SARS-CoV-2 epidemic in Brazil: how the displacement of variants has driven distinct epidemic waves

Abstract

Brazil ranks as third in terms of total number of reported SARS-CoV-2 cases globally. The COVID-19 epidemic in Brazil was characterised by the co-circulation of multiple variants as a consequence of multiple independent introduction events occurring through time. Here, we describe the SARS-CoV-2 variants that are currently circulating and co-circulating in the country, with the aim to highlight which variants have driven the different epidemic waves. For this purpose, we retrieved metadata information of Coronavirus sequences collected in Brazil and available at the GISAID database. SARS-CoV-2 lineages have been identified along with eleven variants, labelled as VOCs (Alpha, Gamma, Beta, Delta and Omicron) VOIs (Lambda and Mu) VUMs (B.1.1.318) and FMVs (Zeta, Eta and B.1.1.519). Here we show that, in the Brazilian context, after 24 months of sustained transmission and evolution of SARS-CoV-2, local variants (among them the B.1.1.28 and B.1.1.33) were displaced by recently introduced VOCs firstly with the Gamma, followed by Delta and more recently Omicron. The rapid spread of some of those VOCs (such as Gamma and Omicron) was also mirror by a large increase in the number of cases and deaths in the country. This in turn reinforces that, due to the emergence of variants that appear to induce a substantial evasion against neutralizing antibody response, it is important to strengthen genomic effort within the country and how vaccination still remains a critical process to protect the vulnerable population, still at risk of infection and death.

Keywords: Brazil; SARS-CoV-2; Surveillance; Variants.

Fig. 1

Diagram of variants detected in Brazil. The diagram represents the evolutionary relation of the twelve VOCs (alpha, beta, gamma, delta, omicron), VOIs (mu, lamda), VUMs (B.1.1.318) and FMVs (zeta, eta and B.1.1.519 detected in Brazil since the beginning of the epidemic until the February 19^th, 2022. Colours indicate WHO variant classification. Main ancestor lineage is B.1. Lineage B.1.1.28 had a crucial impact leading to variants that presented high frequency lately in Brazilian genomes (Gamma and Zeta).

Fig. 2

Dynamics of the SARS-CoV-2 epidemic in Brazil. A) Number of daily COVID-19 cases and the vaccination rates in time; B) Progression in the proportion of circulating variants in Brazil over the first second and third waves of infection, showing the rapid replacement of different VOCs throughout time additionally showing the number of daily COVID-19 deaths.