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Nyagupe, C., De Oliveira Martins, L., Gumbo, H., Mashe, T., Takawira, T., Maeka, K. K., Juru, A., Chikanda, L. K., Tauya, A. R., Page, A. J., Kingsley, R. A. 
ORCID: https://orcid.org/0000-0002-0194-6485, Simbi, R., Chirenda, J., Manasa, J., Ruhanya, V. and Mavenyengwa, R. T.
(2023)
SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe:A retrospective genomic analysis.
South African Medical Journal, 113 (3).
pp. 141-147.
ISSN 0256-9574
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Abstract
Background. SARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccines caused by inequitable distribution. Objective. To monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health. Methods. Here we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples were sequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed. Results. The Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994 mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acid substitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previous infection or vaccination. Conclusion. There were nine lineages circulating in Zimbabwe during the second wave. The B.1.351 was dominant, accounting for >75%. There were over 3 000 mutations on the diagnostic genes and lineage B.1.351, contributing almost two-thirds of the mutations. The S-gene had the most mutations and the E-gene was the least mutated.
| Item Type: | Article |
|---|---|
| Additional Information: | Funding Information: Declaration. This article partially fulfils the requirements of CN’s MPhil degree. Acknowledgements. The authors wish to thank Prof. R T Mavenyengwa, Dr V Ruhanya and Dr J Manasa for their unwavering support and mentorship, and Mr H Gumbo and Dr L de Oliveira Martins for sequencing support. Author contributions. CN wrote the first draft. Funding acquisition: AJP, RAK. Leadership and supervision: AJP, RAK, RTM, VR, AG, RS, JC. Metadata curation: CN, HG, MT, TT. Samples and logistics: CN, KKM, LS. Sequencing and analysis: CN, HG, LdOM. Visualisation: CN, LdOM Funding. The Quadram Institute authors gratefully acknowledge the support of the Biotechnology and Biological Sciences Research Council (BBSRC); their research was funded by the BBSRC Institute Strategic Programme Microbes in the Food Chain BB/R012504/1 and its constituent project BBS/E/F/000PR10352, and Quadram Institute Bioscience BBSRC funded Core Capability Grant (project number BB/CCG1860/1). For open access, the author has applied a cc-by public copyright licence to any author-accepted manuscript version arising from this submission. Conflicts of interest. None. Publisher Copyright: © 2023 South African Medical Association. All rights reserved. |
| Uncontrolled Keywords: | medicine(all),sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/2700 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 31 Oct 2024 15:30 |
| Last Modified: | 03 Nov 2024 00:54 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97387 |
| DOI: | 10.7196/SAMJ.2023.v113i3.16762 |
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