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

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Coutinho, Renato Mendes ; Darcie Marquitti, Flavia Maria ; Ferreira, Leonardo Souto ; Borges, Marcelo Eduardo ; Paixao da Silva, Rafael Lopes ; Canton, Otavio ; Portella, Tatiana P. ; Poloni, Silas ; Franco, Caroline ; Plucinski, Mateusz M. ; Lessa, Fernanda C. ; Moura da Silva, Antonio Augusto ; Kraenkel, Roberto Andre ; de Sousa Mascena Veras, Maria Amelia ; Prado, Paulo Inacio

• Document type: Journal article
• Source: COMMUNICATIONS MEDICINE; v. 1, n. 1, p. 8-pg., 2021-11-15.

Abstract

Background The SARS-CoV-2 variant of concern (VOC) P.1 (Gamma variant) emerged in the Amazonas State, Brazil, in November 2020. The epidemiological consequences of its mutations have not been widely studied, despite detection of P.1 in 36 countries, with local transmission in at least 5 countries. A range of mutations are seen in P.1, ten of them in the spike protein. It shares mutations with VOCs previously detected in the United Kingdom (B.1.1.7, Alpha variant) and South Africa (B.1.351, Beta variant). Methods We estimated the transmissibility and reinfection of P.1 using a model-based approach, fitting data from the national health surveillance of hospitalized individuals and frequency of the P.1 variant in Manaus from December-2020 to February-2021. Results Here we estimate that the new variant is about 2.6 times more transmissible (95% Confidence Interval: 2.4-2.8) than previous circulating variant(s). Manaus already had a high prevalence of individuals previously affected by the SARS-CoV-2 virus and our fitted model attributed 28% of Manaus cases in the period to reinfections by P.1, confirming the importance of reinfection by this variant. This value is in line with estimates from blood donors samples in Manaus city. Conclusions Our estimates rank P.1 as one of the most transmissible among the SARS-CoV-2 VOCs currently identified, and potentially as transmissible as the posteriorly detected VOC B.1.617.2 (Delta variant), posing a serious threat and requiring measures to control its global spread. (AU)

• FAPESP's process: 18/26512-1 - Biological dynamics on networks
• Grantee: Otavio Luiz Canton
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 19/26310-2 - Modelling towards elimination of malaria in Brazilian Amazon
• Grantee: Caroline Franco
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• FAPESP's process: 17/26770-8 - Mathematical models in Population Biology from time-series: applications to Epidemiology and Ecology
• Grantee: Caroline Franco
• Support Opportunities: Scholarships in Brazil - Doctorate
• FAPESP's process: 16/01343-7 - ICTP South American Institute for Fundamental Research: a regional center for theoretical physics
• Grantee: Nathan Jacob Berkovits
• Support Opportunities: Special Projects
• FAPESP's process: 18/24037-4 - Reaction-diffusion equations in Population Biology: persistence and Invasibility conditions
• Grantee: Silas Poloni Lyra
• Support Opportunities: Scholarships in Brazil - Doctorate