto, Pedro S.
Kraemer, Moritz U. G.
Gaburo, Nelson
Camilo, Cecilia da C.
Hoeltgebaum, Henrique
Souza, William M.
Rocha, Esmenia C.
de Souza, Leandro M.
de Pinho, Mariana C.
Araujo, Leonardo J. T.
Malta, Frederico S. V.
de Lima, Aline B.
Silva, Joice do P.
Zauli, Danielle A. G.
Ferreira, Alessandro C. de S.
Schnekenberg, Ricardo P.
Laydon, Daniel J.
Walker, Patrick G. T.
Schlüter, Hannah M.
dos Santos, Ana L. P.
Vidal, Maria S.
Del Caro, Valentina S.
Aguiar, Renato S.
Proença-Modena, José L.
Nelson, Bruce
Hay, James A.
Monod, Mélodie
Coupland, Helen
Sonabend, Raphael
Vollmer, Michaela
Gandy, Axel
Prete, Carlos A.
Nascimento, Vitor H.
Suchard, Marc A.
Bowden, Thomas A.
Pond, Sergei L. K.
Wu, Chieh-Hsi
Ratmann, Oliver
Ferguson, Neil M.
Dye, Christopher
Loman, Nick J.
Lemey, Philippe
Rambaut, Andrew
Fraiji, Nelson A.
Carvalho, Maria do P. S. S.
Pybus, Oliver G.
Flaxman, Seth
Bhatt, Samir
Sabino, Ester C.
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 2021-05-21
Volume: 372
Issue: 6544
Pages: 815-821
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.abh2644
PMC: PMC8139423
OpenAlex: W3156343712
Cited by: 1,461
References: 93
Citations by year: 2026: 48 · 2025: 73 · 2024: 104 · 2023: 227 · 2022: 492 · 2021: 502
FWCI: 105.79
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (vor)
Locations: Science (publishedVersion, cc-by)
medRxiv (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
Edinburgh Research Explorer (University of Edinburgh) (publishedVersion, cc-by)
LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
Spiral (Imperial College London) (submittedVersion, cc-by)
PubMed Central (submittedVersion, cc-by-nc-nd)
ePrints Soton (University of Southampton) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion)
eScholarship (California Digital Library) (submittedVersion, cc-by)
Lirias (KU Leuven) (submittedVersion, other-oa)
TUScholarShare (Temple University) (submittedVersion, cc-by)
Funders: Medical Research Council (MR/S0195/1)
National Institute for Health Research (203141/Z/16/Z, MR/S007555/1, ALTF 869-2019, OPP1175094, 2018/12579-7 CNP)
Wellcome Trust and Royal Society (204311/Z/16/Z)
Topics: Health Sciences › Medicine › Infectious Diseases › SARS-CoV-2 and COVID-19 Research
Physical Sciences › Mathematics › Modeling and Simulation › COVID-19 epidemiological studies
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Keywords: P.1 lineage, SARS-CoV-2, COVID-19 pandemic, variants of concern, spike protein mutations, E484K, N501Y, ACE2 binding, transmissibility, immune evasion, molecular clock, epidemic resurgence, Manaus, genomic surveillance

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

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