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

Autor: Franceschi VB; Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil., Caldana GD; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil., de Menezes Mayer A; Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil., Cybis GB; Department of Statistics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil., Neves CAM; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil., Ferrareze PAG; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil., Demoliner M; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., de Almeida PR; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Gularte JS; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Hansen AW; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Weber MN; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Fleck JD; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Zimerman RA; Irmandade Santa Casa de Misericórdia de Porto Alegre, Porto Alegre, RS, Brazil., Kmetzsch L; Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil., Spilki FR; Molecular Microbiology Laboratory, Universidade Feevale, Novo Hamburgo, RS, Brazil., Thompson CE; Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil. cthompson@ufcspa.edu.br.; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil. cthompson@ufcspa.edu.br.; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), 245/200C Sarmento Leite St, Porto Alegre, RS, 90050-170, Brazil. cthompson@ufcspa.edu.br.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2021 May 20; Vol. 22 (1), pp. 371. Date of Electronic Publication: 2021 May 20.
DOI: 10.1186/s12864-021-07708-w
Abstrakt: Background: Brazil is the third country most affected by Coronavirus disease-2019 (COVID-19), but viral evolution in municipality resolution is still poorly understood in Brazil and it is crucial to understand the epidemiology of viral spread. We aimed to track molecular evolution and spread of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Esteio (Southern Brazil) using phylogenetics and phylodynamics inferences from 21 new genomes in global and regional context. Importantly, the case fatality rate (CFR) in Esteio (3.26%) is slightly higher compared to the Rio Grande do Sul (RS) state (2.56%) and the entire Brazil (2.74%).
Results: We provided a comprehensive view of mutations from a representative sampling from May to October 2020, highlighting two frequent mutations in spike glycoprotein (D614G and V1176F), an emergent mutation (E484K) in spike Receptor Binding Domain (RBD) characteristic of the B.1.351 and P.1 lineages, and the adjacent replacement of 2 amino acids in Nucleocapsid phosphoprotein (R203K and G204R). E484K was found in two genomes from mid-October, which is the earliest description of this mutation in Southern Brazil. Lineages containing this substitution must be subject of intense surveillance due to its association with immune evasion. We also found two epidemiologically-related clusters, including one from patients of the same neighborhood. Phylogenetics and phylodynamics analysis demonstrates multiple introductions of the Brazilian most prevalent lineages (B.1.1.33 and B.1.1.248) and the establishment of Brazilian lineages ignited from the Southeast to other Brazilian regions.
Conclusions: Our data show the value of correlating clinical, epidemiological and genomic information for the understanding of viral evolution and its spatial distribution over time. This is of paramount importance to better inform policy making strategies to fight COVID-19.
Databáze: MEDLINE
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