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Faria NR, Mellan TA, Whittaker C, et al. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. medRxiv. 2021;doi: 10.1101/2021.02.26.21252554.
Faria, N. R., Mellan, T. A., Whittaker, C., Claro, I. M., Candido, D. D. S., Mishra, S., Crispim, M. A. E., Sales, F. C., 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., 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., de S Ferreira, A. C., 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., Modena, J. L. P., Nelson, B., Hay, J. A., Monod, M., Miscouridou, X., Coupland, H., Sonabend, R., Vollmer, M., Gandy, A., 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. (2021). Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. medRxiv : the preprint server for health sciences, . https://doi.org/10.1101/2021.02.26.21252554
Faria, Nuno R, et al. "Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil." medRxiv : the preprint server for health sciences vol. (2021). doi: https://doi.org/10.1101/2021.02.26.21252554
Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, Sabino EC. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil. medRxiv. 2021 Mar 03; doi: 10.1101/2021.02.26.21252554. PMID: 33688664; PMCID: PMC7941639.
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medRxiv. 2021 Mar 03; doi: 10.1101/2021.02.26.21252554.

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.

medRxiv : the preprint server for health sciences

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

Affiliations

  1. Department of Infectious Disease Epidemiology, Imperial College London, UK.
  2. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
  3. Department of Zoology, University of Oxford, UK.
  4. Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.
  5. Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.
  6. Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.
  7. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
  8. Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
  9. Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil.
  10. Institute for Applied Economic Research - Ipea, Brasília, Brazil.
  11. Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil.
  12. DB Diagnósticos do Brasil, São Paulo, Brazil.
  13. CDL Laboratório Santos e Vidal, Manaus, Brazil.
  14. Department of Mathematics, Imperial College London, UK.
  15. Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.
  16. Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil.
  17. Instituto Hermes Pardini, Brazil.
  18. Nuffield Department of Clinical Neurosciences, University of Oxford, UK.
  19. Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.
  20. Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil.
  21. Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.
  22. Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, USA.
  23. Center for Communicable Disease Dynamics, Harvard T H Chan School of Public Health, Boston, MA, USA.
  24. Department of Biomathematics, Department of Biostatistics and Department of Human Genetics, University of California, Los Angeles, CA, USA.
  25. Institute for Genomics and Evolutionary Medicine, Temple University, USA.
  26. Mathematical Sciences, University of Southampton, Southampton, UK.
  27. Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.
  28. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
  29. Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.
  30. Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.
  31. Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK.
  32. Section of Epidemiology, Department of Public Health, University of Copenhagen, Denmark.

PMID: 33688664 PMCID: PMC7941639 DOI: 10.1101/2021.02.26.21252554

Abstract

Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.

ONE-SENTENCE SUMMARY: We report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.

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