Epidemiological situation of the SARS-CoV-2 variants detected in Antioquia, from December 2020 to January 2022
DOI:
https://doi.org/10.33610/01229907.2022v4n1a4Keywords:
Genomics, Nanopore sequencing, Epidemiology, SARS-CoV-2 variantsAbstract
Introduction: Genomic sequencing is a tool that allows the identification of variants of SARS-CoV-2. The genomic surveillance network of Antioquia has been working on the characterization of the circulating variants in the territory to provide scientific evidence to decisionmakers in the pandemic context. The objective of this work is to describe the epidemiological situation of the SARSCoV-2 variants detected in Antioquia from December 2020 to January 2022.
Materials and methods: Descriptive cross-sectional study. The sequenced samples were part of the probabilistic and routine sampling of the National Institute of Health (INS). The Oxford nanopor platform was used for sequencing, additionally, the Sivigila and INS COVID-19 case reporting databases were used for sociodemographic and clinical data. The identification of the lineages and the quality score of the sequences was performed out in Nextclade and Pangolin.
Results: In Antioquia, circulating variants of SARS-CoV-2 were identified in 2 675 samples. Among the variants and/or lineages identified, Delta, Mu and Gamma had the highest proportion, contributing 39 %, 27 % and 14 % respectively, however, the Omicron variant since its identification (December 10, 2021) presented a wide distribution in the department.
Discussion: The lineages determination allowed evidence of the viral genetic diversity circulating in the region, showing a differential Spatio-temporal prevalence compared to the national context. Genomic surveillance will be strengthened with the aim of monitoring characterisitics under sociodemographic variables.
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