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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
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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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“The past several months have witnessed the emergence of four SArS-cov-2 variants of concern (Alpha, beta, Gamma and Delta)”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
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“The Gamma variant contains the RBD mutations N501Y, E484K and K417T (ref. 19 ).”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
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“As the Gamma variant was associated with a surge of infections in a region of Brazil estimated to have achieved a high infection rate, it is suspected of being able to infect and cause illness in persons previously infected with other variants 19,29,30 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
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“It was estimated to result in virus levels 3-4 times higher than earlier variants and to be responsible for an estimated 1.1-fold to 1.8-fold higher mortality 19 .”
From The biological and clinical significance of emerging SARS-CoV-2 variants (2021) · cites this paper as [19]
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“2 and 25.”
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The mRNA vaccine, a swift warhead against a moving infectious disease target
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“The emergence of alpha variant in United king-dom [91], Beta variant in south Africa [92], Gama variant in Brazil [93], delta variant in India [94], Epsilon variant in California [95] and Omicron variant [96] created palpable anxiety among people.”
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“1 lineage (5) and the South African B.”
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“…82 83 84 85 86 87 88 89 90 91 92 INTRODUCTION93 Over a year into the pandemic and with unprecedented reduction in human mobility worldwide, distinct94 SARS-CoV-2 lineages have arisen in multiple geographic areas around the world (Tegally et al., 2020;95 Hodcroft et al., 2021; Faria et al., 2021).”
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“boring three RBD mutation has also been demonstrated with effectively escaped neutralization [11, 12].”
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“To put this estimate into perspective, we also calculated the percentage impact of the treatment effect by re-running regression (2) taking the logarithm of the respective dependent variable (i.”
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Effectiveness of Mass Vaccination in Brazil against Severe COVID-19 CasesPreprint
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The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillancePreprint
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“During the last semester of 2020 and and beginning of 2021, several variants of the SARS-CoV-2 virus have been detected and some of them are considered more contagious and deadly (Faria et al. 2021; Lemieux andLi 2021; Plante et al. 2020;Davies et al. 2021; Leung et al. 2021;Wang et al. 2021).”
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Vaccination with SARS-CoV-2 variants of concern protects mice from challenge with wild-type virus
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“In late 2020, additional variants, termed variants of concern (VoCs) emerged in the United Kingdom [5], in South Africa [6], and in Brazil [7].”
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“Aside from these mutations, three deletions, four silent variants and a four-base insertion were also observed in P1 variant [26].”
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Spread of endemic SARS-CoV-2 lineages in Russia before April 2021
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“This is also a common mutation found in Beta ( Tegally et al., 2021 ) and Gamma ( Faria et al., 2021 ).”
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“Altogether, Omicron BA.5 has critical spike mutations that were previously reported in other VOCs (Alpha, Beta, Gamma, Delta, BA.1, and BA.2).”
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Metadata
- 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
- Published
- 2021-05-21
- Volume
- 372
- Issue
- 6544
- Pages
- 815-821
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- 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
- 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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