Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil

Amanda de Menezes Mayer; Patrícia Aline Gröhs Ferrareze; Luiz Felipe Valter de Oliveira; Tatiana Schäffer Gregianini; Carla Lucia Andretta Moreira Neves; Gabriel Dickin Caldana; Lívia Kmetzsch; Claudia Elizabeth Thompson

doi:10.1016/j.virol.2023.03.005

Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil

Virology. 2023 May:582:1-11. doi: 10.1016/j.virol.2023.03.005. Epub 2023 Mar 16.

Authors

Amanda de Menezes Mayer¹, Patrícia Aline Gröhs Ferrareze², Luiz Felipe Valter de Oliveira³, Tatiana Schäffer Gregianini⁴, Carla Lucia Andretta Moreira Neves², Gabriel Dickin Caldana², Lívia Kmetzsch¹, Claudia Elizabeth Thompson⁵

Affiliations

¹ Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.
² Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
³ BiomeHub, Florianópolis, Brazil.
⁴ Laboratório Central de Saúde Pública do Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, RS, Brazil.
⁵ Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil. Electronic address: cthompson@ufcspa.edu.br.

Abstract

SARS-CoV-2 is the virus responsible for the COVID-19 and has afflicted the world since the end of 2019. Different lineages have been discovered and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.

Keywords: COVID-19; Genomics; Molecular evolution; Phylogenomics; SARS-CoV-2.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Brazil / epidemiology
COVID-19* / epidemiology
Evolution, Molecular
Genomics
Humans
Phylogeny
SARS-CoV-2* / genetics