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

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: COVID-19; Ethiopia; SARS-CoV-2; molecular epidemiology; whole genome sequence.

Figure 1

SARS-CoV-2 epidemiology and variant turnover in Ethiopia: (A) 7-day rolling average for the number of new SARS-CoV-2 cases. Others, represented in blue, comprise mostly B lineages, including B, B.1, and B.1.1 lineages. The size of the dot is indicative of the proportion of variant genomes sampled, whereas the rug plot (bottom segment of (A)) shows the distribution of genomes during the sampling period. (B) The proportion of individuals that have received at least one vaccine dose in Ethiopia compared to the number of new deaths that occurred. (C) Summary of the mean number of detected introductions into Ethiopia binned by month for different regions across the dataset. (D) Summary of the mean number of detected exportations out of Ethiopia to different regions binned by month.

Figure 2

SARS-CoV-2 lineage diversity in Ethiopia. (A) Proportions of SARS-CoV-2 lineages, classified by Pangolin nomenclature, circulating between June 2020 and February 2022 in Ethiopia. (B) Absolute counts of SARS-CoV-2 genomes throughout the study period. Only VOCs and major lineages are listed in the legend. (C) Maximum-Likelihood phylogeny of 353 SARS-CoV-2 genomes. Branches are colored by lineage.