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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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“…was conducted at the end of the year 2020 but since then, as in most countries, the emergence of variants has dramatically altered epidemiological dynamics in France [19,20] and early reports suggest that the Ct value measured could depend on the variant causing the infection [21,22,23,24,25].”
OLIVEIRA, E. A., MAK, R. H. K., Colosimo, E. A., Mendonça, A. C. Q., Vasconcelos, M. A., Júnior, H. M., Silva, L. R., Oliveira, M. C. L., Pinhati, C. C., & Silva, A. C. S. E. (2022) · Pediatric Diabetes · doi:10.1111/pedi.13335 · Cited by 17
“The rationality in separate the sample into two waves was due to the emergence of the Gamma variant identified in January 2021 in the city Manaus, Brazil.(14) This lineage became predominant in Brazil around February 2021 and was characterized by an increased transmissibility and with more severe spectrum of the disea…”
BackgroundYadav, P. D., Mohandas, S., Sarkale, P., Nyayanit, D. A., Shete, A. M., Sahay, R. R., Potdar, V. A., Baradkar, S., Gupta, N., Sapkal, G. N., et al. (2021) · Journal of Infection and Public Health · doi:10.1016/j.jiph.2021.12.009 · Cited by 16
Shah, M., Moon, S. U., Kim, J. H., Thao, T. T., & Woo, H. G. (2022) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2022.04.030 · Cited by 15
“The Gamma variants have been associated with adverse disease symptoms and even infected a person who has recovered from a previous infection, although this claim needded further definitive data support [11].”
Zhou, H., Ni, W., Huang, W., Wang, Z., Cai, M., & Sun, Y.-C. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.834942 · Cited by 17
Wang, H.-I., Sun, K., & Wang, Y. (2022) · International Journal of Environmental Research and Public Health · doi:10.3390/ijerph19148377 · Cited by 16
“Some variants have very high transmissibility, such as the delta variant, which has been shown to be 40% to 60% more transmissible than the alpha variant [2], while others alter the antigenicity of the virus to evade immunity from vaccination or prior infection, such as the beta [3] and gamma [4] variants.”
BackgroundYurkovetskiy, L., Egri, S. B., Kurhade, C., Díaz-Salinas, M. A., Jaimes, J. A., Nyalile, T., Xie, X., Choudhary, M. C., Dauphin, A., Li, J. Z., et al. (2023) · SSRN Electronic Journal · doi:10.1101/2023.03.30.535005 · Cited by 18
Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil
Sant’Anna, F. H., Varela, A. P. M., Prichula, J., Comerlato, J., Comerlato, C. B., Roglio, V. S., Pereira, G. F. M., Moreno, F. F., Seixas, A., & Wendland, E. (2021) · Emerging Microbes & Infections · doi:10.1080/22221751.2021.1949948 · Cited by 16
“considering its higher transmissibility than the previous other Brazilian lineages [22].”
BackgroundIncidence Trends for SARS-CoV-2 Alpha and Beta Variants, Finland, Spring 2021
Kant, R., Nguyen, P. T., Blomqvist, S., Erdin, M., Alburkat, H., Suvanto, M. T., Zakham, F., Salminen, V., Olander, V., Paloniemi, M., et al. (2021) · Emerging infectious diseases · doi:10.3201/eid2712.211631 · Cited by 16
Stability of SARS-CoV-2 and other airborne viruses under different stress conditions
Fumagalli, M. J., Capato, C. F., de Castro-Jorge, L. A., de Souza, W. M., Arruda, E., & Figueiredo, L. T. M. (2021) · Archives of Virology · doi:10.1007/s00705-021-05293-7 · Cited by 16
Self-citationGrubaugh, N. D., & Cobey, S. E. (2021) · Cell · doi:10.1016/j.cell.2021.11.013 · Cited by 16
Repurposing of Drugs for SARS-CoV-2 Using Inverse Docking Fingerprints
Jukič, M., Kores, K., Janežič, D., & Bren, U. (2021) · Frontiers in Chemistry · doi:10.3389/fchem.2021.757826 · Cited by 18
Timofeeva, A. M., Sedykh, S. E., & Nevinsky, G. A. (2022) · Vaccines · doi:10.3390/vaccines10030384 · Cited by 17
de Araújo, J. L. F., Menezes, D., Aguiar, R. S., & de Souza, R. P. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.775246 · Cited by 16
“Some VOCs have been associated with higher viral load, worse prognosis, and lethality (Davies et al., 2021; Faria et al., 2021), thus, confounding factors when evaluating genetic effects.”
Self-citationMartinez, M., Nguyen, P.-V., Su, M., Cardozo, F., Valenzuela, A., Franco, L. X., Galeano, M. E., Rojas, L. E., Acosta, C. C. D., Fernández, J., et al. (2022) · Viruses · doi:10.3390/v14050873 · Cited by 16
“MinION sequencing was well described for SARS-CoV-2 and provides formal confirmation of detected variants and lineages, which cannot be achieved using rRT-PCR alone [4,5,25,31].”
MethodResultSelf-citationMolina-Mora, J. A. (2022) · Gene Reports · doi:10.1016/j.genrep.2022.101554 · Cited by 16
Marco, C. D., Veneziano, C., Massacci, A., Pallocca, M., Marascio, N., Quirino, A., Barreca, G. S., Giancotti, A., Gallo, L., Lamberti, A. G., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.934993 · Cited by 16
Delshad, M., Sanaei, M., Pourbagheri‐Sigaroodi, A., & Bashash, D. (2022) · International Immunopharmacology · doi:10.1016/j.intimp.2022.109128 · Cited by 18
SARS-CoV-2 Variants, Current Vaccines and Therapeutic Implications for COVID-19
Liang, H., Wu, Y., Yau, V., Yin, H.-X., Lowe, S., Bentley, R., Ahmed, M. A., Zhao, W., & Sun, C. (2022) · Vaccines · doi:10.3390/vaccines10091538 · Cited by 16
Localized delivery of nanomedicine and antibodies for combating COVID-19
Tu, B., Gao, Y., An, X., Wang, H., & Huang, Y. (2022) · Acta Pharmaceutica Sinica B · doi:10.1016/j.apsb.2022.09.011 · Cited by 16
SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia
Meganck, R. M., Edwards, C. E., Mallory, M. L., Lee, R. E., Dang, H., Bailey, A. B., Wykoff, J. A., Gallant, S. C., Zhu, D. R., Yount, B. L., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.114076 · Cited by 17
de Souza, U. J. B., dos Santos, R. N., Campos, F. S., Lourenço, K. L., da Fonseca, F. G., Spilki, F. R., & Corona-ômica.BR/MCTI Network (2021) · Viruses · doi:10.3390/v13091806 · Cited by 16
“…the moment, the world’s concern is focused in about four functionally well-defined variants, B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) associated with viral fitness changes (Faria et al., 2021; Hodcroft, 2021; McCallum et al., 2021; Tang et al., 2021; Tegally et al., 2021).”
BackgroundInfluentialNörz, D. S., Grunwald, M., Tang, H. T., Olearo, F., Günther, T., Robitaille, A., Fischer, N., Grundhoff, A. T., Aepfelbacher, M., Pfefferle, S., et al. (2021) · Diagnostics · doi:10.3390/diagnostics11101818 · Cited by 16
de Souza, U. J. B., dos Santos, R. N., de Melo, F. L., Belmok, A., Galvão, J. D., de Rezende, T. C. V., Cardoso, F. D. P., Carvalho, R. F., Oliveira, M. D. S., Júnior, J. C. R., et al. (2022) · Viruses · doi:10.3390/v14040659 · Cited by 15
Virulence Profiles of Wild-Type, P.1 and Delta SARS-CoV-2 Variants in K18-hACE2 Transgenic Mice
Santos, Y. D. S., Gamon, T. H. M., de Azevedo, M. S. P., Telezynski, B. L., de Souza, E. E., Oliveira, D. B. L., Dombrowski, J. G., Rosa-Fernandes, L., Palmisano, G., Carvalho, L. J. M., et al. (2023) · Viruses · doi:10.3390/v15040999 · Cited by 16
“1 variant was identified in Manaus (AM, Brazil), causing widespread infection despite the high seroprevalence against the Wt SARS-CoV-2 strain observed in the city [21].”
BackgroundMallm, J., Bundschuh, C., Kim, H., Weidner, N., Steiger, S., Lander, I., Börner, K., Bauer, K., Hübschmann, D., Beneš, V., et al. (2021) · medRxiv · doi:10.1101/2021.04.27.21254849 · Cited by 16
Huang, D., Liu, Y., Wang, G. A., Lv, S., Tan, Y., & Li, F. (2025) · Chemical Society Reviews · doi:10.1039/d5cs01006c · Cited by 17
Cellular senescence as a source of SARS‐CoV‐2 quasispecies
Karakasiliοtis, I., Lаgopati, N., Evangelou, K., & Gorgoulis, V. G. (2021) · FEBS Journal · doi:10.1111/febs.16230 · Cited by 15
Analysis of SARS-COV2 spike protein variants among Iraqi isolates
Sabir, D. K. (2021) · Gene Reports · doi:10.1016/j.genrep.2021.101420 · Cited by 15
SARS-CoV-2 Variants: Mutations and Effective Changes
Park, G., & Hwang, B. H. (2021) · Biotechnology and Bioprocess Engineering · doi:10.1007/s12257-021-0327-3 · Cited by 17
Li, D., Li, A.-E., Li, Z.-Q., Bao, Y., Liu, T., Qin, X., & Yu, X. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.856757 · Cited by 15
Tyagi, N., Sardar, R., & Gupta, D. K. (2022) · PeerJ · doi:10.7717/peerj.13562 · Cited by 15
A vaccine delivery system promotes strong immune responses against SARS‐CoV‐2 variants
Lei, Z., Zhu, L., Pan, P., Ruan, Z., Gu, Y., Xia, X., Wang, S., Ge, W., Yao, Y., Luo, F., et al. (2023) · Journal of Medical Virology · doi:10.1002/jmv.28475 · Cited by 16
Emergence and competition of virus variants in respiratory viral infections
Bessonov, N., Neverova, D., Попов, В. А., & Volpert, V. A. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2022.945228 · Cited by 15
Challenges in Emerging Vaccines and Future Promising Candidates against SARS‐CoV‐2 Variants
Ghildiyal, T., Rai, N., Rawat, J. M., Singh, M., Anand, J., Pant, G., Kumar, G., & Shidiki, A. (2024) · Journal of Immunology Research · doi:10.1155/2024/9125398 · Cited by 16
“In contrast to VOCs beta, the K417N/T transformation revealed a lower binding af fi nity for gamma VOCs [52].”
ResultTinjauan Molekuler dan Epidemiologi Mutasi pada Virus SARS-CoV-2
Hartono, H., & Yusuf, Y. (2021) · bionature · doi:10.35580/bionature.v22i1.22379 · Cited by 15
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
About these checks
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