Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant
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Preprint
- 5 March 2021
- preprint
- Published by Cold Spring Harbor Laboratory
Abstract
The variant of concern (VOC) P.1 emerged in the Amazonas state (Brazil) in November-2020. It contains a constellation of mutations, ten of them in the spike protein. Consequences of these specific mutations at the population level have been little studied so far, despite the detection of P.1 variant in 26 countries, with local transmission in at least four other countries in the Americas and Europe. Here, we estimate P.1’s transmissibility and reinfection using a model-based approach, by fitting data from the Brazilian national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December 2020 to February 2021, when the city was devastated by four times more cases than in the previous peak (April 2020). The new variant was found to be about 2.6 times more transmissible (95% Confidence Interval (CI): 2.4–2.8) than previous circulating variant(s). The city already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus (estimated as 78%, CI:73–83%), and the fitted model attributed 28% of the cases during the period to reinfections by the variant P.1. Our estimates rank P.1 as the most transmissible among the current identified SARS-CoV-2 VOCs, posing a serious threat and requiring urgent measures to control its global spread.Keywords
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- Published version: Version Communications Medicine, 1, preprints
This publication has 13 references indexed in Scilit:
- Covid-19: Is Manaus the final nail in the coffin for natural herd immunity?BMJ, 2021
- Do antibody positive healthcare workers have lower SARS-CoV-2 infection rates than antibody negative healthcare workers? Large multi-centre prospective cohort study (the SIREN study), England: June to November 2020Published by Cold Spring Harbor Laboratory ,2021
- Three-quarters attack rate of SARS-CoV-2 in the Brazilian Amazon during a largely unmitigated epidemicScience, 2021
- SARS-CoV-2, SARS-CoV, and MERS-CoV viral load dynamics, duration of viral shedding, and infectiousness: a systematic review and meta-analysisThe Lancet Microbe, 2020
- Brazil’s policies condemn Amazonia to a second wave of COVID-19Nature Medicine, 2020
- Projecting contact matrices in 177 geographical regions: an update and comparison with empirical data for the COVID-19 eraPublished by Cold Spring Harbor Laboratory ,2020
- Estimating the burden of SARS-CoV-2 in FranceScience, 2020
- A systematic review and meta-analysis reveals long and dispersive incubation period of COVID-19Published by Cold Spring Harbor Laboratory ,2020
- Nowcasting by Bayesian Smoothing: A flexible, generalizable model for real-time epidemic trackingPLoS Computational Biology, 2020
- Regularization and Variable Selection Via the Elastic NetJournal of the Royal Statistical Society Series B: Statistical Methodology, 2005