Accuracy of CRISPR/Cas-based nucleic acid detection for HIV-1: a systematic review and meta-analysis

Background and aims HIV continues to pose a substantial worldwide public health burden, and achieving the UNAIDS 95–95-95 goals depends on diagnostics that are reliable, rapid, and inexpensive. Because of its exceptional specificity and adaptable design, the CRISPR-Cas platform has emerged as an attractive option for nucleic acid detection. In this systematic review and meta-analysis, we assessed the diagnostic accuracy of CRISPR-Cas-based assays for HIV-1, aiming to clarify their suitability for point-of-care testing and resource-limited settings. Methods Web of Science, PubMed, and CNKI were searched through August 12, 2026. We included original studies that applied CRISPR-Cas assays to detect HIV-1 nucleic acids and reported sufficient data to construct 2 × 2 tables (TP, FP, FN, TN), with RT-qPCR for HIV-1 RNA or qPCR for HIV-1 DNA serving as the reference standard. Pooled sensitivity, specificity, and SROC curves were generated using a bivariate random-effects model. Subgroup analyses and meta-regression were performed to investigate heterogeneity. Results Nine studies met the inclusion criteria. The pooled sensitivity was 0.96 (95% CI 0.90–0.98) and the pooled specificity was 0.98 (95% CI 0.93–1.00), with an AUC of 0.99. The I 2 statistic revealed low heterogeneity (11.82% for sensitivity and 8.91% for specificity). Publication bias was not statistically significant (Deeks’ test, p = 0.925). When stratified by Cas protein, Cas12a yielded a sensitivity of 0.97 and a specificity of 0.98, while Cas13a showed a sensitivity of 0.93 and a specificity of 0.99. However, each subgroup comprised only four to five studies, and between-subgroup differences were not formally examined. The use of fluorescence readout did not significantly influence accuracy ( p > 0.05). Studies using RPA/RAA amplification achieved accuracy comparable to the overall pooled estimates. Conclusion In selected studies, CRISPR-Cas-based assays showed high sensitivity and specificity for HIV-1, but clinical equivalence to qPCR remains unproven. When combined with RPA/RAA isothermal amplification, it holds promise as a rapid, accurate point-of-care testing (POCT) tool. Nevertheless, limited studies and methodological concerns highlight the need for further multicenter validation and real-world implementation data. Systematic review registration This systematic review and meta-analysis was registered with the Open Science Framework (OSF). The registration DOI is 10.17605/OSF.IO/AUTV8 .