{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T03:46:05Z","timestamp":1791517565678,"version":"4.3.4"},"reference-count":38,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T00:00:00Z","timestamp":1740700800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Viruses"],"abstract":"<jats:p>The eastern parts of Ethiopia, including Dire Dawa City, have experienced annual dengue fever (DF) outbreaks since 2013, leading to significant healthcare and economic impacts. However, comprehensive evidence on the specific dengue virus (DENV) serotypes and genotypes involved remains limited. During the 2023 DF outbreak, the National Arbovirus Laboratory received seventy serum samples from suspected DF patients. Positive samples underwent sequencing of the CprM region of the DENV genome, and the obtained sequences were analyzed phylogenetically. Among the patients, 32 (45.7%) displayed early warning signs of severe dengue, and 13 were hospitalized, most showing symptoms indicative of severe dengue. Out of 67 adequate samples, 44 (65.6%) tested positive for DENV RNA by RT-PCR, and 17 successfully underwent CprM sequencing. All sequenced samples were identified as DENV-3, genotype III, major lineage B (DENV-3III_B), with two distinct minor lineages (DENV-3III_B.2 and DENV-3III_B.3). Phylogenetic analysis showed that these lineages were closely related to sequences from the Afar region, suggesting interconnected outbreaks with multiple co-circulating lineages. This study identifies DENV-3III_B as the cause of the 2023 DF outbreak in Dire Dawa City and highlights the need for enhanced viral genomic surveillance in Africa.<\/jats:p>","DOI":"10.3390\/v17030346","type":"journal-article","created":{"date-parts":[[2025,2,28]],"date-time":"2025-02-28T06:45:42Z","timestamp":1740725142000},"page":"346","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Lineage B Genotype III of Dengue Virus Serotype 3 (DENV-3III_B) Is Responsible for Dengue Outbreak in Dire Dawa City, Ethiopia, 2023"],"prefix":"10.3390","volume":"17","author":[{"given":"Abebe Aseffa","family":"Negeri","sequence":"first","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4118-8260","authenticated-orcid":false,"given":"Dawit Hailu","family":"Alemayehu","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saro Abdella","family":"Abrahim","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tsigereda Kifle","family":"Wolde","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-7492-9046","authenticated-orcid":false,"given":"Gutema Bulti","family":"Tura","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7762-8208","authenticated-orcid":false,"given":"Alemnesh Hailemariam","family":"Bedasso","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-6396-8024","authenticated-orcid":false,"given":"Danile Tsega","family":"Geretsion","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ebise Abose","family":"Djirata","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eyilachew Zenebe","family":"Awule","sequence":"additional","affiliation":[{"name":"Dire Dawa City Administration Health Bureau, Dire Dawa P.O. Box 1377, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7902-2231","authenticated-orcid":false,"given":"Diana","family":"Rojas-Gallardo","sequence":"additional","affiliation":[{"name":"Population Biology, Ecology and Evolution Graduate Program, Emory University, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Asefa Konde","family":"Korkiso","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kalkidan","family":"Melaku","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-8915-552X","authenticated-orcid":false,"given":"Raffael","family":"Joseph","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Abaysew","family":"Ayele","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7756-9110","authenticated-orcid":false,"given":"Mesfin Mengesha","family":"Tsegaye","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5942-1534","authenticated-orcid":false,"given":"Anne","family":"Piantadosi","sequence":"additional","affiliation":[{"name":"Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Getachew","family":"Tollera","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alemseged","family":"Abdissa","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1245-8839","authenticated-orcid":false,"given":"Mesay Hailu","family":"Dangiso","sequence":"additional","affiliation":[{"name":"Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adane","family":"Mihret","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2862-0175","authenticated-orcid":false,"given":"Andargachew","family":"Mulu","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0696-3786","authenticated-orcid":false,"given":"Tesfaye","family":"Gelanew","sequence":"additional","affiliation":[{"name":"Armauer Hansen Research Institute, Addis Ababa P.O. Box 1005, Ethiopia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,2,28]]},"reference":[{"key":"ref_1","unstructured":"(2024, April 07). Dengue-Global Situation. Available online: https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2023-DON498."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"taab146","DOI":"10.1093\/jtm\/taab146","article-title":"Global burden for dengue and the evolving pattern in the past 30 years","volume":"28","author":"Yang","year":"2021","journal-title":"J. Travel Med."},{"key":"ref_3","unstructured":"(2024, April 07). Geographical Expansion of Cases of Dengue and Chikungunya Beyond the Historical Areas of Transmission in the Region of the Americas. Available online: https:\/\/www.who.int\/emergencies\/disease-outbreak-news\/item\/2023-DON448."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1139\/cjm-2020-0572","article-title":"Dengue virus: Epidemiology, biology, and disease aetiology","volume":"67","author":"Roy","year":"2021","journal-title":"Can. J. Microbiol."},{"key":"ref_5","unstructured":"(2024, February 25). Dengue and Severe Dengue. Available online: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/dengue-and-severe-dengue."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Mekuriaw, W., Kinde, S., Kindu, B., Mulualem, Y., Hailu, G., Gebresilassie, A., Sisay, C., Bekele, F., Amare, H., and Wossen, M. (2022). Epidemiological, Entomological, and Climatological Investigation of the 2019 Dengue Fever Outbreak in Gewane District, Afar Region, North-East Ethiopia. Insects, 13.","DOI":"10.3390\/insects13111066"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Gutu, M.A., Bekele, A., Seid, Y., Mohammed, Y., Gemechu, F., Woyessa, A.B., Tayachew, A., Dugasa, Y., Gizachew, L., and Idosa, M. (2021). Another dengue fever outbreak in Eastern Ethiopia\u2014An emerging public health threat. PLoS Neglected Trop. Dis., 15.","DOI":"10.1371\/journal.pntd.0008992"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"7207","DOI":"10.2147\/IDR.S368562","article-title":"Dengue Fever Outbreak Investigation in Werder Town, Dollo Zone, Somali Region, Ethiopia","volume":"15","author":"Mesfin","year":"2022","journal-title":"Infect. Drug Resist."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"5680","DOI":"10.1002\/jmv.27116","article-title":"Dengue and COVID-19: A risk of coepidemic in Ethiopia","volume":"93","author":"Mohan","year":"2021","journal-title":"J. Med. Virol."},{"key":"ref_10","first-page":"123","article-title":"Description of Serotype 3 Dengue Fever Virus: Clinical, Surveillance and Geographical Expansion in the Northeastern Ethiopia","volume":"11","author":"Sisay","year":"2023","journal-title":"Sci. J. Public Health"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1116","DOI":"10.1080\/22221751.2021.1935327","article-title":"Clinical signs and symptoms associated with WHO severe dengue classification: A systematic review and meta-analysis","volume":"10","author":"Htun","year":"2021","journal-title":"Emerg. Microbes Infect."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"545","DOI":"10.1128\/jcm.30.3.545-551.1992","article-title":"Rapid detection and typing of dengue viruses from clinical samples by using reverse transcriptase-polymerase chain reaction","volume":"30","author":"Lanciotti","year":"1992","journal-title":"J. Clin. Microbiol."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Hill, V., Cleemput, S., Pereira, J.S., Gifford, R.J., Fonseca, V., Tegally, H., Brito, A.F., Ribeiro, G., de Souza, V.C., and Brcko, I.C. (2024). A New Lineage Nomenclature to Aid Genomic Surveillance of Dengue Virus. PLoS Biol., 22.","DOI":"10.1371\/journal.pbio.3002834"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability","volume":"30","author":"Katoh","year":"2013","journal-title":"Mol. Biol. Evol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies","volume":"32","author":"Nguyen","year":"2015","journal-title":"Mol. Biol. Evol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"W293","DOI":"10.1093\/nar\/gkab301","article-title":"Interactive Tree Of Life (iTOL) v5: An online tool for phylogenetic tree display and annotation","volume":"49","author":"Letunic","year":"2021","journal-title":"Nucleic Acids Res."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"2429653","DOI":"10.1080\/22221751.2024.2429653","article-title":"Introduction of Dengue Virus Serotype 3 in the Afar Region, Ethiopia","volume":"13","author":"Mekonnen","year":"2024","journal-title":"Emerg. Microbes Infect."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1186\/s12985-020-01389-9","article-title":"Association of genotype III of dengue virus serotype 3 with disease outbreak in Eastern Sudan, 2019","volume":"17","author":"Eldigail","year":"2020","journal-title":"Virol. J."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Muthanje, E.M., Kimita, G., Nyataya, J., Njue, W., Mulili, C., Mugweru, J., Mutai, B., Kituyi, S.N., and Waitumbi, J. (2022). March 2019 dengue fever outbreak at the Kenyan south coast involving dengue virus serotype 3, genotypes III and V. PLoS Glob. Public Health, 2.","DOI":"10.1371\/journal.pgph.0000122"},{"key":"ref_20","first-page":"23","article-title":"Dengue Fever Outbreak Investigation and Response in Dire Dawa City Administration, Ethiopia, 2017","volume":"63","author":"Biru","year":"2020","journal-title":"J. Med."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s41182-023-00504-0","article-title":"Epidemiology, biology, pathogenesis, clinical manifestations, and diagnosis of dengue virus infection, and its trend in Ethiopia: A comprehensive literature review","volume":"51","author":"Zerfu","year":"2023","journal-title":"Trop. Med. Health"},{"key":"ref_22","first-page":"49","article-title":"Detection of serotype 1-Dengue fever outbreak in Dire Dawa city, Eastern Ethiopia","volume":"5","author":"Sisay","year":"2022","journal-title":"Ethiop. J. Public Health Nutr. (EJPHN)"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Tsegaye, M.M., Mekonnen, A.T., Gebretsion, D.T., Gelanew, T., Alemayehu, D.H., Tefera, D.A., Woldemichael, T.S., Getaneh, B.A., Abera, E.K., and Jebessa, G.G. (2024). Predominance of Dengue Virus Serotype-1\/Genotype-I in Eastern and Southeastern Ethiopia. Viruses, 16.","DOI":"10.3390\/v16081334"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"800","DOI":"10.3201\/eid0907.030038","article-title":"Emergence and Global Spread of a Dengue Serotype 3, Subtype III Virus","volume":"9","author":"Messer","year":"2003","journal-title":"Emerg. Infect. Dis."},{"key":"ref_25","unstructured":"(2024, March 11). A Malaria Outbreak in Ethiopia Came from an Invasive Asian Mosquito. Available online: https:\/\/www.sciencenews.org\/article\/malaria-outbreak-ethiopia-invasive-mosquito-asia."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3203","DOI":"10.1038\/s41591-023-02641-9","article-title":"Evidence for a role of Anopheles stephensi in the spread of drug- and diagnosis-resistant malaria in Africa","volume":"29","author":"Emiru","year":"2023","journal-title":"Nat. Med."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Degife, L.H., Worku, Y., Belay, D., Bekele, A., and Hailemariam, Z. (2019). Factors associated with dengue fever outbreak in Dire Dawa administration city, October, 2015, Ethiopia\u2014Case control study. BMC Public Health, 19.","DOI":"10.1186\/s12889-019-7015-7"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Nigussie, E., Atlaw, D., Negash, G., Gezahegn, H., Baressa, G., Tasew, A., and Zembaba, D. (2024). A dengue virus infection in Ethiopia: A systematic review and meta-analysis. BMC Infect. Dis., 24.","DOI":"10.1186\/s12879-024-09142-1"},{"key":"ref_29","first-page":"1","article-title":"Circulation of Dengue Virus Type 3 Genotype III in Africa Since 2008","volume":"4","author":"Maquart","year":"2016","journal-title":"J. Hum. Virol. Retrovirol."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"234","DOI":"10.1016\/j.meegid.2017.01.022","article-title":"Genetic diversity and evolution of dengue virus serotype 3: A comparative genomics study","volume":"49","author":"Waman","year":"2017","journal-title":"Infect. Genet. Evol."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Titir, S.R., Paul, S.K., Ahmed, S., Haque, N., Nasreen, S.A., Hossain, K.S., Ahmad, F.U., Nila, S.S., Khanam, J., and Nowsher, N. (2021). Nationwide Distribution of Dengue Virus Type 3 (DENV-3) Genotype I and Emergence of DENV-3 Genotype III During the 2019 Outbreak in Bangladesh. Trop. Med. Infect. Dis., 6.","DOI":"10.3390\/tropicalmed6020058"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1280","DOI":"10.4269\/ajtmh.1986.35.1280","article-title":"Dengue 3 Virus Transmission in Africa","volume":"35","author":"Gubler","year":"1986","journal-title":"Am. J. Trop. Med. Hyg."},{"key":"ref_33","first-page":"1349","article-title":"Dengue Virus Infection in Africa","volume":"17","author":"Amarasinghe","year":"2011","journal-title":"Emerg. Infect. Dis."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Eltom, K., Enan, K., El Hussein, A.R.M., and Elkhidir, I.M. (2021). Dengue Virus Infection in Sub-Saharan Africa Between 2010 and 2020: A Systematic Review and Meta-Analysis. Front. Cell Infect. Microbiol., 11.","DOI":"10.3389\/fcimb.2021.678945"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Gainor, E.M., Harris, E., and LaBeaud, A.D. (2022). Uncovering the Burden of Dengue in Africa: Considerations on Magnitude, Misdiagnosis, and Ancestry. Viruses, 14.","DOI":"10.3390\/v14020233"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1016\/j.ijregi.2021.09.010","article-title":"Severe Dengue in Adults and Children, Ouagadougou (Burkina Faso), West Africa, October 2015\u2013January 2017","volume":"1","author":"Sondo","year":"2021","journal-title":"IJID Reg."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1186\/s40249-021-00908-2","article-title":"Clinical Predictors of Severe Dengue: A Systematic Review and Meta-Analysis","volume":"10","author":"Tsheten","year":"2021","journal-title":"Infect. Dis. Poverty"},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1186\/s12936-023-04723-y","article-title":"Increasing Prevalence of Malaria and Acute Dengue Virus Coinfection in Africa: A Meta-Analysis and Meta-Regression of Cross-Sectional Studies","volume":"22","author":"Gebremariam","year":"2023","journal-title":"Malar. J."}],"container-title":["Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/346\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,9]],"date-time":"2025-10-09T16:44:29Z","timestamp":1760028269000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1999-4915\/17\/3\/346"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,28]]},"references-count":38,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2025,3]]}},"alternative-id":["v17030346"],"URL":"https:\/\/doi.org\/10.3390\/v17030346","relation":{},"ISSN":["1999-4915"],"issn-type":[{"value":"1999-4915","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,28]]}}}