{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,28]],"date-time":"2026-02-28T07:33:12Z","timestamp":1772263992649,"version":"3.50.1"},"reference-count":40,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T00:00:00Z","timestamp":1762819200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background: 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 aimed to analyze the genetic characteristics of the predominant Delta variant in acute febrile illness (AFI) patients in Ethiopia. Method: Nasopharyngeal swab samples were collected from AFI patients in four hospitals from 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 &lt; 30) were sequenced using whole-genome sequencing to identify variants of concern, specific virus lineages and mutation features. Result: Delta variants (21J clade) were 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 was characterized by the double deletion E156-F157- in Spike protein. Conclusions: The findings are 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.<\/jats:p>","DOI":"10.3390\/genes16111366","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T10:56:27Z","timestamp":1762858587000},"page":"1366","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Genomic Characterization of Predominant Delta Variant (B.1.617.2 and AY.120 Sub-Lineages) SARS-CoV-2 Detected from AFI Patients in Ethiopia During 2021\u20132022"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0414-8304","authenticated-orcid":false,"given":"Musse Tadesse","family":"Chekol","sequence":"first","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"},{"name":"Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dejenie Shiferaw","family":"Teklu","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6338-9824","authenticated-orcid":false,"given":"Adamu","family":"Tayachew","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"},{"name":"Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wolde","family":"Shura","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Admikew","family":"Agune","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aster","family":"Hailemariam","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Aynalem","family":"Alemu","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"},{"name":"Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mesfin","family":"Wossen","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Abdulhafiz","family":"Hassen","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Melaku","family":"Gonta","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2348-1199","authenticated-orcid":false,"given":"Neamin","family":"Tesfay","sequence":"additional","affiliation":[{"name":"Public Health Emergency Management Center, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tesfu","family":"Kasa","sequence":"additional","affiliation":[{"name":"Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nigatu","family":"Kebede","sequence":"additional","affiliation":[{"name":"Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,11,11]]},"reference":[{"key":"ref_1","unstructured":"World Health Organization (2025, April 15). Tracking SARS-CoV-2 Variants 2021. Available online: https:\/\/www.who.int\/en\/activities\/tracking-SARS-CoV-2-variants\/."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Domingo, E., Garc\u00eda-Crespo, C., Lobo-Vega, R., and Perales, C. (2021). Mutation rates, mutation frequencies, and proofreading-repair activities in rna virus genetics. 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