Genetic characterization of SARS-CoV-2 isolates in the different pandemic stages of COVID-19 in Cuba
Keywords:
COVID-19, Cuba, genetic diversity, SARS-CoV-2.Abstract
Introduction: The development of safe and effective vaccines against SARS-CoV-2 posed a huge challenge to face the COVID-19 pandemic. The appearance of new variants of SARS-CoV-2 represents a challenge in evaluating the effectiveness of vaccines, different vaccine and therapeutic candidates developed by the scientific community.Objectives: Characterize and analyze the genetic diversity of Cuban viral isolates, in the period between June 2020 and December 2022.
Methods: SARS-CoV-2 RNA was obtained from 27 isolates from cell culture supernatant and the S gene was sequenced. The generated sequences were used for the identification and subsequent molecular characterization of the genetic variants of the virus through phylogenetic analysis and the use of the tools available in the GISEAD database.
Results: The variants detected in the Cuban SARS-CoV-2 isolates corresponded to those identified in the genomic surveillance studies carried out in the different stages of the COVID-19 pandemic in Cuba. 33.3 % of the sequenced isolates corresponded to the different lineages of the Omicron variant, followed by Beta B 1.351 (29.6 %), other SARS-CoV-2 lineages (25.9 %), Alpha B 1.1.7 (7.4 %) and Delta B.1.575 (3.7 %). The D614G mutation was detected in all SARS-CoV-2 isolates studied.
Conclusions: The molecular characterization of the Cuban isolates of SARS-CoV-2 has a high genetic diversity. It makes it possible to evaluate in vitro and in vivo vaccine candidates and therapeutic agents developed by the Cuban biopharmaceutical industry.
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References
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4. Pérez L, Tejero Y, Aguado ME, Valdés O, Álvarez M, Kourí V, et al. Sequencing of S and N genes of SARS-CoV-2 strains circulating in Cuba during March- September 2020. Journal of Microbiology and Infectious Diseases. 2022;12 (3): 78-88. DOI: 10.5799/jmid.1175386
5. Guzmán MG, Pérez L, Tejero Y, Mederos D, Aguado ME, Pintos Y, et al. Emergence and evolution of SARS-CoV-2 genetic variants during the Cuban epidemic. J Clin Virol Plus. 2022; 2(4):100104. DOI: 10.1016/j.jcvp.2022.100104
6. Pérez-Santos L, Kourí-Cardellá V, Tejero-Suárez Y, Macías-Roig L, Pintos-Saavedra Y, Medero-Díaz D, et al. Epidemiological characterization of patients in the first eight weeks following detection of SARS-CoV-2 B.1.529 (omicron) variant in Cuba: MEDICC Review. 2022; 24(3-4):18-23. DOI: 10.37757/MR2022.V24.N3-4.6
7. Noa Romero E, Enriquez Puertas JM, Machado Zaldívar LY, González Sosa NL, Montero González TJ, Falcón Cama V, et al. SARS-CoV-2 Isolation from Cuban COVID-19 Patients. American Journal of Rare Disorders: Diagnosis and Therapy. 2020 [acceso: 26/06/2023]; 3(1):009-015. Disponible en: https://www.sciresliterature.org/RareDisorders/AJRDDT-ID18.pdf
8. CDC. Protocols for SARS-CoV-2 sequencing. U.S. Department of Health & Human Services; 2020. [acceso: 26/06/2023]. Disponible en: https://www.cdc.gov/amd/training/covid-toolkit/module3-6.html
9. Tamura KD, Peterson D. MEGA 5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-39. DOI:10.1093/molbev/msr121
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11. Gouvea dos Santos W. Impact of virus genetic variability and host immunity for the success of COVID-19 vaccines. Biomedicine and Pharmacotherapy. 2021; 136: 111272. DOI: 10.1016/j.biopha 2021.111272
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13. Cathcart AL, Havenar-Daughton C, Lempp FA, Ma D, Schmid MA, Agostini ML, et al. The dual function monoclonal antibodies VIR-7831 and VIR-7832 demonstrate potent in vitro and in vivo activity against SARS-CoV-2. bioRxiv preprint. 2021. DOI: 10.1101/2021.03.09.434607
14. Wang Z, Schmidt F, Weisblum Y, Muecksch F, Barnes CO, Finkin S. mRNA vaccine-elicited antibodies to SARS-CoV-2 and circulating variants. Nature. 2021; 592: 616-622. DOI: 10.1038/s41586-021-03324-6
15. Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone K, Chu HY, et al. Comprehensive mapping of mutations in the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human plasma antibodies. Cell Host & Amp; Microbe. 2021; 29(3):463-76. DOI: 10.1016/j.chom.2021.02.003
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17. Fall A, Eldesouki RE, Sachithanandham J, Paul Morris C, Norton JM, Gaston DC, et al. The displacement of the SARS-CoV-2 variant Delta with Omicron: An investigation of hospital admissions and upper respiratory viral loads. eBioMedicine. 2022; 79:104008. DOI: https://doi.org/10.1016/j.ebiom.2022.104008
18. Mohapatra RK, Tiwari R. Twin combination of Omicron and Delta variants triggering a tsunami wave of ever high surges in COVID-19 cases: A challenging global threat with a special focus on the Indian subcontinent. J Med Virol. 2022; 94(5):1761-5. DOI: 10.1002/jmv.27585
19. Callaway E. Heavily mutated coronavirus variant puts scientists on alert. Nature. 2021; 600(7887): 21. DOI: 10.1038/d41586-021-03552-w
Published
2024-02-23
How to Cite
1.
Machado Zaldívar LY, Noa Romero E, López Rizo LS, Blanco de Armas M, González Sosa NL, Enríquez Puertas J, et al. Genetic characterization of SARS-CoV-2 isolates in the different pandemic stages of COVID-19 in Cuba. Rev Cubana Med Milit [Internet]. 2024 Feb. 23 [cited 2025 Jan. 9];53(1):e024016539. Available from: https://revmedmilitar.sld.cu/index.php/mil/article/view/16539
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