GENOMIC AND MOLECULAR BIOMARKERS OF CRIMEAN–CONGO HEMORRHAGIC FEVER VIRUS FOR RAPID DIAGNOSIS AND ANTIVIRAL DEVELOPMENT

Abstract

Crimean–Congo hemorrhagic fever virus (CCHFV) remains a major public-health concern because of its wide geographic distribution, substantial genetic diversity, high case-fatality potential, and limited availability of specific antiviral therapies. This study aimed to identify conserved genomic and molecular biomarkers that could support rapid diagnosis and antiviral development. A total of 186 complete CCHFV isolates were analyzed, yielding 174 S-segment, 169 M-segment, and 171 L-segment sequences after quality filtering. Comparative genomic analysis showed the highest nucleotide conservation in the S segment (91.8%), followed by the L segment (89.6%), whereas the M segment was more variable (84.3%). Fourteen highly conserved genomic regions with sequence identities above 95% were identified, including a maximum of 98.7% identity within the nucleoprotein-coding region. Primer-design analysis generated 24 preliminary primer pairs, of which 8 fulfilled predefined physicochemical and specificity criteria, with lengths of 19–24 nucleotides, GC contents of 45.0 60.0%, melting temperatures of 58.2–62.4°C, and predicted amplicons of 105–196 bp. Protein-level analysis identified strong conservation within nucleoprotein and RNA-dependent RNA polymerase, with selected RdRp catalytic regions showing 96.4–98.5% amino acid identity. Structural validation supported the reliability of NP, Gc, and RdRp models, while molecular docking revealed binding affinities ranging from −5.8 to −10.2 kcal/mol, with the strongest interaction observed for RdRp. Integrated analysis prioritized 8 diagnostic and 5 therapeutic biomarker candidates. Overall, conserved S- and L-segment regions represent promising diagnostic targets, whereas RdRp and NP emerge as strong candidates for structure-based antiviral development.