Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil-Reference-Cited by-同舟云学术

Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil

Published:2021-05-21 Issue:6544 Volume:372 Page:815-821
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Faria Nuno R.¹²³⁴^ORCID,Mellan Thomas A.¹²^ORCID,Whittaker Charles¹²^ORCID,Claro Ingra M.³⁵^ORCID,Candido Darlan da S.³⁴^ORCID,Mishra Swapnil¹²^ORCID,Crispim Myuki A. E.⁶⁷^ORCID,Sales Flavia C. S.³⁵^ORCID,Hawryluk Iwona¹²^ORCID,McCrone John T.⁸^ORCID,Hulswit Ruben J. G.⁹^ORCID,Franco Lucas A. M.³⁵^ORCID,Ramundo Mariana S.³⁵^ORCID,de Jesus Jaqueline G.³⁵^ORCID,Andrade Pamela S.¹⁰^ORCID,Coletti Thais M.³⁵^ORCID,Ferreira Giulia M.¹¹^ORCID,Silva Camila A. M.³⁵^ORCID,Manuli Erika R.³⁵^ORCID,Pereira Rafael H. M.¹²^ORCID,Peixoto Pedro S.¹³^ORCID,Kraemer Moritz U. G.⁴^ORCID,Gaburo Nelson¹⁴^ORCID,Camilo Cecilia da C.¹⁴^ORCID,Hoeltgebaum Henrique¹⁵^ORCID,Souza William M.¹⁶^ORCID,Rocha Esmenia C.³⁵^ORCID,de Souza Leandro M.³⁵^ORCID,de Pinho Mariana C.³⁵^ORCID,Araujo Leonardo J. T.¹⁷^ORCID,Malta Frederico S. V.¹⁸^ORCID,de Lima Aline B.¹⁸^ORCID,Silva Joice do P.¹⁸^ORCID,Zauli Danielle A. G.¹⁸,Ferreira Alessandro C. de S.¹⁸^ORCID,Schnekenberg Ricardo P.¹⁹^ORCID,Laydon Daniel J.¹²^ORCID,Walker Patrick G. T.¹²^ORCID,Schlüter Hannah M.¹⁵^ORCID,dos Santos Ana L. P.²⁰^ORCID,Vidal Maria S.²⁰^ORCID,Del Caro Valentina S.²⁰^ORCID,Filho Rosinaldo M. F.²⁰,dos Santos Helem M.²⁰,Aguiar Renato S.²¹^ORCID,Proença-Modena José L.²²^ORCID,Nelson Bruce²³^ORCID,Hay James A.²⁴²⁵^ORCID,Monod Mélodie¹⁵,Miscouridou Xenia¹⁵,Coupland Helen¹²^ORCID,Sonabend Raphael¹²^ORCID,Vollmer Michaela¹²^ORCID,Gandy Axel¹⁵^ORCID,Prete Carlos A.²⁶^ORCID,Nascimento Vitor H.²⁶^ORCID,Suchard Marc A.²⁷^ORCID,Bowden Thomas A.⁹^ORCID,Pond Sergei L. K.²⁸,Wu Chieh-Hsi²⁹^ORCID,Ratmann Oliver¹⁵^ORCID,Ferguson Neil M.¹²^ORCID,Dye Christopher⁴^ORCID,Loman Nick J.³⁰^ORCID,Lemey Philippe³¹^ORCID,Rambaut Andrew⁸^ORCID,Fraiji Nelson A.⁶³²,Carvalho Maria do P. S. S.⁶³³^ORCID,Pybus Oliver G.⁴³⁴^ORCID,Flaxman Seth¹⁵^ORCID,Bhatt Samir¹²³⁵^ORCID,Sabino Ester C.³⁵^ORCID

Affiliation:

1. MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK.

2. The Abdul Latif Jameel Institute for Disease and Emergency Analytics (J-IDEA), School of Public Health, Imperial College London, London, UK.

3. Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.

4. Department of Zoology, University of Oxford, Oxford, UK.

5. Departamento de Moléstias Infecciosas e Parasitárias, Faculdade de Medicina da Universidade de São Paulo, São Paulo, Brazil.

6. Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.

7. Diretoria de Ensino e Pesquisa, Fundação Hospitalar de Hematologia e Hemoterapia, Manaus, Brazil.

8. Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.

9. Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.

10. Departamento de Epidemiologia, Faculdade de Saúde Pública da Universidade de São Paulo, Sao Paulo, Brazil.

11. Laboratório de Virologia, Instituto de Ciências Biomédicas, Universidade Federal de Uberlândia, Uberlândia, Brazil.

12. Institute for Applied Economic Research–Ipea, Brasília, Brazil.

13. Institute of Mathematics and Statistics, University of São Paulo, São Paulo, Brazil.

14. DB Diagnósticos do Brasil, São Paulo, Brazil.

15. Department of Mathematics, Imperial College London, London, UK.

16. Virology Research Centre, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil.

17. Laboratory of Quantitative Pathology, Center of Pathology, Adolfo Lutz Institute, São Paulo, Brazil.

18. Instituto Hermes Pardini, Belo Horizonte, Brazil.

19. Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK.

20. CDL Laboratório Santos e Vidal, Manaus, Brazil.

21. Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil.

22. Laboratory of Emerging Viruses, Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas (UNICAMP), São Paulo, Brazil.

23. Instituto Nacional de Pesquisas da Amazônia, Manaus, Brazil.

24. Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

25. Center for Communicable Disease Dynamics, Harvard T. H. Chan School of Public Health, Boston, MA, USA.

26. Departamento de Engenharia de Sistemas Eletrônicos, Escola Politécnica da Universidade de São Paulo, São Paulo, Brazil.

27. Department of Biomathematics, Department of Biostatistics, and Department of Human Genetics, University of California, Los Angeles, CA, USA.

28. Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA, USA.

29. Mathematical Sciences, University of Southampton, Southampton, UK.

30. Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK.

31. Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.

32. Diretoria Clínica, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.

33. Diretoria da Presidência, Fundação Hospitalar de Hematologia e Hemoterapia do Amazonas, Manaus, Brazil.

34. Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, UK.

35. Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark.

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

Funder

Medical Research Council

National Institute for Health Research

Wellcome Trust and Royal Society

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

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