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

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.