NR Faria
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
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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