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. 2023 Jul 14:17:11779322231186477.
doi: 10.1177/11779322231186477. eCollection 2023.

SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia

Gabriella Sgorlon  1   2   3 , Tárcio Peixoto Roca  1   3   4 , Ana Maisa Passos-Silva  1   2   3 , Márlon Grégori Flores Custódio  1 , Jackson Alves da Silva Queiroz  1   2   3 , André Luiz Ferreira da Silva  1   2   3 , Karolaine Santos Teixeira  1   3 , Flávia Serrano Batista  5 , Juan Miguel Villalobos Salcedo  1   2   3 , Rita de Cassia P Rampazzo  6 , Felipe Gomes Naveca  7 , Deusilene Vieira  1   2   3
Affiliations

SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia

Gabriella Sgorlon et al. Bioinform Biol Insights. .

Abstract

The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced. We analyzed the quality and mutations of the genomes and maximum likelihood phylogenetic inference. However, 3 main clusters were observed, referring to Gamma (52.91%), Delta (24.38%), and Omicron (20.38%) VOCs with wide distribution in all health regions of the Rondônia state. Regarding the vaccination profile, there was a higher percentage of unvaccinated and partially vaccinated individuals, with more representatives by the Gamma variant. A total of 1412 sequences were suitable for mutation analysis in the S gene region. The Omicron VOC showed 38 mutations, with the Delta and Gamma variants with 16 and 17, respectively. The VOC Omicron and Gamma shared 4 mutations E484K, H655Y, N501Y, and N679K with high frequency, and Delta and Omicron 2 mutations (T478K and T95I). Regarding the comparison between the frequency of mutations for each variant concerning the vaccination groups, there were no changes in mutations for each group. In conclusion, the study showed a temporal increase in mutations and subvariants for characterized strains. Furthermore, the vaccination profile did not impact significant changes in the mutational profile yet remains a determining factor for severe disease.

Keywords: SARS-CoV-2; mutations; sequences; vaccination; variants.

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Conflict of interest statement

The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.

Figures

Figure 1.
Figure 1.
Maximum likelihood phylogenetic tree showing 1412 sequences with “good” quality in NEXTCLADE obtained in this study and 47 reference genomes retrieved from GISAID. The tree was rooted with the most ancestral sequence (EPI_ISL_402123). Gamma, Omicron, and Delta clades are shaded in yellow, blue, and green, respectively. AY. indicates Delta; BA., Omicron; P., Gamma; GISAID, Global Initiative on Sharing All Influenza Data.
Figure 2.
Figure 2.
Dispersion map of cases per variant in the 7 health regions in the state of Rondônia.
Figure 3.
Figure 3.
Area plot showing the distribution of subvariants during the study period. AY. indicates Delta; BA., Omicron; P., Gamma.
Figure 4.
Figure 4.
Mutations located in the S gene region in the Gamma, Delta, and Omicron variants. A frequency above 2% was set for visualization of the graph.
Figure 5.
Figure 5.
Immunization groups compared with proportions of mutations for each variant. (A) Gamma vaccinated. (B) Gamma nonvaccinated/partially. (C) Delta vaccinated. (D) Delta nonvaccinated/partially. (E) Omicron vaccinated. (F) Omicron nonvaccinated/partially.
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