SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia
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 individ...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
SAGE Publishing
2023-07-01
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| Series: | Bioinformatics and Biology Insights |
| Online Access: | https://doi.org/10.1177/11779322231186477 |
| _version_ | 1797780056427200512 |
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| author | Gabriella Sgorlon Tárcio Peixoto Roca Ana Maisa Passos-Silva Márlon Grégori Flores Custódio Jackson Alves da Silva Queiroz André Luiz Ferreira da Silva Karolaine Santos Teixeira Flávia Serrano Batista Juan Miguel Villalobos Salcedo Rita de Cassia P. Rampazzo Felipe Gomes Naveca Deusilene Vieira |
| author_facet | Gabriella Sgorlon Tárcio Peixoto Roca Ana Maisa Passos-Silva Márlon Grégori Flores Custódio Jackson Alves da Silva Queiroz André Luiz Ferreira da Silva Karolaine Santos Teixeira Flávia Serrano Batista Juan Miguel Villalobos Salcedo Rita de Cassia P. Rampazzo Felipe Gomes Naveca Deusilene Vieira |
| author_sort | Gabriella Sgorlon |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-12T23:38:07Z |
| format | Article |
| id | doaj.art-cfc9b7cbf3504365841f93e655fe4434 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-03-12T23:38:07Z |
| publishDate | 2023-07-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-cfc9b7cbf3504365841f93e655fe44342023-07-15T06:03:25ZengSAGE PublishingBioinformatics and Biology Insights1177-93222023-07-011710.1177/11779322231186477SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western AmazoniaGabriella Sgorlon0Tárcio Peixoto Roca1Ana Maisa Passos-Silva2Márlon Grégori Flores Custódio3Jackson Alves da Silva Queiroz4André Luiz Ferreira da Silva5Karolaine Santos Teixeira6Flávia Serrano Batista7Juan Miguel Villalobos Salcedo8Rita de Cassia P. Rampazzo9Felipe Gomes Naveca10Deusilene Vieira11Centro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilLaboratório de Hepatites Virais, Instituto Oswaldo Cruz (IOC), FIOCRUZ, Rio de Janeiro, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilLaboratório de Virologia Molecular, Fundação Oswaldo Cruz Rondônia (FIOCRUZ/RO), Porto Velho, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilCoordenação Estadual do Covid-19, AGEVISA/RO, Porto Velho, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilInstituto de Biologia Molecular do Paraná (IBMP), Curitiba, BrazilLaboratório de Virologia do Instituto Leônidas e Maria Deane, FIOCRUZ/AM, Manaus, BrazilCentro de Pesquisa em Medicina Tropical de Rondônia (CEPEM/RO), Porto Velho, BrazilThe 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.https://doi.org/10.1177/11779322231186477 |
| spellingShingle | Gabriella Sgorlon Tárcio Peixoto Roca Ana Maisa Passos-Silva Márlon Grégori Flores Custódio Jackson Alves da Silva Queiroz André Luiz Ferreira da Silva Karolaine Santos Teixeira Flávia Serrano Batista Juan Miguel Villalobos Salcedo Rita de Cassia P. Rampazzo Felipe Gomes Naveca Deusilene Vieira SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia Bioinformatics and Biology Insights |
| title | SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia |
| title_full | SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia |
| title_fullStr | SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia |
| title_full_unstemmed | SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia |
| title_short | SARS-CoV-2 Spike Protein Mutations in Different Variants: A Comparison Between Vaccinated and Unvaccinated Population in Western Amazonia |
| title_sort | sars cov 2 spike protein mutations in different variants a comparison between vaccinated and unvaccinated population in western amazonia |
| url | https://doi.org/10.1177/11779322231186477 |
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