Background: Crimean–Congo haemorrhagic fever virus (CCHFV) exhibits substantial genetic diversity that can compromise sequence-dependent molecular diagnostics. CRISPR-Cas13a offers a rapid and adaptable approach for nucleic-acid detection, but its diagnostic performance and tolerance to viral sequence variation require systematic evaluation.
Objective: This systematic review evaluated the analytical performance, sequence-variation tolerance, and point-of-care potential of CRISPR-Cas13a-based molecular detection of CCHFV.
Method: The review followed PRISMA 2020 and PRISMA-DTA guidance. PubMed, Web of Science, and NCBI PMC were searched for eligible molecular diagnostic studies. Data on assay design, target region, analytical sensitivity, specificity, limit of detection, detection time, cross-reactivity, and operational characteristics were extracted. Risk of bias was assessed using QUADAS-2, and findings were synthesised narratively because of substantial methodological heterogeneity.
Results: Of 142 identified records, 16 studies were included in the qualitative synthesis. CCHFV showed substantial sequence diversity, with approximately 20.152% nucleotide divergence across the S segment. The degenerate CRISPR-Cas13a SHERLOCK assay demonstrated detection across seven CCHFV clades, with an analytical limit of detection of 1 copy/μL (25 copies/reaction) and detection within approximately 30–40 minutes. Degenerate crRNA design also maintained detection of target variants that compromised conventional sequence-specific targeting, while no cross-reactivity was observed with the related viruses evaluated. However, the principal evidence remained largely analytical, with limited prospective clinical validation.
Conclusion: CRISPR-Cas13a demonstrates promising analytical sensitivity, rapid detection, and adaptability to CCHFV sequence variation. Degenerate crRNA design may improve diagnostic resilience against emerging viral variants. However, the current evidence is insufficient to establish clinical diagnostic accuracy or routine point-of-care implementation. Prospective multicentre studies using diverse clinical specimens and validated reference methods are required before clinical adoption.