Detection of Multiple Dengue Virus Serotypes Circulating in Somalia

Abstract

Dengue virus (DENV) is widely distributed across Africa but underreported due to limited surveillance and diagnostic capacity. Under an acute febrile illness surveillance protocol, we collected and screened 374 samples from patients with fever in Mogadishu, Somalia. Samples were screened for DENV serotypes using real-time reverse transcription polymerase chain reaction, and positive samples were sequenced and phylogenetically analyzed. We identified 55 samples containing orthoflavivirus RNA (14.7%). Of these 55 samples, three dengue serotypes, DENV serotype 1 (DENV-1, n = 24), DENV serotype 2 (DENV-2, n = 21), and DENV serotype 3 (DENV-3, n = 12), were identified. Two cases of coinfections were detected: 1) between DENV-1 and DENV-2 and 2) between DENV-2 and DENV-3. DENV-1 had two genetic clusters, both related to lineages from Asia. DENV-2 grouped within a set of sequences from Asia and Africa, particularly close to a DENV-2 outbreak in Kenya. The DENV-3 grouped with isolates from Oceania Asia, clustering with a case of dengue fever identified in Italy in 2023 and Ethiopia in 2023. Our findings suggest concurrent infections of the three serotypes with DENV-3 being more widely spread in East Africa.