Molecular Cloning, Sequence Analysis, and 3D Structure Prediction of Alkhumra Hemorrhagic Fever Virus Envelope (E) Protein Gene.

Background: Alkhumra hemorrhagic fever virus is a newly discovered tick-borne flavivirus that was first identified in 1994 - 1995 in the Alkhumra district of Jeddah, Kingdom of Saudi Arabia. AHFV was detected in a butcher who developed severe hemorrhagic fever. Since then, a total of 604 confirmed cases have been reported in KSA between 1995 - 2020. Currently, there are no routine screenings or treatments available for AHFV.

Methods: In this study, the AHFV-E gene was amplified and cloned into a pET-28a (+) vector. The recombinant clones were confirmed through colony PCR, restriction enzyme digestion, and sequencing. The resulting sequence was submitted to GenBank with the accession number OR785376, and the 3D structure of the E protein was determined using Phyre2 and visualized using PayMol software.

Results: The sequence identity matrix ranged from 98 - 99% with other isolates from human and animal samples. The phylogenetic tree analysis revealed that AHFV-E gene formed a closed cluster with AHFV isolates. The 3D structure showed a confidence score of 100%, indicating a strong alignment between the target sequence and template.

Conclusions: The successful cloning, sequencing, of the E gene in this study holds promise for developing diagnostic assays, screening, of AHFV in the Kingdom of Saudi Arabia.