SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis

Authors

  • C Nyagupe Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe; National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • L de Oliveira Martins Quadram Institute Bioscience, Norwich, UK
  • H Gumbo National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • T Mashe National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • T Takawira National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • KK Maeka National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • A Juru National Microbiology Reference Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • LK Chikanda Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
  • AR Tauya Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
  • AJ Page Quadram Institute Bioscience, Norwich, UK
  • RA Kingsley Quadram Institute Bioscience, Norwich, UK
  • R Simbi Directorate of Laboratory, Ministry of Health and Child Care, Harare, Zimbabwe
  • J Chirenda Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
  • J Manasa Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
  • V Ruhanya Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe
  • RT Mavenyengwa Microbiology Unit, Faculty of Medicine and Health Sciences, University of Zimbabwe, Harare, Zimbabwe

DOI:

https://doi.org/10.7196/SAMJ.2023.v113i3.16762

Keywords:

SARS-CoV

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.

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Published

2023-03-02

Issue

Vol. 113 No. 3 (2023)

Section

Research

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Copyright (c) 2023 C Nyagupe, L de Oliveira Martins, H Gumbo, T Mashe, T Takawira, KK Maeka, A Juru, LK Chikanda, AR Tauya, AJ Page, RA Kingsley, R Simbi, J Chirenda, J Manasa, V Ruhanya, RT Mavenyengwa

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How to Cite

1.
Nyagupe C, de Oliveira Martins L, Gumbo H, Mashe T, Takawira T, Maeka K, et al. SARS-CoV-2 mutations on diagnostic gene targets in the second wave in Zimbabwe: A retrospective genomic analysis. S Afr Med J [Internet]. 2023 Mar. 2 [cited 2025 Oct. 30];113(3):141-7. Available from: https://samajournals.co.za/index.php/samj/article/view/821