Volume 10, Issue 3 (9-2022)                   JoMMID 2022, 10(3): 135-140 | Back to browse issues page

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Institut de Recherche en Sciences de la Santé (IRSS) /Laboratoire de Recherche Biomédicale (LaReBio), Ouagadougou, Burkina Faso
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Introduction: In Sub-Saharan Africa, the data on the mutations and variants of circulating SARS-CoV-2 is limited. This study aimed to screen specific mutations and variants of SARS-CoV-2 circulating in Burkina Faso. Methods: This study included symptomatic and asymptomatic individuals who underwent diagnostic testing for SARS-CoV-2 by RT-PCR on nasopharyngeal and oropharyngeal swabs from 7 December 2021 to 12 January 2022. Samples from individuals with a Ct value ≤ 33 were selected for the variants-specific mutation screening. The screening was performed using two kits, “SNPsig® SARS-COV-2 (Escape PLEX)" and "SNPsig® VariPLEX™ (COVID-19) Real-Time PCR Assay". Results: SARS-CoV-2 prevalence was 18.9% (332/1758). A total of 113 samples (34.04%) had a Ct value less than (≤ 33), with only 20.35% (23/113) belonging to symptomatic patients. The mean age was 39.01±13 years. The Beta variant (B.1.351) was the most detected one comprising 78.8% (89/113) of variants. Gamma and Delta variants were detected at a low proportion of 0.9% (1/113). No mutation or variant was detected in seven (6.2%) samples. Conclusion: Specific mutation screening detected Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2) variants of SARS-CoV-2 circulating in Burkina Faso. The absence of mutations in some samples might suggest variants other than those detected.
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Type of Study: Original article | Subject: Diagnostic/screening methods and protocols
Received: 2022/07/1 | Accepted: 2022/09/19 | Published: 2022/10/12

1. Li R, Pei S, Chen B, Song Y, Zhang T, Yang W, et al. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV-2). Science (New York, NY). 2020; 368 (6490): 489-93. [DOI:10.1126/science.abb3221]
2. Nguyen HT, Zhang S, Wang Q, Anang S, Wang J, Ding H, et al. Spike Glycoprotein and Host Cell Determinants of SARS-CoV-2 Entry and Cytopathic Effects. J Virol. 2021; 95 (5): e02304-20. [DOI:10.1128/JVI.02304-20]
3. Cucinotta D, Vanelli M. WHO Declares COVID-19 a Pandemic. Acta Biomed. 2020; 91 (1):157-60.
4. John Hopkins. COVID-19 Dashboard. https://coronavirus.jhu.edu/map.html (Accessed on 25 April, 2022)
5. Malone B, Urakova N, Snijder EJ, Campbell EA. Structures and functions of coronavirus replication-transcription complexes and their relevance for SARS-CoV-2 drug design. Nat Rev Mol Cell Biol. 2022; 23 (1): 21-39. [DOI:10.1038/s41580-021-00432-z]
6. Petrosillo N, Viceconte G, Ergonul O, Ippolito G, Petersen E. COVID-19, SARS and MERS: are they closely related? Clin Microbiol and Infect. 2020; 26 (6): 729-34. [DOI:10.1016/j.cmi.2020.03.026]
7. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Genome Composition and Divergence of the Novel Coronavirus (2019-nCoV) Originating in China. Cell Host Microbe. 2020; 27 (3): 325-8. [DOI:10.1016/j.chom.2020.02.001]
8. Aleem A, Akbar Samad AB, Slenker AK. Emerging Variants of SARS-CoV-2 And Novel Therapeutics Against Coronavirus (COVID-19). 2022 Feb 6. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2022 Jan.
9. Pachetti M, Marini B, Benedetti F, Giudici F, Mauro E, Storici P, et al. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant. J Transl Med. 2020; 18 (1): 179. [DOI:10.1186/s12967-020-02344-6]
10. Wu A, Peng Y, Huang B, Ding X, Wang X, Niu P, et al. Antibody resistance of SARS-CoV-2 variants B.1.351 and B.1.1.7. Nature. 2021; 593 (7857): 130-5. [DOI:10.1038/s41586-021-03398-2]
11. Tchesnokova V, Kulasekara H, Larson L, Bowers V, Rechkina E, Kisiela D, et al. Acquisition of the L452R Mutation in the ACE2-Binding Interface of Spike Protein Triggers Recent Massive Expansion of SARS-CoV-2 Variants. J Clin Microbiol. 2021; 59 (11): e00921-21. [DOI:10.1128/JCM.00921-21]
12. Greaney AJ, Loes AN, Crawford KHD, Starr TN, Malone KD, 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 Microbe. 2021; 29 (3): 463-76.e6. [DOI:10.1016/j.chom.2021.02.003]
13. Xing Y, Li X, Gao X, Dong Q. Natural Polymorphisms Are Present in the Furin Cleavage Site of the SARS-CoV-2 Spike Glycoprotein. Front Genet. 2020; 11: 783. [DOI:10.3389/fgene.2020.00783]
14. Hassine IH. COVID-19 vaccines and variants of concern: A review. Rev Med Virol. 2021: e2313.
15. CDC. SARS-CoV-2 Variant Classifications and Definitions. https://www.cdc.gov/coronavirus/2019-ncov/variants/variant-classifications.html (Accessed on 25 April, 2022)
16. World Health Organization. 2022. Suivi des variants du SARS-CoV-2. https://www.who.int/fr/activities/tracking-SARS-CoV-2-variants (Accessed on 04 April 2022)
17. Boudet A, Stephan R, Bravo S, Sasso M, Lavigne J-P. Limitation of Screening of Different Variants of SARS-CoV-2 by RT-PCR. Diagnostics (Basel). 2021; 11 (7): 1241. [DOI:10.3390/diagnostics11071241]
18. CORUS. Evolution des cas de COVID-19 au Burkina Faso. http://www.corus.gov.bf/statistiques (Accessed on 04 April 2022)
19. Al Bayat S, Mundodan J, Hasnain S, Sallam M, Khogali H, Ali D, et al. Can the cycle threshold (Ct) value of RT-PCR test for SARS CoV2 predict infectivity among close contacts? J Infect Public Health. 2021; 14 (9): 1201-5. [DOI:10.1016/j.jiph.2021.08.013]
20. Platten M, Hoffmann D, Grosser R, Wisplinghoff F, Wisplinghoff H, Wiesmüller G, et al. SARS-CoV-2, CT-Values, and Infectivity-Conclusions to Be Drawn from Side Observations. Viruses. 2021; 13 (8): 1459. [DOI:10.3390/v13081459]
21. World Health Organization. Western and Southern Africa Initiative to build molecular capacities. WHO AFRO COVID Lab Team. Webinar
22. Oran DP, Topol EJ. Prevalence of Asymptomatic SARS-CoV-2 Infection: A Narrative Review. Ann Intern Med. 2020; 173 (5): 362-7. [DOI:10.7326/M20-3012]
23. Wilkinson E, Giovanetti M, Tegally H, San JE, Lessells R, Cuadros D, et al. A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa. Science (New York, NY). 2021; 374 (6566): 423-31. [DOI:10.1126/science.abj4336]
24. Mandolo J, Msefula J, Henrion MYR, Brown C, Moyo B, Samon A, et al. SARS-CoV-2 exposure in Malawian blood donors: an analysis of seroprevalence and variant dynamics between January 2020 and July 2021. BMC Med. 2021; 19 (1): 303. [DOI:10.1186/s12916-021-02187-y]
25. Service d'information du Gouvernement (SIG). Vaccin contre la COVID-19 : Des autorités reçoivent les premières doses. 2021. https://www.google.com/urlsa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwivxJ2e_rP3AhXmi_0HHYO3B6oQFnoECA8QAQ&url=https%3A%2F%2Fwww.sig.gov.bf%2Fdetails%3Ftx_news_pi1%255Baction%255D%3Ddetail%26tx_news_pi1%255Bcontroller%255D%3DNews%26tx_news_pi1%255Bnews%255D%3D1219%26cHash%3D18a7642988fafeffa44401a63226a3f0&usg=AOvVaw2XA7NKuNHqfJshCcw4Lws1 (Accessed on 22 April, 2022)
26. Cele S, Gazy I, Jackson L, Hwa SH, Tegally H, Lustig G, et al. Escape of SARS-CoV-2 501Y.V2 from neutralization by convalescent plasma. Nature. 2021; 593 (7857): 142-6. [DOI:10.1038/s41586-021-03471-w]
27. Moyo-Gwete T, Madzivhandila M, Makhado Z, Ayres F, Mhlanga D, Oosthuysen B, et al. SARS-CoV-2 501Y.V2 (B.1.351) elicits cross-reactive neutralizing antibodies. bioRxiv: Preprint. 2021. [DOI:10.1101/2021.03.06.434193]
28. Pearson CA, Russell1 TW, Davies NG, Kucharski AJ, CMMID COVID-19 working group, Edmunds WJ, et al. (2021)' Estimates of severity and transmissibility of novel South Africa SARS-CoV-2 variant 501Y.V2'. Preprint. 2021. 50; 1-4.
29. Shinde V, Bhikha S, Hoosain Z, Archary M, Bhorat Q, Fairlie L, et al. Efficacy of NVX-CoV2373 COVID-19 Vaccine against the B.1.351 Variant. N Engl J Med. 2021; 384 (20): 1899-909. [DOI:10.1056/NEJMoa2103055]
30. Francisco RDS, Jr., Benites LF, Lamarca AP, de Almeida LGP, Hansen AW, Gularte JS, et al. Pervasive transmission of E484K and emergence of VUI-NP13L with evidence of SARS-CoV-2 co-infection events by two different lineages in Rio Grande do Sul, Brazil. Virus Res. 2021; 296: 198345. [DOI:10.1016/j.virusres.2021.198345]
31. Ong SWX, Chiew CJ, Ang LW, Mak T-M, Cui L, Toh MPHS, et al. Clinical and virological features of SARS-CoV-2 variants of concern: a retrospective cohort study comparing B.1.1.7 (Alpha), B.1.315 (Beta), and B.1.617.2 (Delta). Clin Infect Dis. 2022: 75 (1): e1128-e36. [DOI:10.1093/cid/ciab721]

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