Genes (Mar 2023)
Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020–2022
- Abay Sisay,
- Derek Tshiabuila,
- Stephanie van Wyk,
- Abraham Tesfaye,
- Gerald Mboowa,
- Samuel O. Oyola,
- Sofonias Kifle Tesema,
- Cheryl Baxter,
- Darren Martin,
- Richard Lessells,
- Houriiyah Tegally,
- Monika Moir,
- Jennifer Giandhari,
- Sureshnee Pillay,
- Lavanya Singh,
- Yajna Ramphal,
- Arisha Maharaj,
- Yusasha Pillay,
- Akhil Maharaj,
- Yeshnee Naidoo,
- Upasana Ramphal,
- Lucious Chabuka,
- Eduan Wilkinson,
- Tulio de Oliveira,
- Adey Feleke Desta,
- James E. San
Affiliations
- Abay Sisay
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Derek Tshiabuila
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Stephanie van Wyk
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Abraham Tesfaye
- Department of Medical Laboratory Sciences, College of Health Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Gerald Mboowa
- Institute of Pathogen Genomics, Africa Centers for Disease Control and Prevention (Africa CDC), African Union Commission, Roosevelt Street W21 K19, Addis Ababa P.O. Box 3243, Ethiopia
- Samuel O. Oyola
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya
- Sofonias Kifle Tesema
- Institute of Pathogen Genomics, Africa Centers for Disease Control and Prevention (Africa CDC), African Union Commission, Roosevelt Street W21 K19, Addis Ababa P.O. Box 3243, Ethiopia
- Cheryl Baxter
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Darren Martin
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Cape Town 7925, South Africa
- Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Monika Moir
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Jennifer Giandhari
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Sureshnee Pillay
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Lavanya Singh
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Yajna Ramphal
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Arisha Maharaj
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Yusasha Pillay
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Akhil Maharaj
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Yeshnee Naidoo
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Upasana Ramphal
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Lucious Chabuka
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch 7600, South Africa
- Adey Feleke Desta
- Department of Microbial, Cellular, and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- James E. San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- DOI
- https://doi.org/10.3390/genes14030705
- Journal volume & issue
-
Vol. 14,
no. 3
p. 705
Abstract
Ethiopia is the second most populous country in Africa and the sixth most affected by COVID-19 on the continent. Despite having experienced five infection waves, >499,000 cases, and ~7500 COVID-19-related deaths as of January 2023, there is still no detailed genomic epidemiological report on the introduction and spread of SARS-CoV-2 in Ethiopia. In this study, we reconstructed and elucidated the COVID-19 epidemic dynamics. Specifically, we investigated the introduction, local transmission, ongoing evolution, and spread of SARS-CoV-2 during the first four infection waves using 353 high-quality near-whole genomes sampled in Ethiopia. Our results show that whereas viral introductions seeded the first wave, subsequent waves were seeded by local transmission. The B.1.480 lineage emerged in the first wave and notably remained in circulation even after the emergence of the Alpha variant. The B.1.480 was outcompeted by the Delta variant. Notably, Ethiopia’s lack of local sequencing capacity was further limited by sporadic, uneven, and insufficient sampling that limited the incorporation of genomic epidemiology in the epidemic public health response in Ethiopia. These results highlight Ethiopia’s role in SARS-CoV-2 dissemination and the urgent need for balanced, near-real-time genomic sequencing.
Keywords