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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
Open accessPublished version of a preprint
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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“1), emerging in Brazil in November of that year carried similar (K417T, E484K, and N501Y) in the Spike protein, resulting also in rapid spread across the globe.(7) The two Epsilon (B.”
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“The Beta variant predominated in South Africa in late 2020, and the Gamma variant was prevalent in Brazil in late 2020 [13,14].”
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“2 lineages, previously designated as Alpha and Gamma VOCs, respectively) (Faria et al., 2021; Franceschi et al., 2021; Nonaka et al., 2021; Resende et al., 2020).”
High-Integrity Sequencing of Spike Gene for SARS-CoV-2 Variant Determination
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“2 Delta variant, have been detected.(14,15) In Bangladesh, by November 2021, only 18% of the whole population was fully vaccinated against this disease.”
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Prerequisite for COVID-19 Prediction: A Review on Factors Affecting the Infection Rate
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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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