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

Faria, NR; Mellan, TA; Whittaker, C; Claro, IM; Candido, DD; 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, CD; Hoeltgebaum, H; Souza, WM; Rocha, EC; de Souza, LM; de Pinho, MC; Araujo, LJT; Malta, FSV; de Lima, AB; Silva, JD; Zauli, DAG; Ferreira, ACD; Schnekenberg, RP; Laydon, DJ; Walker, PGT; Schluter, HM; dos Santos, ALP; Vidal, MS; Del Caro, VS; Filho, RMF; dos Santos, HM; Aguiar, RS; Proenca-Modena, JLP; Nelson, B; Hay, JA; Monod, M; Miscouridou, X; Coupland, H; Sonabend, R; Vollmer, M; Gandy, A; Prete, CA; Nascimento, VH; Suchard, MA; Bowden, TA; Pond, SLK; Wu, CH; Ratmann, O; Ferguson, NM; Dye, C; Loman, NJ; Lemey, P; Rambaut, A; Fraiji, NA; Carvalho, MDSS; Pybus, OG; Flaxman, S; Bhatt, S; Sabino, EC

Authors

NR Faria

TA Mellan

C Whittaker

IM Claro

DD Candido

S Mishra

MAE Crispim

FC Sales

I Hawryluk

JT McCrone

RJG Hulswit

LAM Franco

MS Ramundo

JG de Jesus

PS Andrade

TM Coletti

GM Ferreira

CAM Silva

ER Manuli

RHM Pereira

PS Peixoto

MU Kraemer

N Gaburo

CD Camilo

H Hoeltgebaum

WM Souza

EC Rocha

LM de Souza

MC de Pinho

LJT Araujo

FSV Malta

AB de Lima

JD Silva

DAG Zauli

ACD Ferreira

RP Schnekenberg

DJ Laydon

PGT Walker

HM Schluter

ALP dos Santos

MS Vidal

VS Del Caro

RMF Filho

HM dos Santos

RS Aguiar

JLP Proenca-Modena

B Nelson

JA Hay

M Monod

X Miscouridou

H Coupland

R Sonabend

M Vollmer

A Gandy

CA Prete

VH Nascimento

MA Suchard

TA Bowden

SLK Pond

CH Wu

O Ratmann

NM Ferguson

C Dye

NJ Loman

P Lemey

A Rambaut

NA Fraiji

MDSS Carvalho

OG Pybus

S Flaxman

S Bhatt

EC Sabino



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.

Citation

Faria, N., Mellan, T., Whittaker, C., Claro, I., Candido, D., Mishra, S., …Sabino, E. (2021). Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil. Science, 372(6544), 815-+. https://doi.org/10.1126/science.abh2644

Journal Article Type Article
Acceptance Date Apr 11, 2021
Publication Date 2021
Deposit Date Jan 13, 2022
Publicly Available Date Feb 4, 2022
Print ISSN 0036-8075
Publisher American Association for the Advancement of Science
Peer Reviewed Peer Reviewed
Volume 372
Issue 6544
Pages 815-+
DOI https://doi.org/10.1126/science.abh2644
Keywords RESPIRATORY-SYNDROME-CORONAVIRUS; RECEPTOR-BINDING DOMAIN; LOCAL TRANSMISSION; MOLECULAR CLOCK; PERFORMANCE; DYNAMICS; COVID-19; SITES
Public URL https://rvc-repository.worktribe.com/output/1555689

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