Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant

R.M. Coutinho; F.M.D. Marquitti; L.S. Ferreira; M.E. Borges; R.L.P. da Silva; O. Canton; T.P. Portella; S. Poloni; C. Franco; M.M. Plucinski; F.C. Lessa; A.A.M. da Silva; R.A. Kraenkel; M.A. de Sousa Mascena Veras; P.I. Prado

doi:10.1101/2021.03.03.21252706

Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant

R.M. Coutinho^* (Corresponding Author), F.M.D. Marquitti^* (Corresponding Author), L.S. Ferreira, M.E. Borges, R.L.P. da Silva, O. Canton, T.P. Portella, S. Poloni, C. Franco, M.M. Plucinski, F.C. Lessa, A.A.M. da Silva, R.A. Kraenkel, M.A. de Sousa Mascena Veras, P.I. Prado

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Article number	48
Number of pages	8
Journal	Communications Medicine
Volume	1
Early online date	15 Nov 2021
DOIs	https://doi.org/10.1101/2021.03.03.21252706 https://doi.org/10.1038/s43856-021-00048-6
Publication status	Published - 15 Nov 2021
Externally published	Yes

Bibliographical note

Acknowledgements
We are grateful for the collaborative work of the reviewers and the entire group of the Observatório COVID-19 BR. In particular, we thank Verônica Coelho for critical inputs. We also thank the research funding agencies: the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brazil (Finance Code 001 to F.M.D.M., L.S.F. and T.P.P.), Conselho Nacional de Desenvolvimento Científico e Tecnológico—Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.S., 313055/2020-3 to P.I.P., 312559/2020-8 to M.A.S.M.V., 311832/2017-2 to R.A.K., 305703/2019-6 to A.A.M.S.) and Fundação de Amparo à Pesquisa do Estado de São Paulo—Brazil (grant number: 2019/26310-2 and 2017/26770-8 to C.F., 2018/26512-1 to O.C., 2018/24037-4 to S.P. and contract number: 2016/01343-7 to R.A.K.). The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of the Centers of Disease Control and Prevention.

Data Availability Statement

Data availability
The hospitalization data were obtained from the Brazilian epidemiological syndrome surveillance system for influenza, SIVEP-Gripe (https://opendatasus.saude.gov.br). Time-series of frequency of sequenced genomes identified as P.1 in Manaus were extracted from published datasets3,12. Data that support the findings of this study, including source data underlying the main figures in the manuscript, can be accessed via the link: https://zenodo.org/record/559460013 or through the Github repository https://github.com/covid19br/model-P1-variant/tree/main/DATA.

Code availability
The codes used for perform the analysis are available in the following link: https://zenodo.org/record/559460013, and in the Github repository https://github.com/covid19br/model-P1-variant.

Supplementary information
The online version contains supplementary material available at https://doi.org/10.1038/s43856-021-00048-6.

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Cite this

Coutinho, R. M., Marquitti, F. M. D., Ferreira, L. S., Borges, M. E., da Silva, R. L. P., Canton, O., Portella, T. P., Poloni, S., Franco, C., Plucinski, M. M., Lessa, F. C., da Silva, A. A. M., Kraenkel, R. A., de Sousa Mascena Veras, M. A., & Prado, P. I. (2021). Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant. Communications Medicine, 1, Article 48. https://doi.org/10.1101/2021.03.03.21252706, https://doi.org/10.1038/s43856-021-00048-6

Coutinho, RM, Marquitti, FMD, Ferreira, LS, Borges, ME, da Silva, RLP, Canton, O, Portella, TP, Poloni, S, Franco, C, Plucinski, MM, Lessa, FC, da Silva, AAM, Kraenkel, RA, de Sousa Mascena Veras, MA & Prado, PI 2021, 'Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant', Communications Medicine, vol. 1, 48. https://doi.org/10.1101/2021.03.03.21252706, https://doi.org/10.1038/s43856-021-00048-6

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title = "Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant",

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{\textquoteright}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.",

author = "R.M. Coutinho and F.M.D. Marquitti and L.S. Ferreira and M.E. Borges and {da Silva}, R.L.P. and O. Canton and T.P. Portella and S. Poloni and C. Franco and M.M. Plucinski and F.C. Lessa and {da Silva}, A.A.M. and R.A. Kraenkel and {de Sousa Mascena Veras}, M.A. and P.I. Prado",

note = "Acknowledgements We are grateful for the collaborative work of the reviewers and the entire group of the Observat{\'o}rio COVID-19 BR. In particular, we thank Ver{\^o}nica Coelho for critical inputs. We also thank the research funding agencies: the Coordena{\c c}{\~a}o de Aperfei{\c c}oamento de Pessoal de N{\'i}vel Superior—Brazil (Finance Code 001 to F.M.D.M., L.S.F. and T.P.P.), Conselho Nacional de Desenvolvimento Cient{\'i}fico e Tecnol{\'o}gico—Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.S., 313055/2020-3 to P.I.P., 312559/2020-8 to M.A.S.M.V., 311832/2017-2 to R.A.K., 305703/2019-6 to A.A.M.S.) and Funda{\c c}{\~a}o de Amparo {\`a} Pesquisa do Estado de S{\~a}o Paulo—Brazil (grant number: 2019/26310-2 and 2017/26770-8 to C.F., 2018/26512-1 to O.C., 2018/24037-4 to S.P. and contract number: 2016/01343-7 to R.A.K.). The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of the Centers of Disease Control and Prevention.",

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AU - Coutinho, R.M.

AU - Marquitti, F.M.D.

AU - Ferreira, L.S.

AU - Borges, M.E.

AU - da Silva, R.L.P.

AU - Canton, O.

AU - Portella, T.P.

AU - Poloni, S.

AU - Franco, C.

AU - Plucinski, M.M.

AU - Lessa, F.C.

AU - da Silva, A.A.M.

AU - Kraenkel, R.A.

AU - de Sousa Mascena Veras, M.A.

AU - Prado, P.I.

N1 - Acknowledgements We are grateful for the collaborative work of the reviewers and the entire group of the Observatório COVID-19 BR. In particular, we thank Verônica Coelho for critical inputs. We also thank the research funding agencies: the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior—Brazil (Finance Code 001 to F.M.D.M., L.S.F. and T.P.P.), Conselho Nacional de Desenvolvimento Científico e Tecnológico—Brazil (grant number: 315854/2020-0 to M.E.B., 141698/2018-7 to R.L.P.S., 313055/2020-3 to P.I.P., 312559/2020-8 to M.A.S.M.V., 311832/2017-2 to R.A.K., 305703/2019-6 to A.A.M.S.) and Fundação de Amparo à Pesquisa do Estado de São Paulo—Brazil (grant number: 2019/26310-2 and 2017/26770-8 to C.F., 2018/26512-1 to O.C., 2018/24037-4 to S.P. and contract number: 2016/01343-7 to R.A.K.). The findings and conclusions in this article are those of the authors and do not necessarily represent the official position of the Centers of Disease Control and Prevention.

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Model-based estimation of transmissibility and reinfection of SARS-CoV-2 P.1 variant

Abstract

Bibliographical note

Data Availability Statement

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