Dataset Information

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.

ABSTRACT: 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.

SUBMITTER: Faria NR

PROVIDER: S-EPMC7941639 | biostudies-literature | 2021 Mar

REPOSITORIES: biostudies-literature

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Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.

Faria Nuno R NR Mellan Thomas A TA Whittaker Charles C Claro Ingra M IM Candido Darlan da S DDS Mishra Swapnil S Crispim Myuki A E MAE Sales Flavia C FC Hawryluk Iwona I McCrone John T JT Hulswit Ruben J G RJG Franco Lucas A M LAM Ramundo Mariana S MS de Jesus Jaqueline G JG Andrade Pamela S PS Coletti Thais M TM Ferreira Giulia M GM Silva Camila A M CAM Manuli Erika R ER Pereira Rafael H M RHM Peixoto Pedro S PS Kraemer Moritz U MU Gaburo Nelson N Camilo Cecilia da C CDC Hoeltgebaum Henrique H Souza William M WM Rocha Esmenia C EC de Souza Leandro M LM de Pinho Mariana C MC Araujo Leonardo J T LJT Malta Frederico S V FSV de Lima Aline B AB Silva Joice do P JDP Zauli Danielle A G DAG de S Ferreira Alessandro C AC Schnekenberg Ricardo P RP Laydon Daniel J DJ Walker Patrick G T PGT Schlüter Hannah M HM Dos Santos Ana L P ALP Vidal Maria S MS Del Caro Valentina S VS Filho Rosinaldo M F RMF Dos Santos Helem M HM Aguiar Renato S RS Modena José L P JLP Nelson Bruce B Hay James A JA Monod Melodie M Miscouridou Xenia X Coupland Helen H Sonabend Raphael R Vollmer Michaela M Gandy Axel A Suchard Marc A MA Bowden Thomas A TA Pond Sergei L K SLK Wu Chieh-Hsi CH Ratmann Oliver O Ferguson Neil M NM Dye Christopher C Loman Nick J NJ Lemey Philippe P Rambaut Andrew A Fraiji Nelson A NA Carvalho Maria do P S S MDPSS Pybus Oliver G OG Flaxman Seth S Bhatt Samir S Sabino Ester C EC

medRxiv : the preprint server for health sciences 20210303

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 t ...[more]

PMID: 33688664

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Project description:BackgroundThe city of Manaus, north Brazil, was stricken by a second epidemic wave of SARS-CoV-2 despite high seroprevalence estimates, coinciding with the emergence of the Gamma (P.1) variant. Reinfections were postulated as a partial explanation for the second surge. However, accurate calculation of reinfection rates is difficult when stringent criteria as two time-separated RT-PCR tests and/or genome sequencing are required. To estimate the proportion of reinfections caused by Gamma during the second wave in Manaus and the protection conferred by previous infection, we identified anti-SARS-CoV-2 antibody boosting in repeat blood donors as a mean to infer reinfection.MethodsWe tested serial blood samples from unvaccinated repeat blood donors in Manaus for the presence of anti-SARS-CoV-2 IgG antibodies using two assays that display waning in early convalescence, enabling the detection of reinfection-induced boosting. Donors were required to have three or more donations, being at least one during each epidemic wave. We propose a strict serological definition of reinfection (reactivity boosting following waning like a V-shaped curve in both assays or three spaced boostings), probable (two separate boosting events) and possible (reinfection detected by only one assay) reinfections. The serial samples were used to divide donors into six groups defined based on the inferred sequence of infection and reinfection with non-Gamma and Gamma variants.ResultsFrom 3655 repeat blood donors, 238 met all inclusion criteria, and 223 had enough residual sample volume to perform both serological assays. We found 13.6% (95% CI 7.0-24.5%) of all presumed Gamma infections that were observed in 2021 were reinfections. If we also include cases of probable or possible reinfections, these percentages increase respectively to 22.7% (95% CI 14.3-34.2%) and 39.3% (95% CI 29.5-50.0%). Previous infection conferred a protection against reinfection of 85.3% (95% CI 71.3-92.7%), decreasing to respectively 72.5% (95% CI 54.7-83.6%) and 39.5% (95% CI 14.1-57.8%) if probable and possible reinfections are included.ConclusionsReinfection by Gamma is common and may play a significant role in epidemics where Gamma is prevalent, highlighting the continued threat variants of concern pose even to settings previously hit by substantial epidemics.

Dataset Information

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.

Publications

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.

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