Comparison of mRNA-based and next-generation sequencing HPV assays in a population-based cervical cancer screening program in China

Objective: To evaluate and compare the diagnostic performance of the Food and Drug Administration-approved APTIMA human papillomavirus (HPV) assay (E6/E7 mRNA-based) and the Mygene HPV-STI Assay (MHSA) in detecting cervical intraepithelial neoplasia (CIN) 2+ and CIN3+ lesions among Chinese women in a screening setting.Methods: A total of 3,166 women were enrolled from Wuxiang County, Shanxi Province, China, and followed for 3 years.APTIMA and MHSA were performed using cervical cytology specimens.Histopathology served as the reference standard.Diagnostic accuracy (sensitivity, specificity, and predictive values), assay concordance, and receiver operating characteristic (ROC) analyses were conducted for baseline and longitudinal detection of CIN2+/CIN3+.Results: Among 2,683 women with complete follow-up, the prevalence of high-risk-HPV was 17.22% by APTIMA and 20.16% by MHSA.Substantial concordance was observed (=0.798).APTIMA showed higher specificity than MHSA when combined with cytology (CIN2+: 88.42% vs. 87.96%,p=0.038;CIN3+: 87.28% vs. 86.87%,p=0.063), while sensitivity and predictive values were comparable.The MHSA demonstrated broader HPV genotyping, while APTIMA yielded slightly superior performance in post-test probability for CIN3+ over 3 years.ROC analysis confirmed comparable diagnostic discrimination.Conclusion: Both assays offer high clinical accuracy within 3 years.While APTIMA remains the validated standard, the MHSA may serve as a promising next-generation sequencingbased alternative, particularly in expanded genotyping.