Abstract

Cases of 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 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 1.7-2.4-fold more transmissible, and that previous (non-P.1) infection provides 54-79% 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.

Rights

This content is not covered by the Open Government Licence. Please see source record or item for information on rights and permissions.

Cite as

Faria, N., Mellan, T., Whittaker, C., Claro, I., Candido, D., Mishra, S., Crispim, M., Sales, F., Hawryluk, I., McCrone, J., Hulswit, R., Franco, L., Ramundo, M., de Jesus, J., Andrade, P., Coletti, T., Ferreira, G., Silva, C., Manuli, E., Pereira, R., Peixoto, P., Kraemer, M., Gaburo, N., Camilo, C., Hoeltgebaum, H., Souza, W., Rocha, E., de Souza, L., de Pinho, M., Araujo, L., Malta, F., de Lima, A., Silva, J., Zauli, D., Ferreira, A., Schnekenberg, R., Laydon, D., Walker, P., Schlüter, H., Dos Santos, A., Vidal, M., Del Caro, V., Filho, R., Dos Santos, H., Aguiar, R., Proença-Modena, J., Nelson, B., Hay, J., Monod, M., Miscouridou, X., Coupland, H., Sonabend, R., Vollmer, M., Gandy, A., Prete, C., Nascimento, V., Suchard, M., Bowden, T., Pond, S., Wu, C., Ratmann, O., Ferguson, N., Dye, C., Loman, N., Lemey, P., Rambaut, A., Fraiji, N., Carvalho, M., Pybus, O., Flaxman, S., Bhatt, S. & Sabino, E. 2021, 'Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil', Science. https://doi.org/10.1126/science.abh2644

Downloadable citations

Download HTML citationHTML Download BIB citationBIB Download RIS citationRIS
Last updated: 17 June 2023
Was this page helpful?