Dynamics of SARS-CoV-2 Variants of Concern in Brazil, Early 2021

Abstract

Brazil is the country with the second-largest number of deaths due to the coronavirus disease-2019 (COVID-19). Two variants of concern (VOCs), Alpha (B.1.1.7) and Gamma (P.1), were first detected in December 2020. While Alpha expanded within an expected rate in January and February 2021, its prevalence among new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cases started to decrease in March, which coincided with the explosion of Gamma variant incidence all over the country, being responsible for more than 95% of the new cases over the following months. A significantly higher viral load [i.e., mean cycle threshold (Ct) values] for Gamma in comparison to non-VOC samples was verified by the analysis of a large data set of routine reverse transcription-PCR (RT-PCR) exams. Moreover, the rate of reinfections greatly increased from March 2021 onward, reinforcing the enhanced ability of Gamma to escape the immune response. It is difficult to predict the outcomes of competition between variants since local factors like frequency of introduction and vaccine coverage play a key role. Genomic surveillance is of uttermost importance for the mitigation of the pandemic.

Keywords: SARS-CoV-2; alpha; gamma; reinfections; variants of concern.

Figure 1

Temporal evolution of B.1.1.7 (S-gene target failure, SGTF) in three Brazilian states with more than 5,000 samples tested. Blue lines, actual frequencies, orange lines, projections with a 10-day doubling time fixed rate. (A) Santa Catarina state; (B) Goiás state; and (C) São Paulo state.

Figure 2

Putative reinfections considering all positive real-time (RT)-polymerase chain reactions (PCRs). (A) Monthly rate over a total number of reinfections from March 2020 to June 2021. (B) Absolute number of reinfections that occurred after the periods of: blue bars, 120 days (4 months); orange bars, 150 days (5 months); green bars, 180 days (6 months).