Detection of Potentially Novel Dengue Lineages in EMRO Region Through Integrated Phylogenomic and Protein Analysis

Abstract

Despite decades of confirmed dengue circulation in the Eastern Mediterranean region (EMRO), genomic data remains limited and underrepresented. This research aimed to examine the DENV genome, focusing on nucleotide and E protein levels, using various computer simulation methods, so as to analyze DENV transmission dynamics closely. Using multiple computational approaches and costume python pipelines, we examined nucleotide and envelope (E) protein sequences to assess evolutionary relationships, divergence, and substitution patterns. Our results show that recent strains (2023–2025) from Pakistan, UAE, and Djibouti are genetically diverse and closely aligned with global variants from Cuba, India, and China. Nucleotide and amino acid phylogenies supported by PCA and time-resolved tree models revealed tight clustering among the collected isolates. They suggested a potential regional convergence with newly reported lineages from Asia and the Americas. In particular, a new lineage of DENV-3 (AII) of Cuban origin was found to be related to Saudi and Israeli strains, which caused concern regarding silent spread in other regions. Moreover, amino acid analyses of the envelope protein (E) identified common substitution sites within 2025 samples, with some mutations possibly being related to immune evasion and changes in viral fitness. Our data suggest a pattern of changing transmission routes and emerging silent lineages, but a crucial limitation is the lack of real-time surveillance and the limited number of contributed sequences from important countries in the EMRO region. Finally, we emphasize a pressing need for genomic surveillance, detailed analyses of functional mutations, and data sharing regarding DENV spread in order to monitor and control potential DENV outbreaks before they lead to large-scale outbreaks.