Full-genome sequencing and analysis of DENV-3 serotype isolated from Yemen

Abstract

Background: Dengue virus causes the dengue fever as well as hemorrhagic fever in tropical and sub-tropical countries. It is now endemic in most parts of the South East Asia. Full-genome information of dengue virus 3 is not available from Yemen.

Methods: In this study, the dengue virus 3 was detected by diagnostic tools like serology and RT-PCR in the samples isolated from a patient in Yemen. The full-genome was sequenced, and the identity, phylogenetic relationship and recombination analysis was performed by using BioEdit, MEGA X and RDP4 softwares.

Results: The full-genome of the Yemen isolate was found to be 10,643 nt long with 3390 amino acids. The Yemen dengue virus 3 isolate showed the sequence similarity (98.5-92.4%) with dengue virus 3 isolates from China, Pakistan, India and Bangladesh respectively. The significant non-synonymous substitutions of amino acid in Yemen isolate were observed with selected isolates. The phylogenetic tree of Yemen isolate formed a unique clade within genotype III and sub-clade into lineage III. The Dengue virus isolate from Jeddah formed separated cluster with lineage IV.

Conclusions: This reveals the unique genetic variability among DENV-3 serotypes from Jeddah and earlier reported isolates from other regions.

Keywords: Dengue virus; Genetic variation; Genome; Recombination; Yemen.