Evaluating the impacts of relaxation and mutation in the SARS-CoV-2 on the COVID-19 epidemic based on a mathematical model: a case study of São Paulo State (Brazil)

At the beginning of 2020, SARS-CoV-2 spread to all continents, and many countries adopted quarantine to flatten the COVID-19 outbreak, resulting in the containment of transmission. However, the persistent transmission of SARS-CoV-2, an RNA virus, resulted in the appearance of mutations in the original virus. The appearance of more virulent mutations in different regions of the world resulted in an increased number of severe COVID-19 cases. A mathematical model based on the COVID-19 natural history encompassing the mutations was applied to evaluate the SARS-CoV-2 epidemic. The model parameters were fitted against the observed data from São Paulo State (Brazil) considering quarantine, relaxation, and mutation. The estimated data from São Paulo State showed that the original SARS-CoV-2 transmission better explained the COVID-19 epidemic during the quarantine. However, the increased number of fatalities beyond that predicted by the relaxation indicated the occurrence of mutations. Hence, the relaxation in association with the transmission of a more virulent SARS-CoV-2 better estimated the COVID-19 epidemic from February 26, 2020, to June 15, 2021, in São Paulo State.