The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon
Genomic surveillance represents a strategy to understanding the evolutionary mechanisms, transmission, and infectivity of different SARS-CoV-2 variants. We evaluated 603 individuals positive for SARS-CoV-2 from 34 municipalities of Rondônia between December 2021 to December 2022. Nasopharyngeal samp...
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| creator | Sgorlon, Gabriella Roca, Tárcio P Passos-Silva, Ana Maisa Queiroz, Jackson A. S Teixeira, Karolaine S Araújo, Adrhyan Batista, Flávia S Souza, Valquiria R Oliveira, Franciane M Morello, Luis G Marchini, Fabricio K Salcedo, Juan M.V Rampazzo, Rita de Cassia P Naveca, Felipe G Vieira, Deusilene |
| description | Genomic surveillance represents a strategy to understanding the evolutionary mechanisms, transmission, and infectivity of different SARS-CoV-2 variants. We evaluated 603 individuals positive for SARS-CoV-2 from 34 municipalities of Rondônia between December 2021 to December 2022. Nasopharyngeal samples were collected, RNA was extracted and screened using RT-qPCR for VOCs. RNA of the samples were sequenced and further analyzed for phylogeny, mutations, and lineages, totaling 96.19% of samples positive for Omicron VOC in this cohort. We observed that most individuals had at least two doses, however 18.97% were not vaccinated with any dose. 554 sequences were amenable to analysis for alignment and phylogenetic characterization; this group corresponded to the 27 subvariants of the Omicron VOC; a total of 100 mutations were identified, 48% of which were found in the S gene. In conclusion, the data demonstrated the rapid spread and persistence of Omicron VOC in Rondônia during the 12-month study period. Although high frequency of mutations was found in the analyzed samples, there were no individuals with a severe clinical profile, demonstrating that vaccination had a positive effect in those cases. |
| doi_str_mv | 10.1371/journal.pone.0285742 |
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S ; Teixeira, Karolaine S ; Araújo, Adrhyan ; Batista, Flávia S ; Souza, Valquiria R ; Oliveira, Franciane M ; Morello, Luis G ; Marchini, Fabricio K ; Salcedo, Juan M.V ; Rampazzo, Rita de Cassia P ; Naveca, Felipe G ; Vieira, Deusilene</creator><creatorcontrib>Sgorlon, Gabriella ; Roca, Tárcio P ; Passos-Silva, Ana Maisa ; Queiroz, Jackson A. S ; Teixeira, Karolaine S ; Araújo, Adrhyan ; Batista, Flávia S ; Souza, Valquiria R ; Oliveira, Franciane M ; Morello, Luis G ; Marchini, Fabricio K ; Salcedo, Juan M.V ; Rampazzo, Rita de Cassia P ; Naveca, Felipe G ; Vieira, Deusilene</creatorcontrib><description>Genomic surveillance represents a strategy to understanding the evolutionary mechanisms, transmission, and infectivity of different SARS-CoV-2 variants. We evaluated 603 individuals positive for SARS-CoV-2 from 34 municipalities of Rondônia between December 2021 to December 2022. Nasopharyngeal samples were collected, RNA was extracted and screened using RT-qPCR for VOCs. RNA of the samples were sequenced and further analyzed for phylogeny, mutations, and lineages, totaling 96.19% of samples positive for Omicron VOC in this cohort. We observed that most individuals had at least two doses, however 18.97% were not vaccinated with any dose. 554 sequences were amenable to analysis for alignment and phylogenetic characterization; this group corresponded to the 27 subvariants of the Omicron VOC; a total of 100 mutations were identified, 48% of which were found in the S gene. In conclusion, the data demonstrated the rapid spread and persistence of Omicron VOC in Rondônia during the 12-month study period. 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| subjects | Analysis Biology and life sciences Computer and Information Sciences COVID-19 Disease transmission Genomes Health aspects Infectivity Maximum likelihood method Medicine and health sciences Mutation People and places Phylogeny Prevention Research and analysis methods Ribonucleic acid RNA S gene Severe acute respiratory syndrome coronavirus 2 Software Statistical analysis Surveillance Vaccination |
| title | The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-03T11%3A13%3A31IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=The%20emergence%20of%20Omicron%20VOC%20and%20its%20rapid%20spread%20and%20persistence%20in%20the%20Western%20Amazon&rft.jtitle=PloS%20one&rft.au=Sgorlon,%20Gabriella&rft.date=2023-08-17&rft.volume=18&rft.issue=8&rft.spage=e0285742&rft.epage=e0285742&rft.pages=e0285742-e0285742&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0285742&rft_dat=%3Cgale_plos_%3EA761278761%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2852603805&rft_id=info:pmid/&rft_galeid=A761278761&rft_doaj_id=oai_doaj_org_article_bd9943986a3849d1bd59b1bf8542c652&rfr_iscdi=true |