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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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“Along with some less successful novel lineages (termed variants of interest or VOIs), these VOCs were characterized by a combination of increased intrinsic transmissibility, sometimes enhanced immune evasion capabilities, and increased pathogenicity.4 Each of the VOCs was associated initially with increasing SARS-CoV-…”
BackgroundInfluentialSelf-citationA SARS-CoV-2 Nucleocapsid Variant that Affects Antigen Test Performance
Bourassa, L. A., Perchetti, G. A., Phung, Q., Lin, M. J., Mills, M. G., Roychoudhury, P., Harmon, K. G., Reed, J. C., & Greninger, A. L. (2021) · Journal of Clinical Virology · doi:10.1016/j.jcv.2021.104900 · Cited by 66
Staquicini, D. I., Tang, F. H. F., Markosian, C., Yao, V. J., Staquicini, F. I., Dodero‐Rojas, E., Contessoto, V. G., Davis, D., O’Brien, P., Habib, N., et al. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2105739118 · Cited by 69
SARS-CoV-2 variants and effectiveness of vaccines: a review of current evidence
Tatsi, E., Filippatos, F., & Michos, A. G. (2021) · Epidemiology and Infection · doi:10.1017/s0950268821002430 · Cited by 68
“Compared to previous circulating strains, it seems that generation of NAbs levels is suggestively lower against B.1.351 and B.1.617.2 [85, 86].”
BackgroundInfluentialOne year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages
Gónzález‐Candelas, F., Shaw, M., Phan, T. G., Kulkarni‐Kale, U., Paraskevis, D. N., Luciani, F., Kimura, H., & Sironi, M. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.104869 · Cited by 65
SARS-CoV-2 infects adipose tissue in a fat depot- and viral lineage-dependent manner
Saccon, T. D., Mousovich‐Neto, F., Ludwig, R. G., Carregari, V. C., Souza, A. B. D. A., dos Passos, A. S. C., Martini, M. C., Barbosa, P. P., de Souza, G. F., Muraro, S. P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33218-8 · Cited by 70
Defending against SARS-CoV-2: The T cell perspective
Almendro-Vázquez, P., Laguna‐Goya, R., & Paz‐Artal, E. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1107803 · Cited by 67
Molecular mechanism of ensitrelvir inhibiting SARS-CoV-2 main protease and its variants
Lin, M.-M., Zeng, X., Duan, Y., Yang, Z., Ma, Y., Yang, H., Yang, X., & Liu, X. (2023) · Communications Biology · doi:10.1038/s42003-023-05071-y · Cited by 65
Carreño, J. M., Alshammary, H., Singh, G., Raskin, A. J., Amanat, F., Amoako, A. A., Gonzalez-Reiche, A. S., van de Guchte, A., PARIS study group, Awawda, M. H., et al. (2021) · EBioMedicine · doi:10.1016/j.ebiom.2021.103626 · Cited by 61
“The emergence of variant viruses, first in Europe in the summer of 2020 [3 5] - including in minks in Denmark - and then in late 2020 in the UK [6], South Africa [7] and Brazil [8] was a surprising event.”
Chung, H., Jian, M., Chang, C.-K., Lin, J., Yeh, K., Chen, C., Hsieh, S., Hung, K., Tang, S. W., Perng, C., et al. (2022) · Microbiology Spectrum · doi:10.1128/spectrum.02513-21 · Cited by 84
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SARS-CoV-2’s Variants of Concern: A Brief Characterization
Scovino, A. M., Dahab, E. C., Vieira, G. F., Freire‐de‐Lima, L., Freire-de-Lima, C. G., & Morrot, A. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.834098 · Cited by 69
Nonaka, C. K. V., Gräf, T., Barcia, C. A. D. L., Costa, V. F., de Oliveira, J. L., Passos, R. D. H., Bastos, I. N., de Santana, M. C. B., Santos, I. M., de Sousa, K. A. F., et al. (2021) · International Journal of Infectious Diseases · doi:10.1016/j.ijid.2021.08.003 · Cited by 63
Chiuppesi, F., Nguyen, V. H., Park, Y., Contreras, H., Karpinski, V., Faircloth, K., Nguyen, J., Kha, M., Johnson, D., Martinez, J., et al. (2022) · npj Vaccines · doi:10.1038/s41541-022-00436-6 · Cited by 61
Evolution of the SARS-CoV-2 Omicron Variants: Genetic Impact on Viral Fitness
Liu, W., Huang, Z., Xiao, J., Wu, Y., Xia, N., & Yuan, Q. (2024) · Viruses · doi:10.3390/v16020184 · Cited by 68
Overcoming Brazil’s monumental COVID-19 failure: an urgent call to action
Hallal, P. C., & Victora, C. G. (2021) · Nature Medicine · doi:10.1038/s41591-021-01353-2 · Cited by 62
Cerutti, G., Rapp, M., Guo, Y., Bahna, F. A., Bimela, J. S., Reddem, E. R., Yu, J., Wang, P., Liu, L., Huang, Y., et al. (2021) · Structure · doi:10.1016/j.str.2021.05.014 · Cited by 59
Chen, K., Pun, C. S., & Wong, H. Y. (2021) · European Journal of Operational Research · doi:10.1016/j.ejor.2021.11.012 · Cited by 62
Banho, C. Á., Sacchetto, L., Campos, G. R. F., Bittar, C., Possebon, F. S., Ullmann, L. S., Marques, B. D. C., da Silva, G. C. D., Moraes, M. M., Parra, M. C. P., et al. (2022) · Communications Medicine · doi:10.1038/s43856-022-00108-5 · Cited by 63
SARS-CoV-2 variants – Evolution, spike protein, and vaccines
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Spatial and temporal fluctuations in COVID-19 fatality rates in Brazilian hospitals
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Self-citationContributions of adaptation and purifying selection to SARS-CoV-2 evolution
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“The Gamma variants carry the E484K mutation, causing a 10- to 1,000-fold reduction in the neutralization activities of RBS antibodies, including REGN10933 and LYCoV555, upon monotherapeutic usage (Wang et al., 2021b).”
InfluentialThe ins and outs of SARS-CoV-2 variants of concern (VOCs)
Salehi-Vaziri, ., Fazlalipour, M., Khorrami, S. M. S., Azadmanesh, K., Pouriayevali, M. H., Jalali, T., Shoja, Z., & Maleki, A. (2022) · Archives of Virology · doi:10.1007/s00705-022-05365-2 · Cited by 61
Recent Chronology of COVID-19 Pandemic
Siddiqui, S., Alhamdi, H. W. S., & Alghamdi, H. A. (2022) · Frontiers in Public Health · doi:10.3389/fpubh.2022.778037 · Cited by 80
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“However, even locations that have been hardest hit by the first wave of the epidemic have not gained a lasting protection against future waves (Faria et al., 2021; Sabino et al., 2021).”
BackgroundImpact of temperature on the affinity of SARS-CoV-2 Spike glycoprotein for host ACE2
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Herd immunity is an important—and often misunderstood—public health phenomenon
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SARS-CoV-2 Infectivity and Severity of COVID-19 According to SARS-CoV-2 Variants: Current Evidence
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“Additionally, the VOC P1 was significantly associated with lower Ct values and with an increase in positive samples from 0 to 87% in Manaus, Brazil, between 2 November 2020, and 4 January 2021, suggesting high transmissibility [38].”
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Recent insights into SARS‐CoV‐2 omicron variant
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Rapid replacement of the Beta variant by the Delta variant in South AfricaPreprint
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Preclinical evaluation of a SARS-CoV-2 mRNA vaccine PTX-COVID19-B
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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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