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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Bibliographic Details
Published in:	PloS one Vol. 18; no. 8; p. e0285742
Main Authors:	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
Format:	Journal Article
Language:	English
Published:	San Francisco Public Library of Science 17-08-2023 Public Library of Science (PLoS)
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 Brazil United States > US
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Summary:	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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Competing Interests: At the time of submission, R.C.P.R, L.G.M and F.K.M were employees at IBMP, which manufactures and commercializes the test described in this study. The other authors declare no potential conflict of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0285742