Model-based evaluation of transmissibility and reinfection for the P.1 variant of the SARS-CoV-2

The variant of concern (VOC) P.1 emerged in the Amazonas state (Brazil) and was sequenced for the first time on 6-Jan-2021 by the Japanese National Institute of Infectious Diseases. It contains a constellation of mutations, ten of them in the spike protein. Consequences of these mutations at the populational level have been little studied so far. From December-2020 to February-2021, Manaus was devastated by four times more cases compared to the previous peak (April-2020). Here, data from the national health surveillance of hospitalized individuals and frequency of the P.1 variant were analysed using a model-based approach to estimate P.1 parameters of transmissibility and reinfection by maximum likelihood. Sensitivity analysis was performed changing pathogenicity and the period analysed (including/excluding the health system collapse period). The new variant transmissibility was found to be about 2.5 times higher (Confidence Interval (95%CI): 2.3-2.8) compared to the previous variant in Manaus. A low probability of reinfection by the new variant (6.4%, 95%CI: 5.7-7.1%).) was estimated, even under initial high prevalence (68%, 95%CI: 63- 74%), by the time P.1 emerged. Consequences of a higher transmissibility were already observed with VOC B.1.1.7 in the UK and Europe. Urgent measures must be taken to control the spread of P.1.