HPV genotyping and E6/E7 transcript assays for cervical lesion detection in an Asian screening population—Cobas and Aptima HPV tests

•This study compared the clinical performance of AHPV with another well-established HPV test Cobas on an Asian population.•Overall, the two tests showed moderate concordance, with AHPV showing significantly lower test positivity rate.•Both tests showed high sensitivity in detecting biopsy prove HSIL + but AHPV was significantly more specific.•Both AHPV and Cobas HPV tests successfully highlighted all ASC-US which developed HSIL + within 2 years, but AHPV had a significantly higher specificity than Cobas HPV. High-risk human papillomavirus (hrHPV) detection and genotyping by Cobas HPV test has become an important technical platform in cervical cancer screening. It may be used as a co-test with cervical cytology or as a standalone test. Aptima HPV assay (AHPV) is another hrHPV test detecting 13 genotypes through qPCR based amplification of viral E6/E7 transcripts. Partial genotyping with Aptima HPV 16 18/45 genotype assay (AHPV GT) on positive samples is possible. Evidence supporting the performance of AHPV in Asian populations is scarce. To compare the performances of Cobas and AHPV in detection of cervical squamous intraepithelial lesions (SIL) and triage of cytologically equivocal smears in a cohort of Hong Kong women. 442 liquid based cytology (LBC) residues with biopsy confirmed diagnoses were evaluated by both AHPV and Cobas HPV tests. Overall, there was a moderate agreement between AHPV and Cobas (κ = 0.5082, 95% CI: 0.492–0.672). The sensitivities of AHPV and Cobas for detecting biopsy confirmed HSIL or worse lesions (HSIL+) were 96.71% (95% CI: 92.49%–98.92%) and 97.37% (95% CI: 93.40%–99.28%) respectively. AHPV demonstrated significantly higher specificity than Cobas (37.85% vs 23.96%, p