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Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
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 nove...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Association for the Advancement of Science
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139423/ https://www.ncbi.nlm.nih.gov/pubmed/33853970 http://dx.doi.org/10.1126/science.abh2644 |
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author | 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. Schlter, Hannah M. dos Santos, Ana L. P. Vidal, Maria S. Del Caro, Valentina S. Filho, Rosinaldo M. F. dos Santos, Helem M. Aguiar, Renato S. Proena-Modena, Jos L. Nelson, Bruce Hay, James A. Monod, Mlodie Miscouridou, Xenia 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. |
author_facet | 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. Schlter, Hannah M. dos Santos, Ana L. P. Vidal, Maria S. Del Caro, Valentina S. Filho, Rosinaldo M. F. dos Santos, Helem M. Aguiar, Renato S. Proena-Modena, Jos L. Nelson, Bruce Hay, James A. Monod, Mlodie Miscouridou, Xenia 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. |
author_sort | Faria, Nuno R. |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8139423 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | American Association for the Advancement of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-81394232021-05-25 Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil 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. Schlter, Hannah M. dos Santos, Ana L. P. Vidal, Maria S. Del Caro, Valentina S. Filho, Rosinaldo M. F. dos Santos, Helem M. Aguiar, Renato S. Proena-Modena, Jos L. Nelson, Bruce Hay, James A. Monod, Mlodie Miscouridou, Xenia 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. Science Research Articles 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. American Association for the Advancement of Science 2021-05-21 2021-04-14 /pmc/articles/PMC8139423/ /pubmed/33853970 http://dx.doi.org/10.1126/science.abh2644 Text en Copyright 2021 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution license (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles 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. Schlter, Hannah M. dos Santos, Ana L. P. Vidal, Maria S. Del Caro, Valentina S. Filho, Rosinaldo M. F. dos Santos, Helem M. Aguiar, Renato S. Proena-Modena, Jos L. Nelson, Bruce Hay, James A. Monod, Mlodie Miscouridou, Xenia 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. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title_full | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title_fullStr | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title_full_unstemmed | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title_short | Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil |
title_sort | genomics and epidemiology of the p.1 sars-cov-2 lineage in manaus, brazil |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8139423/ https://www.ncbi.nlm.nih.gov/pubmed/33853970 http://dx.doi.org/10.1126/science.abh2644 |
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