Analytical and Diagnostic Validation of a Fluorescence-Based Hybridization Chain Reaction Assay for Detection of HPV 16/35 E6 Transcripts

Cervical cancer is associated with persistent human papillomavirus (HPV) infections. The early detection of HPV is one of the key strategies for the effective treatment of cervical cancer. Current HPV molecular detection methods use enzyme-based nucleic acid amplification strategies that, although specific and sensitive, involve extensive workflows. Enzyme-free isothermal amplification detection strategies with the potential to adapt to low-resource settings for HPV oncogenic transcripts remain limited. This study aimed to validate a fluorescence-based branched hybridization chain reaction (bHCR) assay for the targeted detection of HPV 16/35 E6 oncogenic transcripts. Analytical performance was evaluated using a synthetic target and a negative clinical matrix, whereas the diagnostic performance of the bHCR assay was evaluated using clinically characterized samples (n = 67). The study demonstrated assay linearity over an analyte concentration range of 0.625–40 µM, with a statistically significant correlation between the fluorescence signal and target concentration (r2 = 0.928, p < 0.0001). Analytical accuracy was assessed by pre-extraction spike recovery; achieved recoveries ranged from 70% to 86%, indicating potential RNA loss during the assay workflow. Analytical sensitivity determined the background signal threshold limit of blank (LoB) as 16,251.6 RFU, with detection and quantification at concentrations of 0.0625 µM (≈2.6 × 1011 copies per reaction, limit of detection (LoD) and 0.125 µM (≈5.3 × 1011 copies per reaction, limit of quantification (LoQ). The assay exhibited high diagnostic performance, with a diagnostic cut-off of 16,481 RFU and an area under the curve (AUC) of 0.9194. Specificity and sensitivity of the assay were 94% and 86%, respectively, with a Negative Predictive Value (NPV) of 85% and a Positive Predictive Value (PPV) of 94%. These findings demonstrate a reliable analytical assay with excellent diagnostic discrimination and warrant further optimization and expanded clinical validation.