Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

The SARS-CoV-2 Omicron Variant of Concern and its Rapid Spread throughout the Western Brazilian Amazon

Version 1 : Received: 27 April 2022 / Approved: 28 April 2022 / Online: 28 April 2022 (03:28:50 CEST)

How to cite: Sgorlon-Oliveira, G.; Queiroz, J.A.D.S.; Gasparelo, N.W.F.; Roca, T.P.; Passos-Silva, A.M.; Teixeira, K.S.; Oliveira, A.A.D.S.; Souza, P.R.F.D.; Silva, E.D.S.; Silva, C.C.D.; Maia, A.C.S.; Azzi, C.F.G.; Batista, F.S.; Souza, V.R.D.; Oliveira, F.M.; Salcedo, J.M.V.; Pereira, S.D.S.; Naveca, F.G.; Rampazzo, R.D.C.P.; Morello, L.G.; Marchini, F.K.; Vieira, D. The SARS-CoV-2 Omicron Variant of Concern and its Rapid Spread throughout the Western Brazilian Amazon. Preprints 2022, 2022040266 (doi: 10.20944/preprints202204.0266.v1). Sgorlon-Oliveira, G.; Queiroz, J.A.D.S.; Gasparelo, N.W.F.; Roca, T.P.; Passos-Silva, A.M.; Teixeira, K.S.; Oliveira, A.A.D.S.; Souza, P.R.F.D.; Silva, E.D.S.; Silva, C.C.D.; Maia, A.C.S.; Azzi, C.F.G.; Batista, F.S.; Souza, V.R.D.; Oliveira, F.M.; Salcedo, J.M.V.; Pereira, S.D.S.; Naveca, F.G.; Rampazzo, R.D.C.P.; Morello, L.G.; Marchini, F.K.; Vieira, D. The SARS-CoV-2 Omicron Variant of Concern and its Rapid Spread throughout the Western Brazilian Amazon. Preprints 2022, 2022040266 (doi: 10.20944/preprints202204.0266.v1).

Abstract

Genomic surveillance represents an important strategy for understanding evolutionary mechanisms, transmission profile, and infectivity of different SARS-CoV-2 variants. We assessed the epidemiological profile of 366 individuals who tested positive for SARS-CoV-2 from 29 municipalities in Rondônia between December 2021 to March 2022. Samples were collected, RNA was ex-tracted and screened using RT-qPCR for Alpha, Beta, Gamma, Delta and Omicron VOCs and viral quantification was performed. Sequences were analyzed for phylogeny, mutations and lineages. Of the samples analyzed, 93.71% were positive for the Omicron variant and 6.28% were positive for the Delta variant. The symptoms observed were cough, sore throat, and fever, with a mean duration of 5 days; no hospitalizations or deaths were reported. We noted that among the positive individuals, 51% had been immunized with two doses, 22% received three doses, 13% received one dose, and 13% were not immunized. Just 242 samples were amenable to analysis for alignment and phylogenetic characterization; corresponding to variants BA.1 and BA.1.1; a total of 120 mutations were identified, 36% of which were found in the S gene. In conclusion, there was a high frequency of mutations in the SARS-CoV-2 genome, but no record of clinical severity, demonstrating the positive effect of vaccination.

Keywords

SARS CoV-2; Variant of Concern; Omicron; mutation; genomic surveillance

Subject

BIOLOGY, Other

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