The emergence of Omicron VOC and its rapid spread and persistence in the Western Amazon.
Journal
PloS one
ISSN: 1932-6203
Titre abrégé: PLoS One
Pays: United States
ID NLM: 101285081
Informations de publication
Date de publication:
2023
2023
Historique:
received:
22
01
2023
accepted:
30
04
2023
medline:
21
8
2023
pubmed:
17
8
2023
entrez:
17
8
2023
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 37590264
doi: 10.1371/journal.pone.0285742
pii: PONE-D-23-01948
pmc: PMC10434903
doi:
Substances chimiques
RNA
63231-63-0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e0285742Informations de copyright
Copyright: © 2023 Sgorlon et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Déclaration de conflit d'intérêts
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
Références
Nat Med. 2022 Jun;28(6):1297-1302
pubmed: 35322239
J Chem Inf Model. 2022 Jan 24;62(2):412-422
pubmed: 34989238
Cell. 2022 Feb 3;185(3):447-456.e11
pubmed: 35026151
Braz J Microbiol. 2022 Sep;53(3):1313-1319
pubmed: 35778549
Cell Host Microbe. 2023 Jan 11;31(1):9-17.e3
pubmed: 36476380
Front Immunol. 2022 Jan 03;12:809244
pubmed: 35046961
Bioinformatics. 2018 Dec 1;34(23):4121-4123
pubmed: 29790939
Geroscience. 2022 Apr;44(2):619-637
pubmed: 35258772
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Clin Infect Dis. 2022 Aug 03;:
pubmed: 35917440
Nat Microbiol. 2020 Nov;5(11):1403-1407
pubmed: 32669681
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
J Med Virol. 2022 Apr;94(4):1641-1649
pubmed: 34914115
J Travel Med. 2022 May 31;29(3):
pubmed: 35262737
Cell Rep Med. 2022 Jul 19;3(7):100679
pubmed: 35798000
Int J Infect Dis. 2021 Mar;104:373-378
pubmed: 33434663
Gene. 2022 Mar 10;814:146134
pubmed: 34990799
Cell Rep. 2021 Jan 12;34(2):108630
pubmed: 33417835
Virus Evol. 2021 Jul 30;7(2):veab064
pubmed: 34527285
Elife. 2021 Aug 26;10:
pubmed: 34435953
Microbiol Spectr. 2022 Feb 23;10(1):e0236621
pubmed: 35196783
Mem Inst Oswaldo Cruz. 2023 Jan 20;117:e220155
pubmed: 36700580
J Cell Physiol. 2021 Oct;236(10):7045-7057
pubmed: 33755190
J Virol. 2022 Oct 12;96(19):e0130122
pubmed: 36121299
Cell. 2020 Oct 29;183(3):739-751.e8
pubmed: 32991842
Nat Methods. 2017 Jun;14(6):587-589
pubmed: 28481363
J Med Virol. 2022 Jul;94(7):3410-3415
pubmed: 35233783