Comparative performance of L1- and E6/E7-targeted HPV genotyping assays based on a unified MeltArray platform

ABSTRACT Human papillomavirus (HPV) molecular testing is central to cervical cancer screening. Commercial assays commonly target either the L1 gene or the E6/E7 oncogenes, yet comparative performance data under standardized conditions remain limited. We developed two HPV genotyping assays targeting L1 and E6/E7 regions, respectively, using the same MeltArray platform to minimize technical variability. Both assays detect 18 high-risk and potential high-risk HPV types. A total of 2,477 clinical samples (2,034 liquid-based cytology [LBC] and 413 formalin-fixed paraffin-embedded [FFPE] specimens) were analyzed. Concordance in HPV detection and genotyping was assessed using Cohen’s kappa statistics. The assays showed 98.8% overall agreement in HPV detection (Cohen’s kappa [ κ ] = 0.976), with high concordance across LBC and FFPE samples, including high-grade squamous intraepithelial lesion, cervical intraepithelial neoplasia (CIN) 2/CIN 3, and cervical cancer. Discordant genotyping results were rare and concentrated in types with differing limits of detection (e.g., HPV39, HPV52, and HPV66). No substantial detection bias favoring either target gene was observed in cancer cases. When performed under matched analytical conditions, L1 and E6/E7-based assays provide equivalent performance in HPV detection and genotyping. These findings support their interchangeable use in cervical cancer screening, with both targets demonstrating high reliability across the full spectrum of cervical lesions. IMPORTANCE Human papillomavirus (HPV) testing is the principal strategy for cervical cancer screening, with most commercially available assays targeting either the L1 gene or the E6/E7 oncogenes. However, the comparisons of L1 and E6/E7 targets under standardized technical conditions remain limited. In this study, we developed and evaluated two parallel HPV genotyping assays targeting the L1 gene and E6/E7 genes, respectively, using the same MeltArray platform and unified reaction conditions. Analysis of a clinical cohort comprising 2,477 patients demonstrated equivalent performance between L1 and E6/E7 assays in both cervical swab and tissue samples, supporting their interchangeable use in cervical cancer screening.