Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil
Author:
Faria Nuno R.ORCID, 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. 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., Schlüter 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., Modena José L. P., Nelson Bruce, Hay James A., Monod Melodie, Miscouridou Xenia, Coupland Helen, Sonabend Raphael, Vollmer Michaela, Gandy Axel, 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.
Abstract
AbstractCases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that 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 early 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 1.4–2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with 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.One-Sentence SummaryWe report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.
Publisher
Cold Spring Harbor Laboratory
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