Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study

Patrícia Aline Gröhs Ferrareze; Gabriela Betella Cybis; Luiz Felipe Valter de Oliveira; Ricardo Ariel Zimerman; Dieine Estela Bernieri Schiavon; Camila Peter; Claudia Elizabeth Thompson

doi:10.1016/j.micinf.2023.105216

Intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil: a SARS-CoV-2 genomic epidemiology study

Microbes Infect. 2024 Jan-Feb;26(1-2):105216. doi: 10.1016/j.micinf.2023.105216. Epub 2023 Oct 10.

Authors

Patrícia Aline Gröhs Ferrareze¹, Gabriela Betella Cybis², Luiz Felipe Valter de Oliveira³, Ricardo Ariel Zimerman⁴, Dieine Estela Bernieri Schiavon⁵, Camila Peter⁶, Claudia Elizabeth Thompson⁷

Affiliations

¹ Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil.
² Department of Statistics, Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil.
³ BiomeHub, Florianópolis, Brazil.
⁴ Hospital da Brigada Militar, Porto Alegre, RS, Brazil.
⁵ Undergraduate Program in Biomedical Informatics, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Rio Grande do Sul, Brazil.
⁶ Laboratório Exame, Novo Hamburgo, Brazil.
⁷ 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, RS, Brazil. Electronic address: cthompson@ufcspa.edu.br.

PMID: 37827275
DOI: 10.1016/j.micinf.2023.105216

Abstract

The analyses of genetic traits, dispersion patterns and phylogenomics are essential for understanding the evolutionary forces driving SARS-CoV-2 viruses in these three years of COVID-19 pandemics. Brazil is one of the most affected countries in the world and not sufficient genomic studies have been performed. The emergence of P.1 lineage led to one of the most serious public health crises on record. Our study presents the genomic sequencing and characterization of 412 samples from Rio Grande do Sul state, in the Brazilian Southern region, during Gamma and Delta epidemic waves, in 2021. Additionally, molecular evolution tests were performed to identify positively selected sites in Brazil between 2020 and 2022, as well as offer some evolutionary perspective about the maintenance of multiple spike mutations in Omicron lineages. Genomic epidemiology analysis has indicated an intense P.1 (Gamma) diversification followed by rapid Delta substitution in Southern Brazil.

Keywords: COVID-19; Genomic epidemiology; Molecular evolution; Phylodynamics; SARS-CoV-2.

MeSH terms

Brazil / epidemiology
COVID-19* / epidemiology
Genomics
Humans
Phylogeny
Public Health
SARS-CoV-2* / genetics