• C Nyagupe, L de Oliveira Martins, H Gumbo, T Mashe, T Takawira, K K Maeka, A Juru, L K Chikanda, A R Tauya, A J Page, R A Kingsley, R Simbi, J Chirenda, J Manasa, V Ruhanya, and R T Mavenyengwa.
• 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. nyagupecharles@gmail.com.
• S. Afr. Med. J. 2023 Mar 2; 113 (3): 141147141-147.

BackgroundSARS-CoV-2 continues to be a major issue in resource-limited settings, particularly owing to the limited supply of vaccinescaused by inequitable distribution.ObjectiveTo monitor diagnostic gene targets to identify potential test failures caused by mutations, which is important for public health.MethodsHere we analysed the genome sequence of SARS-CoV-2 from the second wave in Zimbabwe. A total of 377 samples weresequenced at Quadram Institute Bioscience. After quality control, 192 sequences passed and were analysed.ResultsThe Beta variant was dominant during this period, contributing 77.6% (149) of the genomes sequenced and having a total of 2994mutations in diagnostic polymerase chain reaction target genes. Many single nucleotide polymorphism mutations resulted in amino acidsubstitution that had the potential to impact viral fitness by increasing the rate of transmission or evading the immune response to previousinfection or vaccination.ConclusionThere 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-genehad the most mutations and the E-gene was the least mutated.

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