Cargando…

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Association for the Advancement of Science 2021
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
_version_ 1783696003694592000
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
work_keys_str_mv AT farianunor genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT mellanthomasa genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT whittakercharles genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT claroingram genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT candidodarlandas genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT mishraswapnil genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT crispimmyukiae genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT salesflaviacs genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT hawrylukiwona genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT mccronejohnt genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT hulswitrubenjg genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT francolucasam genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT ramundomarianas genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT dejesusjaquelineg genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT andradepamelas genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT colettithaism genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT ferreiragiuliam genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT silvacamilaam genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT manulierikar genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT pereirarafaelhm genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT peixotopedros genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT kraemermoritzug genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT gaburonelson genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT camiloceciliadac genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT hoeltgebaumhenrique genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT souzawilliamm genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT rochaesmeniac genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT desouzaleandrom genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT depinhomarianac genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT araujoleonardojt genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT maltafredericosv genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT delimaalineb genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT silvajoicedop genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT zaulidanielleag genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT ferreiraalessandrocdes genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT schnekenbergricardop genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT laydondanielj genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT walkerpatrickgt genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT schlterhannahm genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT dossantosanalp genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT vidalmarias genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT delcarovalentinas genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT filhorosinaldomf genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT dossantoshelemm genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT aguiarrenatos genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT proenamodenajosl genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT nelsonbruce genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT hayjamesa genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT monodmlodie genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT miscouridouxenia genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT couplandhelen genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT sonabendraphael genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT vollmermichaela genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT gandyaxel genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT pretecarlosa genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT nascimentovitorh genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT suchardmarca genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT bowdenthomasa genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT pondsergeilk genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT wuchiehhsi genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT ratmannoliver genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT fergusonneilm genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT dyechristopher genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT lomannickj genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT lemeyphilippe genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT rambautandrew genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT fraijinelsona genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT carvalhomariadopss genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT pybusoliverg genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT flaxmanseth genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT bhattsamir genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil
AT sabinoesterc genomicsandepidemiologyofthep1sarscov2lineageinmanausbrazil