Journal
SCIENCE
Volume 372, Issue 6544, Pages 815-+Publisher
AMER ASSOC ADVANCEMENT SCIENCE
DOI: 10.1126/science.abh2644
Keywords
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Categories
Funding
- Medical Research Council-Sao Paulo Research Foundation (FAPESP) CADDE partnership award [MR/S0195/1, FAPESP 18/14389-0]
- FAPESP [2018/25468-9, 2018/17176-8, 2019/12000-1, 18/14389-0, 2019/07544-2, 2019/21301-5, 2017/13981-0, 2019/24251-9, 2020/04272-9, 2019/21568-1, 2018/12579-7, 2019/21858-0, 16/18445-7, 2020/04558-0]
- Wellcome Trust
- Royal Society [204311/Z/16/Z]
- Wellcome Trust [203141/Z/16/Z]
- Clarendon Fund and Department of Zoology, University of Oxford
- Medical Research Council [MR/S007555/1]
- European Molecular Biology Organisation [ALTF 869-2019]
- CNPq [312688/2017-2, 439119/2018-9, 408338/2018-0, 304714/2018-6]
- FAPERJ [202.922/2018]
- FFMUSP [206.706]
- Imperial College COVID-19 Research Fund
- CAPES [001]
- Wellcome Trust Collaborator Award [206298/Z/17/Z]
- European Research Council [725422-ReservoirDOCS]
- European Union's Horizon 2020 project MOOD [874850]
- U.S. National Institutes of Health [U19 AI135995]
- Oxford Martin School
- Branco Weiss Fellowship
- Covid-19 Research Fund
- EPSRC [EP/V002910/1]
- BMGF
- Novo Nordisk Foundation
- Academy of Medical Sciences
- BRC
- MRC
- Bill & Melinda Gates Foundation [OPP1175094]
- Rede Corona-oica BR MCTI/FINEP [FINEP 01.20.0029.000462/20]
- Rede Corona-oica BR MCTI/FINEP (CNPq) [404096/2020-4]
- EPSRC Centre for Doctoral Training in Modern Statistics and Statistical Machine Learning at Imperial and Oxford
- UK Medical Research Council
- UK Department for International Development
- Community Jameel
- NIHR Health Protection Research Unit in Modelling Methodology
- Oxford Nanopore Technologies
- NVIDIA Corporation
- Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [16/18445-7, 19/12000-1, 19/21858-0, 20/04558-0, 18/14389-0] Funding Source: FAPESP
- MRC [MR/S019510/1] Funding Source: UKRI
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A new variant of concern, P.1, with 17 mutations including three spike protein mutations associated with increased binding to human ACE2 receptors, emerged in Manaus, Brazil between November 2020 and January 2021. Molecular analysis suggests P.1 may be 1.7- to 2.4-fold more transmissible and that previous infection may provide 54 to 79% protection against P.1 infection compared to other lineages. Enhanced global genomic surveillance of such variants is crucial for pandemic response.
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.
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