Genomic surveillance of the variants of SARS CoV-2 that circulated in Cuba between March 2020 to September 2022
Keywords:
VOC, Non-VOC, S gene, SARS CoV-2, CubaAbstract
Introduction: In the face of the COVID-19 pandemic caused by the new SARS CoV-2 coronavirus, Cuba early established a strategic plan for its confrontation, confirming the first cases in March 2020. The objective of this work was to identify the variants of SARS CoV-2 that circulated in Cuba from March 2020 to September 2022 and their relationship with certain sociodemographic and clinical-epidemiological variables.
Methods: It was carried out a descriptive cross-sectional study. They were included 2,105 positive patient samples from all over the country. They were performed viral RNA extraction, amplification and sequencing of the N (nucleocapsid) and S (spicule) genes. They were performed mutation profiles and variant assignment using the GISAID database.
Results: During the year 2020, the D614G variant (84.2%) and the wild strain from Wuhan (5.2%) circulated. In 2021, they were detected 18 variants, among them Alpha, Beta, Gamma, Delta and Omicron (of concern). The most frequent were Beta (34.77%), Delta (24.89%), D614G (19%) and Omicron (7.6%). Delta was associated with a higher incidence of the disease and Beta with clinical severity. The Omicron variant displaced Delta at the end of 2021, with no increase in lethality. During 2022 circulated the variants of Omicron, BA.1, BA.2 and BA.5. Conclusions: Genomic surveillance made it possible to demonstrate the circulation of multiple variants in Cuba and their relationship with clinical severity and transmissibility. The relatively milder behavior of the disease caused by the Omicron variant could be influenced by the high vaccination coverage and the natural immunity acquired during the Delta wave.
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