Molecular Epidemiology and Diversity of SARS-CoV-2 in Ethiopia, 2020-2022

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...

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Published in:Genes 2023-03, Vol.14 (3), p.705
Main Authors: Sisay, Abay, Tshiabuila, Derek, van Wyk, Stephanie, Tesfaye, Abraham, Mboowa, Gerald, Oyola, Samuel O, Tesema, Sofonias Kifle, Baxter, Cheryl, Martin, Darren, Lessells, Richard, Tegally, Houriiyah, Moir, Monika, Giandhari, Jennifer, Pillay, Sureshnee, Singh, Lavanya, Ramphal, Yajna, Maharaj, Arisha, Pillay, Yusasha, Maharaj, Akhil, Naidoo, Yeshnee, Ramphal, Upasana, Chabuka, Lucious, Wilkinson, Eduan, de Oliveira, Tulio, Desta, Adey Feleke, San, James E
Format: Article
Language:English
Subjects:
Coronaviruses
COVID-19
COVID-19 - epidemiology
COVID-19 - genetics
COVID-19 diagnostic tests
Disease transmission
Epidemics
Epidemiology
Ethiopia - epidemiology
Genomes
Genomics
Humans
Medical laboratories
Molecular Epidemiology
Pandemics
Public health
SARS-CoV-2 - genetics
Severe acute respiratory syndrome coronavirus 2
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Summary: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.
ISSN:2073-4425
2073-4425
DOI:10.3390/genes14030705