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

Author(s):Show less -

Faria, Nuno R. ^{[1, 2, 3, 4]} ; Mellan, Thomas A. ^{[2, 4]} ; Whittaker, Charles ^{[2, 4]} ; Claro, Ingra M. ^{[3, 5]} ; Candido, Darlan da S. ^{[1, 3]} ; Mishra, Swapnil ^{[2, 4]} ; Crispim, Myuki A. E. ^{[6, 7]} ; Sales, Flavia C. ^{[3, 5]} ; Hawryluk, Iwona ^{[2, 4]} ; McCrone, John T. ^[8] ; Hulswit, Ruben J. G. ^[9] ; Franco, Lucas A. M. ^{[3, 5]} ; Ramundo, Mariana S. ^{[3, 5]} ; de Jesus, Jaqueline G. ^{[3, 5]} ; Andrade, Pamela S. ^[10] ; Coletti, Thais M. ^{[3, 5]} ; Ferreira, Giulia M. ^[11] ; Silva, Camila A. M. ^{[3, 5]} ; Manuli, Erika R. ^{[3, 5]} ; Pereira, Rafael H. M. ^[12] ; Peixoto, Pedro S. ^[13] ; Kraemer, Moritz U. ^[1] ; Gaburo, Jr., Nelson ^[14] ; Camilo, Cecilia da C. ^[14] ; Hoeltgebaum, Henrique ^[15] ; Souza, William M. ^[16] ; Rocha, Esmenia C. ^{[3, 5]} ; de Souza, Leandro M. ^{[3, 5]} ; de Pinho, Mariana C. ^{[3, 5]} ; Araujo, Leonardo J. T. ^[17] ; Malta, V, Frederico S. ; de Lima, Aline B. ^[18] ; Silva, Joice do P. ^[18] ; Zauli, Danielle A. G. ^[18] ; Ferreira, Alessandro C. de S. ^[18] ; Schnekenberg, Ricardo P. ^[19] ; Laydon, Daniel J. ^{[2, 4]} ; Walker, Patrick G. T. ^{[2, 4]} ; Schlueter, Hannah M. ^[15] ; dos Santos, Ana L. P. ^[20] ; Vidal, Maria S. ^[20] ; Del Caro, Valentina S. ^[20] ; Filho, Rosinaldo M. F. ^[20] ; dos Santos, Helem M. ^[20] ; Aguiar, Renato S. ^[21] ; Proenca-Modena, Jose L. P. ^[22] ; Nelson, Bruce ^[23] ; Hay, James A. ^{[24, 25]} ; Monod, Melodie ^[15] ; Miscouridou, Xenia ^[15] ; Coupland, Helen ^{[2, 4]} ; Sonabend, Raphael ^{[2, 4]} ; Vollmer, Michaela ^{[2, 4]} ; Gandy, Axel ^[15] ; Prete, Jr., Carlos A. ^[26] ; Nascimento, Vitor H. ^[26] ; Suchard, Marc A. ^{[27, 28]} ; Bowden, Thomas A. ^[9] ; Pond, Sergei L. K. ^[29] ; Wu, Chieh-Hsi ^[30] ; Ratmann, Oliver ^[15] ; Ferguson, Neil M. ^{[2, 4]} ; Dye, Christopher ^[1] ; Loman, Nick J. ^[31] ; Lemey, Philippe ^[32] ; Rambaut, Andrew ^[8] ; Fraiji, Nelson A. ^{[33, 6]} ; Carvalho, Maria do P. S. S. ^{[33, 6]} ; Pybus, Oliver G. ^{[1, 34]} ; Flaxman, Seth ^[15] ; Bhatt, Samir ^{[2, 4, 35]} ; Sabino, Ester C. ^{[3, 5]}

Affiliation:Show less -

^[1] Univ Oxford, Dept Zool, Oxford - England

^[2] Imperial Coll London, MRC Ctr Global Infect Dis Anal, Sch Publ Hlth, London - England

^[3] Univ Sao Paulo, Inst Med Trop, Fac Med, Sao Paulo - Brazil

^[4] Imperial Coll London, Abdul Latif Lamed Inst Dis & Emergency Analyt J I, Sch Publ Hlth, London - England

^[5] Univ Sao Paulo, Fac Med, Dept Molestias Infecciosas & Parasitaries, Sao Paulo - Brazil

^[6] Fundacao Hosp Hematol & Hemoterapia, Manaus, Amazonas - Brazil

^[7] Fundacao Hosp Hematol & Hemoterapia, Ensino & Pesquisa, Manaus, Amazonas - Brazil

^[8] Univ Edinburgh, Inst Evolutionary Biol, Edinburgh, Midlothian - Scotland

^[9] Univ Oxford, Wellcome Ctr Human Genet, Div Struct Biol, Oxford - England

^[10] Univ Sao Paulo, Fac Saude Publ, Dept Epidemiol, Sao Paulo - Brazil

^[11] Univ Fed Uberlandia, Inst Ciencias Biomed, Lab Virol, Uberlandia, MG - Brazil

^[12] Inst Appl Econ Res IPEA, Brasilia, DF - Brazil

^[13] Univ Sao Paulo, Inst Math & Stat, Sao Paulo - Brazil

^[14] DB Diagndst Brasil, Sao Paulo - Brazil

^[15] Imperial Coll London, Dept Math, London - England

^[16] Univ Sao Paulo, Ribeirao Preto Med Sch, Virol Res Ctr, Ribeirao Preto, SP - Brazil

^[17] Adolfo Lutz Inst, Ctr Pathol, Lab Quantitat Pathol, Sao Paulo - Brazil

^[18] Malta, Frederico S., V, Inst Hermes Pardini, Belo Horizonte, MG - Brazil

^[19] Univ Oxford, Nuffield Dept Clin Neurosci, Oxford - England

^[20] CDL Lab Santos & Vidal, Manaus, Amazonas - Brazil

^[21] Univ Fed Minas Gerais, Inst Ciencias Biol, Dept Genet Ecol & Evolucao, Belo Horizonte, MG - Brazil

^[22] Univ Estadual Campinas, UNICAMP, Inst Biol, Dept Genet Evolut Microbiol & Immunol, Lab Emergin, Sao Paulo - Brazil

^[23] Inst Nacl de Pesquisas da Amazonia, Manaus, Amazonas - Brazil

^[24] Harvard TH Chan Sch Publ Hlth, Dept Epidemiol, Boston, MA - USA

^[25] Harvard TH Chan Sch Publ Hlth, Ctr Communicable Dis Dynam, Boston, MA - USA

^[26] Univ Sao Paulo, Escola Politecn, Dept Engn Sistemas Eletron, Sao Paulo - Brazil

^[27] Univ Calif Los Angeles, Dept Biomath, Dept Blostat, Los Angeles, CA - USA

^[28] Univ Calif Los Angeles, Dept Human Genet, Los Angeles, CA - USA

^[29] Temple Univ, Inst Genom & Evolutionary Med, Philadelphia, PA 19122 - USA

^[30] Univ Southampton, Math Sci, Southampton, Hants - England

^[31] Univ Birmingham, Inst Microbiol & Infect, Birmingham, W Midlands - England

^[32] Katholieke Univ Leuven, Rega Inst, Dept Microbiol Immunol & Transplantat, Leuven - Belgium

^[33] Fundacao Hosp Hematol & Hemoterapia Amazonas, Manaus, Amazonas - Brazil

^[34] Royal Vet Coll, Dept Pathobiol & Populat Sci, London - England

^[35] Univ Copenhagen, Sect Epidemiol, Dept Publ Hlth, Copenhagen - Denmark

• Document type: Journal article
• Source: Science; v. 372, n. 6544, p. 815+, MAY 21 2021.
• Web of Science Citations: 224

Abstract

Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-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 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against 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. (AU)

• FAPESP's process: 20/04558-0 - Characterization of intrinsic risk factors and the development of new diagnostic and treatment alternatives for COVID-19
• Grantee: José Luiz Proença Módena
• Support Opportunities: Regular Research Grants
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• FAPESP's process: 19/12000-1 - Modeling of the spatiotemporal dispersion of emergent arboviruses using heterogeneous data sources in the State of São Paulo
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