Phylogeography and Genomic Characterization of Dengue Virus 1 in Nigeria
Dengue virus has been endemic in Nigeria for six decades, yet the evolutionary history and spatiotemporal spread of circulating lineages remain poorly understood due to limited genomic surveillance. Here we sequenced and assembled 15 complete dengue virus genomes from clinical blood samples collected in southwest Nigeria (Ondo State) in 2024, and used these genomes to determine circulating genotypic diversity and transmission dynamics in Nigeria. Using Nextclade, all sequences were assigned to the DENV1-III.A.2 lineage. Bayesian phylogeographic inference showed that this lineage has persisted in Nigeria since approximately 2015, with East Asia identified as the likely source, though the introduction into Nigeria lacked robust posterior support. Two recurrent capsid mutations (L46M and N90S) were observed within a predicted apoE3 binding pocket, potentially affecting host-virus lipid interactions and virion assembly. These findings underscore the need for expanded genomic surveillance in underrepresented regions and highlight how specific structural mutations may inform future antiviral strategies. This study was conducted by: Ibrahima Diallo, Olusola Ogunsanya, Edyth Parker, Ayotunde Sijuwola, Oludayo Ope-Ewe, Kehinde Ogundana, Agnes Folefac, Nicholas Oyejide, Emilola Kolade, Sylvester Abah, Etim Nta Henshaw, Ian Baudi, Marietou Faye Paye, Colby Wilkason, Iguosadolo Nosamiefan, Anise Happi, Pardis Sabeti,  Christian Happi.
Dengue virus has been endemic in Nigeria for six decades, yet the evolutionary history and spatiotemporal spread of circulating lineages remain poorly understood due to limited genomic surveillance. Here we sequenced and assembled 15 complete dengue virus genomes from clinical blood samples collected in southwest Nigeria (Ondo State) in 2024, and used these genomes to determine circulating genotypic diversity and transmission dynamics in Nigeria. Using Nextclade, all sequences were assigned to the DENV1-III.A.2 lineage. Bayesian phylogeographic inference showed that this lineage has persisted in Nigeria since approximately 2015, with East Asia identified as the likely source, though the introduction into Nigeria lacked robust posterior support. Two recurrent capsid mutations (L46M and N90S) were observed within a predicted apoE3 binding pocket, potentially affecting host-virus lipid interactions and virion assembly. These findings underscore the need for expanded genomic surveillance in underrepresented regions and highlight how specific structural mutations may inform future antiviral strategies. This study was conducted by: Ibrahima Diallo, Olusola Ogunsanya, Edyth Parker, Ayotunde Sijuwola, Oludayo Ope-Ewe, Kehinde Ogundana, Agnes Folefac, Nicholas Oyejide, Emilola Kolade, Sylvester Abah, Etim Nta Henshaw, Ian Baudi, Marietou Faye Paye, Colby Wilkason, Iguosadolo Nosamiefan, Anise Happi, Pardis Sabeti,  Christian Happi.
Institute of Genomics and Global Health