Genomic characterization of SARS-CoV-2 during the COVID-19 pandemic in Villa Clara, Cuba
1 Department of Molecular Biology, Provincial Center of Hygiene, Epidemiology and Microbiology of Villa Clara, Cuba.
2 Department of Virology, Pedro Kourí Institute of Tropical Medicine (IPK), Cuba.
3 President of the Board EurAsia Heart Foundation, Switzerland.
4 Department of Hygiene and Epidemiology, Faculty of Health Technology and Nursing (FHTN), University of Medical Sciences of Villa Clara (UMS-VC), Cuba.
Research Article
Open Access Research Journal of Multidisciplinary Studies, 2026, 11(01), 036-046.
Article DOI: 10.53022/oarjms.2026.11.1.0018
Publication history:
Received on 20 December 2025; revised on 05 February 2026; accepted on 07 February 2026
Abstract:
Severe Acute Respiratory Syndrome Coronavirus 2 was declared a public health emergency of international concern in March 2020. This virus evolved into different genetic variants that circulated worldwide. Local genomic surveillance was crucial for the pandemic response. The objective of the research consisted in characterize the genomic surveillance of SARS-CoV-2 from confirmed cases at the Villa Clara LBM (Base Laboratory) during the study period. A cross-sectional descriptive study was conducted from December 2020 to May 2023. The study utilized 106 nasopharyngeal swab samples from patients confirmed by RT-PCR at the Villa Clara LBM, which were sent for nucleotide sequencing to the LNR-IVR-IPK (National Reference Laboratory-Insect Vector Department at the Pedro Kourí Institute). Patients infected with the Delta variant presented severe forms of the disease in 43.75% of cases. The Delta variant had the lowest median cycle threshold value (18.50). 100% of patients with the Delta variant had the mutations found in subgroup 3 (D614G, L452R, P681H, T478K). In the phylogenetic tree, the branch grouping the Omicron variant showed high genetic diversity. The use of genomic surveillance during the COVID-19 pandemic was essential for understanding the clinical-epidemiological dynamics linked to each circulating SARS-CoV-2 variant in Villa Clara province.
Keywords:
Genetic variants; Genomic surveillance; Severe Acute Respiratory Syndrome Coronavirus 2
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Copyright © 2026 Author(s) retain the copyright of this article. This article is published under the terms of the Creative Commons Attribution Liscense 4.0