Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.
Faria NR., Mellan TA., Whittaker C., Claro IM., Candido DDS., Mishra S., Crispim MAE., Sales FC., Hawryluk I., McCrone JT., Hulswit RJG., Franco LAM., Ramundo MS., de Jesus JG., Andrade PS., Coletti TM., Ferreira GM., Silva CAM., Manuli ER., Pereira RHM., Peixoto PS., Kraemer MU., Gaburo N., Camilo CDC., Hoeltgebaum H., Souza WM., Rocha EC., de Souza LM., de Pinho MC., Araujo LJT., Malta FSV., de Lima AB., Silva JDP., Zauli DAG., de S Ferreira AC., Schnekenberg RP., Laydon DJ., Walker PGT., Schlüter HM., Dos Santos ALP., Vidal MS., Del Caro VS., Filho RMF., Dos Santos HM., Aguiar RS., Modena JLP., Nelson B., Hay JA., Monod M., Miscouridou X., Coupland H., Sonabend R., Vollmer M., Gandy A., Suchard MA., Bowden TA., Pond SLK., Wu C-H., Ratmann O., Ferguson NM., Dye C., Loman NJ., Lemey P., Rambaut A., Fraiji NA., Carvalho MDPSS., Pybus OG., Flaxman S., Bhatt S., Sabino EC.
Cases 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 Summary: We report the evolution and emergence of a SARS-CoV-2 lineage of concern associated with rapid transmission in Manaus.