Genetic diversity of sars-cov-2 in southern province of Zambia.

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Katowa, Ben
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The University of Zambia
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), has spread globally with catastrophic effects on the public health system. Four main Variants of Concern (VOCs), namely Alpha, Beta, Delta and Omicron, have been associated with waves of high transmission throughout the world. This study aimed at characterizing the SARS-CoV-2 variants that were circulating in Southern Province, Zambia. Nasopharyngeal swabs samples were collected between December 2020 and April 2022 from eight districts in Southern Province. A total of 198 samples were transported to Macha Research Trust (MRT) for Whole Genome Sequencing (WGS). Detection of the SARS-CoV-2 genome was done using the CDC protocol (Lu et al., 2020). The Oxford Nanopore and Nextseq illumina platforms were used for WGS. From the 198 samples collected, a total of 40 whole genomes were sequenced. Genetic analysis of 40 SARS-CoV-2 whole genomes revealed the circulation of Alpha (B.1.1.7), Beta (B.1.351), Delta (AY.116) and four Omicron lineages (BA.1, BA 1.1, BA 1.1.4 and BA2). From the seven lineages 42 percent, 15 percent, 13 percent, 10 percent, 10 percent, seven percent and three percent belonged to BA.1, B.1.351, BA.2, BA 1.1., AY.116, B.1.17 and BA 1.1.4 lineages, respectively. Across the 40 genomes analysed, a total of 292 mutations were observed from the original Wuhan/Hu 1/2019/EPI 1SL 402125 reference genome, of which 281 (96.2 percent) were found in the coding region of the genome, including 182 missense mutations, 66 synonymous mutations, 23 deletions, 9 insertions, 1 stop codon, and 11 mutations in the non-coding region. The Spike region had 82 mutations followed by the NSP3 region with 42 mutations. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Zambia from different European and African countries. This study stresses the need for continued genomic monitoring of SARS-CoV-2 circulation in Zambia to inform public health mitigation measures, particularly in strategically positioned regions such as the Southern Province which could be at increased risk of introduction of novel VOCs.
Thesis of Master of Science in Infectious Diseases.