Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethical Considerations
2.2. Study Design, Period, and Setting
2.3. Quality Assurance
2.4. RNA-Extraction and Next-Generation Sequencing
2.5. Sample Preparation
2.6. Genome Sequencing
2.6.1. Genome Sequencing Using Illumina Sequencing Technologies
Tiling-Based Polymerase Chain Reaction
2.6.2. Genome Sequencing Using Oxford Nanopore Technologies
2.6.3. Metadata Management
2.6.4. Sequence Assembly, Alignment, and Phylogenetic Analysis
2.6.5. Data Analysis and Visualization
3. Results
3.1. Socio-Demographic Characteristics of the Study Participants
3.2. Local Epidemic Dynamics
3.3. Phylogenetic Reconstruction and Variant Detection in Ethiopia
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
AAPHREML | Addis Ababa Public Health Research and Emergency Management Laboratory |
AAU | Addis Ababa University |
ACDC | Africa Center for Disease Prevention and Control |
CERI | Centre for Epidemic Response and Innovation |
CI | Confidence interval |
CT | Cycle threshold |
GISAID | Global Initiative on Sharing All Influenza Data |
KRISP | KwaZulu-Natal Research Innovation and Sequencing Platform |
NAAT | Nucleic acid amplification tests |
PCR | Polymerase chain reaction |
RNA | Ribose nucleic acid |
RT-PCR | Reverse transcriptase polymerase chain reaction |
SARS-CoV-2 | Severe acute respiratory syndrome novel coronavirus-2 |
VOCs | Variants of concern |
VTM | Virus transport medium |
WHO | World Health Organization |
SDG | Sustainable development goal |
COVID-19 | Coronavirus disease 2019 |
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Variable | Class | Frequency (%) | Variant (VOC) | |||
---|---|---|---|---|---|---|
Alpha | Beta | Delta | Omicron | |||
Sex | Female | 181 (51.3) | 10 | 2 | 99 | 57 |
Male | 172 (48.7) | 7 | 1 | 102 | 46 | |
Age range (years) | 1–20 | 40 (11.3) | 7 | 1 | 19 | 8 |
21–30 | 121 (34.3) | 1 | 1 | 80 | 25 | |
31–40 | 84 (23.8) | 5 | 1 | 43 | 30 | |
41–50 | 41 (11.6) | 2 | 0 | 25 | 12 | |
51–60 | 21 (10.2) | 2 | 0 | 18 | 15 | |
>60 | 31 (8.8) | 0 | 0 | 16 | 13 | |
Reason for testing (during sampling) | Suspect | 107 (30.3) | 6 | 1 | 133 | 2 |
Contacts of confirmed cases | 79 (22.4) | 8 | 2 | 45 | 1 | |
Community Surveillance | 167 (47.3) | 3 | 0 | 23 | 100 | |
Clinical status of the clients while sampling | Asymptomatic * | 53 (15) | 3 | 0 | 37 | 5 |
Mild | 273 (77.3) | 14 | 3 | 142 | 94 | |
Severe | 27 (7.7) | 0 | 0 | 22 | 4 |
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Sisay, A.; Tshiabuila, D.; van Wyk, S.; Tesfaye, A.; Mboowa, G.; Oyola, S.O.; Tesema, S.K.; Baxter, C.; Martin, D.; Lessells, R.; et al. Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022. Genes 2023, 14, 705. https://doi.org/10.3390/genes14030705
Sisay A, Tshiabuila D, van Wyk S, Tesfaye A, Mboowa G, Oyola SO, Tesema SK, Baxter C, Martin D, Lessells R, et al. Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022. Genes. 2023; 14(3):705. https://doi.org/10.3390/genes14030705
Chicago/Turabian StyleSisay, Abay, Derek Tshiabuila, Stephanie van Wyk, Abraham Tesfaye, Gerald Mboowa, Samuel O. Oyola, Sofonias Kifle Tesema, Cheryl Baxter, Darren Martin, Richard Lessells, and et al. 2023. "Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022" Genes 14, no. 3: 705. https://doi.org/10.3390/genes14030705