The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019 and spread across the world. Brazil is an important centre of the COVID-19 pandemic, with significant infection and death rates. However, a limited number of works reported viral strains, genomic signatures or mutations in the circulating virus in the country, mainly reporting and characterizing variants that emerged. Herein we analysed the SARS- CoV-2 genome strains circulating in Brazil from May to September 2020 using 720 sequences deposited in the GISAID database to better understand the variability in the viral genome during this period and its impacts on the current and future scenario of the pandemic in Brazil. Our data demonstrated that some of the mutations identified here are present in variants of interest and variants of concern (VOCs), and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. The most frequent substitutions identified have been described globally, such as the G614-carrying virus and V1176F, enhancing viral transmissibility and infectivity. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants were not influenced by mutations in UTR regions, since it maintained its conformational structure in most analysed sequences. In phylogenetic analysis, the spread of SARS-CoV-2 from the large urban centres to the countryside during these months could be explained by the flexibilization of social isolation measures and also be associated with possible new waves of infection. The results described here demonstrate possible genomic signatures, suggest a geography transmission chain, viral adaptability, and emphasize the importance of active viral genomic surveillance, since important mutations in VOCs were found in periods before its appearance.