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SARS-CoV-2 Genetic Variants Identified in Selected Regions of Ethiopia Through Whole Genome Sequencing: Insights from the Fifth Wave of COVID-19

Year: 2025

Type: article

Abstract: Background: During the COVID-19 pandemic, global sequencing highlighted SARS-CoV-2 variants with increased transmissibility and immune evasion. In Ethiopia, where COVID-19 cases surged, little was known about the virus's dynamics. This study aimed to analyze SARS-CoV-2 variants during the fifth wave of the pandemic, crucial for vaccine, therapeutic, and diagnostic selection, as well as understanding of disease progression and severity. Method: From the samples collected from different parts of the country between June and August 2022, a total of 150 SARS-CoV-2 positive samples were randomly retrieved from the repository of the national SARS-CoV-2 reference laboratory of Ethiopian Public Health Institute (EPHI). Samples were re-analyzed using BIO-RAD, CFX96 Deep Well™ Real-Time PCR Detection system. Only 70 samples with a Ct value <30 were selected for next-generation sequencing using NextSeq 550 platform (Illumina platform). Out of 70, 63 genome sequences passed the bioinformatics quality and were chosen for further analysis. The genomic data was analyzed using bioinformatics and statistical tools. The reference genome "hCoV-19/Wuhan/WIV04/2019" was used for phylogeny. In addition, 117 sequence pairs were downloaded from GISAID, originating from 18 neighbouring countries and different parts of the world, in order to estimate the average evolutionary divergence across all sequence pairs. Results: Of the 63 genome sequences, 44 (69.8%) were from male and 19 (30.2%) were from Female. The median age of patient was 34 years. The dominant variant was Omicron (97%, 61/63), followed by Delta (3.2%, 2/63). Within Omicron, clade 22A was most prevalent (64%, 40/63), while other clades like 22B (18%, 11/63) and 21K (14%, 9/63) also present. Evolutionary divergence was limited, with Ethiopian sequences showing less genetic diversity compared to global sequences. Conclusion:The Omicron variant dominated the fifth wave in Ethiopia, with evidence of recent community transmission. Despite slight differences in genetic diversity with global sequences, the study underscores the importance of ongoing surveillance for variant tracking and public health interventions.

Source: Genes

DOI: 10.3390/genes16030351