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

Author

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

Subjects
Human Genome, Immunization, Pneumonia & Influenza, Lung, Prevention, Genetics, Vaccine Related, Biotechnology, Pneumonia, Emerging Infectious Diseases, Biodefense, Infectious Diseases, Infection, Good Health and Well Being, Angiotensin-Converting Enzyme 2, Brazil, COVID-19, Communicable Diseases, Emerging, Epidemiological Monitoring, Genome, Viral, Genomics, Humans, Models, Theoretical, Molecular Epidemiology, Mutation, Protein Binding, SARS-CoV-2, Spike Glycoprotein, Coronavirus, Viral Load, General Science & Technology
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.

Published
2021

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

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., 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., 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., 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., Schlueter, 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., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, 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., Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C., 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., 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., 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., Schlueter, 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., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, 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, and Sabino, Ester C.

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.

Published
2021

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