Relative frequency of genomic mutations in SARS-CoV-2 recovered from southern Brazilian cases of COVID-19 through the Gamma, Delta and Omicron waves.

Autor: Filippi M; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil. Electronic address: michelifilippi@hotmail.com., Demoliner M; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., Gularte JS; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., de Abreu Goes Pereira VM; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., da Silva MS; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., Girardi V; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., Hansen AW; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil., Spilki FR; Laboratório de Microbiologia Molecular, Departamento de Virologia, Universidade Feevale, Novo Hamburgo, Rio Grande do Sul, Brazil.
Jazyk: angličtina
Zdroj: Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases [Infect Genet Evol] 2024 Jun; Vol. 120, pp. 105590. Date of Electronic Publication: 2024 Apr 03.
DOI: 10.1016/j.meegid.2024.105590
Abstrakt: The presence of different mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome can be related to changes in coronavirus disease (COVID-19) infection. Besides, these viral alterations associated with factors such as massive number of positive cases, vaccination and reinfections can be important in the viral evolution process. As well as, mutations found at low frequencies may have a more neutral action and consequently be less inclined to negative selection, facilitating their spread through the population. Related to that, we aimed to present mutations that are possibly relevant in the process of viral evolution found in 115 SARS-CoV-2 sequences from samples of individuals residing in the metropolitan region of Porto Alegre in the state of Rio Grande do Sul, Brazil. The genome from clinical samples was sequenced using High-Throughput Sequencing (HTS) and analyzed using a workflow to map reads and find variations/SNPs. The samples were separated into 3 groups considering the sample lineage. Of the total number of analyzed sequences, 35 were from the Gamma lineage, 35 from Delta and 45 from Omicron. Amino acid changes present in frequencies lower than 80% of the reads in the sequences were evaluated. 11 common mutations among the samples were found in the Gamma lineage, 1 in the ORF1ab gene, 7 in the S gene, 2 in the ORF6 gene and 1 in the ORF7a gene. While in the Delta lineage, a total of 11 mutations distributed in the ORF1ab, S, ORF7a and N genes, 2, 7, 1 and 1 mutation were found in each gene, respectively. And finally, in the Omicron, 16 mutations were identified, 2 in the ORF1ab gene, 12 in the S gene and 2 in the M gene. In conclusion, we emphasize that genomic surveillance can be a useful tool to assess how mutations play a key role in virus adaptation, and its process of susceptibility to new hosts showing the possible signs of viral evolution.
Competing Interests: Declaration of competing interest The authors report no declarations of interest.
(Copyright © 2024 The Author(s). Published by Elsevier B.V. All rights reserved.)
Databáze: MEDLINE
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