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Article

Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia; A Retrospective Genomic Surveillance Study

1
Churches Health Association of Zambia, Lusaka 10101, Zambia
2
Virology Unit, Central Veterinary Research Institute, Ministry of Fisheries and Livestock, Lusaka 10101, Zambia
3
Global Fund to Fight AIDS, Tuberculosis and Malaria (GFATM), 1201 Geneva, Switzerland
4
Department of Pharmacy, School of Health Sciences, University of Zambia School of Health Sciences, Lusaka 10101, Zambia
5
University Teaching Hospital, Ministry of Health, Lusaka 10101, Zambia
6
Department of Epidemiology and Biostatistics, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
7
Public Health Department, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola 21692, Zambia
8
Department of Biomedical Sciences, School of Health Sciences, University of Zambia School of Health Sciences, Lusaka 10101, Zambia
9
Zambia National Public Health Institute Ministry of Health, Lusaka 10101, Zambia
10
Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia
11
Macha Research Trust, Choma 20100, Zambia
*
Authors to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(12), 6338; https://doi.org/10.3390/ijms25126338
Submission received: 9 April 2024 / Revised: 27 May 2024 / Accepted: 30 May 2024 / Published: 7 June 2024

Abstract

Mutations have driven the evolution and development of new variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with potential implications for increased transmissibility, disease severity and vaccine escape among others. Genome sequencing is a technique that allows scientists to read the genetic code of an organism and has become a powerful tool for studying emerging infectious diseases. Here, we conducted a cross-sectional study in selected districts of the Eastern Province of Zambia, from November 2021 to February 2022. We analyzed SARS-CoV-2 samples (n = 76) using high-throughput sequencing. A total of 4097 mutations were identified in 69 SARS-CoV-2 genomes with 47% (1925/4097) of the mutations occurring in the spike protein. We identified 83 unique amino acid mutations in the spike protein of the seven Omicron sublineages (BA.1, BA.1.1, BA.1.14, BA.1.18, BA.1.21, BA.2, BA.2.23 and XT). Of these, 43.4% (36/83) were present in the receptor binding domain, while 14.5% (12/83) were in the receptor binding motif. While we identified a potential recombinant XT strain, the highly transmissible BA.2 sublineage was more predominant (40.8%). We observed the substitution of other variants with the Omicron strain in the Eastern Province. This work shows the importance of pandemic preparedness and the need to monitor disease in the general population.
Keywords: SARS-CoV-2; SAR-CoV-2 mutations; Omicron variant; Eastern Province; Zambia; genomic surveillance SARS-CoV-2; SAR-CoV-2 mutations; Omicron variant; Eastern Province; Zambia; genomic surveillance

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MDPI and ACS Style

Shempela, D.M.; Chambaro, H.M.; Sikalima, J.; Cham, F.; Njuguna, M.; Morrison, L.; Mudenda, S.; Chanda, D.; Kasanga, M.; Daka, V.; et al. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia; A Retrospective Genomic Surveillance Study. Int. J. Mol. Sci. 2024, 25, 6338. https://doi.org/10.3390/ijms25126338

AMA Style

Shempela DM, Chambaro HM, Sikalima J, Cham F, Njuguna M, Morrison L, Mudenda S, Chanda D, Kasanga M, Daka V, et al. Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia; A Retrospective Genomic Surveillance Study. International Journal of Molecular Sciences. 2024; 25(12):6338. https://doi.org/10.3390/ijms25126338

Chicago/Turabian Style

Shempela, Doreen Mainza, Herman M. Chambaro, Jay Sikalima, Fatim Cham, Michael Njuguna, Linden Morrison, Steward Mudenda, Duncan Chanda, Maisa Kasanga, Victor Daka, and et al. 2024. "Detection and Characterisation of SARS-CoV-2 in Eastern Province of Zambia; A Retrospective Genomic Surveillance Study" International Journal of Molecular Sciences 25, no. 12: 6338. https://doi.org/10.3390/ijms25126338

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