Genomic Characterization of Predominance Delta Variant (B.1.617.2 and AY.120 sub-lineages) SARS-CoV-2 Detected from AFI Patients in Ethiopia during 2021-2022

The Delta variant of SARS-CoV-2 virus, one of the alarming variants of concern (VOC) with a distinct mutation characteristic, was immensely detrimental and a significant cause of the prolonged pandemic waves. This study intends to analyze the genetic characteristics of the predominant Delta variant detected from Acute Febrile Illness (AFI) patients in Ethiopia. Nasopharyngeal samples were collected from AFI patients in four hospitals during February 2021 to June 2022 and tested for SARS-CoV-2 by using RT-qPCR. Of 101 positive samples, 48 stored specimens were re-tested, and 26 with sufficient RNA quality (Ct < 30) were sequenced using whole-genome sequencing to identify variants of concern, specific virus lineages and mutation features. Delta variants (21J clade) found predominant among all the sequenced SARS-CoV-2 isolate (80.8%, 21/26). AY.120 (46.2%) and B.1.617.2 (26.9%) were the predominant sub lineages of the delta variant. Omicron (21k, Pango BA.1.1/BA.1.17/ BA.1) and Alpha (20I, Pango B.1.1.7) variants accounted for 11.5% and 7.7% of the total sequenced samples. Phylogenetic analysis showed evidence of local transmission and possible multiple introductions of SARS-CoV-2 VOCs in Ethiopia. The number of mutations increases dramatically from Alpha (~35 avg) to Delta (~42 avg) to Omicron (~56 avg). The Delta variant revealed a spike mutation on L452R and T478K and P681R, and characterized by the double deletion E156-F157- in Spike protein. The findings observed in this study is indicative of a gradual change in the genetic coding of the virus underscoring the importance of ongoing genomic surveillance to track the evolution and spread of SARS-CoV-2 and other emerging virus.