Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic

Abstract

The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health.

Keywords: Brazil; Delta; Gamma; Genomic monitoring; variants replacment.

Figure 1.

Replacement of the Gamma by the Delta variant in Brazil. (A) Dynamics of the SARS-CoV-2 epidemic in Brazil showing the number of daily COVID-19 deaths and the progression in the proportion of circulating variants in the country over time, with the rapid replacement of the Gamma by the Delta variant. (B–C) The modelled proportion of SARS-CoV-2 variants over time in Brazil in a linear and in a logarithmic scale (respectively), showing that Gamma became the dominant variant in Brazil by the beginning of 2021 and was rapidly outcompeted by Delta from June 2021. Model fits are based on a multinomial logistic regression. The size of the dots corresponds to the weekly sample size of SARS-CoV-2 genomes (independently of variants, such that each week will have the same point size across all variant curves). (D) Prevalence maps following the progression in the monthly average of a daily number of cases and proportions of each variant (Alpha, Zeta, Gamma, and Delta) per region (North, Northeast, Midwest, Southeast, and South) in Brazil from October 2020 to October 2021. The scale 0–1 used represents the time-relative prevalence of each variant calculated independently of all the others (i.e. variant prevalence divided by its maximum across time). It shows the spatio-temporal evolution of each variant’s spread.

Figure 2.

Phylogenetic analysis of the Delta variant in Brazil. (A) Time-resolved maximum clade credibility phylogeny of 11,147 SARS-CoV-2 Delta sequences from Brazil, from which 6,626 were generated by our National Network for Pandemic Alert of SARS-CoV-2 along with global Delta sequences (grey). Only Brazilian genomes have been highlighted in the figure. Colours indicate different Brazilian regions (North in green; Midwest in orange; Northeast in yellow; Southeast in red; and South in light pink). (B) Inferred locations of importations of the Delta variant into Brazil. (C) Inferred locations of exportation of the Delta variant from Brazil.