Genomic Epidemiology of SARS-CoV-2 in Esteio, Rio Grande do Sul, Brazil

Abstract

Brazil is the third country most affected by Covid-19 pandemic. In spite of this, viral evolution in municipality resolution is poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We identified four main circulating lineages in Esteio (Southern Brazil) and their relationship with global, national and regional lineages using phylogenetics and phylodynamics inferences from 21 SARS-CoV-2 genome sequences. We provided a comprehensive view of viral mutations from a time- and age-representative sampling from May to October 2020, in Esteio (RS, Brazil), highlighting two frequent mutations in Spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in Spike Receptor Binding Domain (RBD) characteristic of the South African lineage B.1.351, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). A significant viral diversity was evidenced with the identification of 80 different SNPs. The E484K replacement was found in two genomes (9.5%) from samples obtained in mid-October, which is to our best knowledge the earliest description of E484K harboring SARS-CoV-2 in South Brazil. This mutation identified in a small municipality from the RS state demonstrates that it was probably widely distributed in the Brazilian territory, but went unnoticed so far by the lack of genomic surveillance in Brazil. The introduction of E484K mutants shows temporal correlation with later increases in new cases in our state. Importantly, since it has been associated with immune evasion and enhanced interaction with hACE-2, lineages containing this substitution must be the subject of intense surveillance. Our date demonstrates multiple introductions of the most prevalent lineages (B.1.1.33 and B.1.1.248) and the major role of community transmission in viral spreading and the establishment of Brazilian lineages. This represents an important contribution to the epidemiology of SARS-CoV-2.

Spatiotemporal dissemination pattern of SARS-CoV-2 B1.1.28-derived lineages introduced into Uruguay across its southeastern border with Brazil

“…We found a sharp increase of P.2 frequency in Rocha, with partial replacement of earlier circulating B.1.1.28 lineages, as previously reported in RS and many other Brazilian states [7,[15][16][17]. The dissemination of the VOI P.2 in Rocha may have been facilitated by the notorious increment in mobility and lax social distancing in that department (a popular holiday destination for Uruguayans) that occurred at the beginning of 2021.…”

“…The VOI P.2 reached the southernmost Brazilian state of Rio Grande do Sul (RS) in October, 2020 and then spread massively in that region [15][16][17][18]. Given the high viral flux between RS and Uruguay detected during 2020 [11], it is likely that the introduction of the VOI P.2 from Brazil could have been associated with the epidemic worsening in Uruguay by the end of 2020 and beginning of 2021.…”

Priorities for the COVID-19 pandemic at the start of 2021: statement of the Lancet COVID-19 Commission

“…The high rates of community transmission (>100 new COVID-19 cases per million per day) 2 in the USA, Europe, South Africa, and other countries show the emergence of new variants of SARS-CoV-2, such as lineage B.1.1.7 in the UK, [3][4][5][6][7] 501Y.V2 in South Africa, 8 and additional variants emerging in California, USA, 9,10 and in Brazil. 11,12 New lineages are increasing transmission of infection and raising risks in regions that have been less affected by COVID-19, including in sub-Saharan Africa. [13][14][15] Additionally, acquired immunity from earlier COVID-19 infections might be less protective against reinfection with some of the new SARS-CoV-2 variants.…”

Mutation hotspots, geographical and temporal distribution of SARS-CoV-2 lineages in Brazil, February 2020-2021: insights and limitations from uneven sequencing efforts

“…Studies from Rio de Janeiro (Southeast) and Rio Grande do Sul (South) identified B.1.1.28 and B.1.1.33 in higher proportion from April to December 2020 (Voloch et al 2020; Franceschi et al 2021; Francisco Jr et al 2021). The emergence of a B.1.1.28-derived lineage carrying the E484K mutation (after named P.2) was dated in July 2020, however it began to appear more frequently and almost simultaneously in October 2020 in the Rio de Janeiro state (Voloch et al 2020) and in the small municipality of Esteio, Rio Grande do Sul (Franceschi et al 2021), suggesting its wide distribution in the Southern and Southeastern regions of Brazil and uncertainty regarding its origin. This assumption and the frequency increase of B.1.1.28 and derived lineages were corroborated by another study from several municipalities of Rio Grande do Sul, which found that 86% of the sequenced genomes were classified as B.1.1.28 and ∼50% of these belong to the new lineage P.2 (Francisco Jr et al 2021).…”