Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics

Abstract

Since the beginning of the SARS-CoV-2 spread in Brazil, few studies have been published analysing the variability of viral genome. Herein, we described the dynamic of SARS-CoV-2 strains circulating in Brazil from May to September 2020, to better understand viral changes that may affect the ongoing pandemic. Our data demonstrate that some of the mutations identified are currently observed in variants of interest and variants of concern, and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5 %) in the spike, that has replaced the old variant; the V1167F in the spike (41 %), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39 %) in the N protein. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants was 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 could be associated with possible new waves of infection. These results allow a better understanding of SARS-CoV-2 strains that have circulated in Brazil, and thus, with relevant infomation, provide the potential viral changes that may have affected and/or contributed to the current and future scenario of the COVID-19 pandemic.

Molecular epidemiology of SARS‐CoV‐2 variants in circulation in the state of Maranhão, Brazil

“…In mid-2021, the Delta variant became dominant in the sequenced samples, suppressing the Gamma variant in the country. 7 In January 2022, the Delta variant was supplanted by the Omicron variant, which in a short time becomes the predominant variant in the sequenced genomes, with all SARS-CoV-2 peaks occurring in 2022 related to the sub-lineages of this variant. 8,9 The Maranhão state accounts for more than 1 million cases of COVID-19 and has already recorded more than 7000 deaths since the beginning of the pandemic, corresponding to a lethality rate of 2.720%.…”

“…Brazilian variants Gamma and Zeta were linked to the second wave of COVID‐19 case peaks in Brazil after January 2021. In mid‐2021, the Delta variant became dominant in the sequenced samples, suppressing the Gamma variant in the country 7 . In January 2022, the Delta variant was supplanted by the Omicron variant, which in a short time becomes the predominant variant in the sequenced genomes, with all SARS‐CoV‐2 peaks occurring in 2022 related to the sub‐lineages of this variant 8,9 …”

Evolutionary Profile of Mayaro Virus in the Americas: An Update into Genome Variability

“…Amino acid substitutions were analyzed in comparison to the reference sequence. The selective pressure analysis was performed on MAYV protein-coding sequence subsets through the Datamonkey Adaptive Evolution Server [19], to identify and localize statistically supported positive and negative selective pressure sites, as previously described [20]. To predict the impact of each substitution in protein selection, the fast unconstrained Bayesian approximation (FUBAR) model was used, which applies a maximum-likelihood (ML) approach to infer nonsynonymous (dN) and synonymous (dS) substitution rates on a per-site basis for a given coding alignment and corresponding phylogeny [21].…”

Produção e validação de cartilha digital sobre uso de máscaras no contexto pandêmico da COVID-19

“…Essa forma de comunicação precisa atingir todas as camadas populacionais de modo a sensibilizar a população acerca das formas de transmissão e prevenção da doença, principalmente, com relação ao uso correto das máscaras. Além disso, devido à alta transmissibilidade e mutação do vírus, surgiram variantes que se apresentaram como um risco para a saúde pública, resultando em novos surtos da doença, 6 reforçando a necessidade de sensibilização pública sobre o uso de máscaras. Desse modo, o uso de ferramentas digitais, como cartilhas informativas, vídeos, posts, jogos e websites, constitui estratégia eficaz para facilitar a disseminação do conhecimento, além de promover apoio às atividades de educação em saúde.…”