Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2023 Aug 17;18(8):e0285742.
doi: 10.1371/journal.pone.0285742. eCollection 2023.

The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon

Gabriella Sgorlon  1   2   3 , Tárcio P Roca  1   3   4 , Ana Maisa Passos-Silva  1   2   3 , Jackson A S Queiroz  1   2   3 , Karolaine S Teixeira  1   3 , Adrhyan Araújo  1   3 , Flávia S Batista  5 , Valquiria R Souza  6 , Franciane M Oliveira  6 , Luis G Morello  7   8 , Fabricio K Marchini  7   8 , Juan M V Salcedo  1   2   3 , Rita de Cassia P Rampazzo  7 , Felipe G Naveca  9 , Deusilene Vieira  1   2   3
Affiliations

The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon

Gabriella Sgorlon et al. PLoS One. .

Abstract

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.

PubMed Disclaimer

Conflict of interest statement

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

Figures

Fig 1
Fig 1. Viral load measured by the number of days after onset of symptoms.
Fig 2
Fig 2. Maximum likelihood phylogenetic tree presenting 554 sequences obtained in this study and 363 genomes retrieved from GISAID.
The samples are indicated as blue circles. The tree was rooted with the most ancestral sequence (EPI_ISL_402123).
Fig 3
Fig 3. Dot plot demonstrating the frequency of mutations identified in the set of 554 samples analyzed by NGS.
The labels of mutations with frequencies <2% have been hidden.
See this image and copyright information in PMC

References

    1. Papanikolaou V, Chrysovergis A, Ragos V, Tsiambas E, Katsinis S, Manoli A, et al.. From delta to Omicron: S1-RBD/S2 mutation/deletion equilibrium in SARS-CoV-2 defined variants. Gene. 2022;814. doi: 10.1016/j.gene.2021.146134 - DOI - PMC - PubMed
    1. Mistry P, Barmania F, Mellet J, Peta K, Strydom A, Viljoen IM, et al.. SARS-CoV-2 Variants, Vaccines, and Host Immunity. Front Immunol. 2022;12: 5400. doi: 10.3389/fimmu.2021.809244 - DOI - PMC - PubMed
    1. Tracking SARS-CoV-2 variants. [cited 10 Mar 2022]. Available: https://www.who.int/en/activities/tracking-SARS-CoV-2-variants/
    1. Sgorlon Oliveira G, Silva-Flannery L, da Silva JF, Siza C, Esteves RJ, Marston BJ, et al.. Active surveillance and early detection of community transmission of SARS-CoV-2 Mu variant (B.1.621) in the Brazilian Amazon. J Med Virol. 2022. [cited 15 Mar 2022]. doi: 10.1002/JMV.27686 - DOI - PMC - PubMed
    1. A rede–Genomahcov–Fiocruz. [cited 25 Oct 2022]. Available: https://www.genomahcov.fiocruz.br/a-rede/

Publication types

Supplementary concepts