Comparison of the clinical and analytical performance of Alinity m HR HPV and cobas 4800 HPV assays in a population-based screening setting

•Alinity compared vs. cobas 4800 on 4334 women attending regular cervical screening.•Alinity's clinical sensitivity and specificity is non-inferior to cobas 4800.•Excellent overall and genotype-specific agreement was observed between two assays.•Alinity's extended genotyping could assist in management of HPV-positive women. The recently launched Abbott Alinity m HR HPV (Alinity) assay separately identifies high-risk human papillomavirus (hrHPV) genotypes HPV16, HPV18, and HPV45, and reports 11 other genotypes as two aggregates. Clinical and analytical performance of Alinity was compared with the cobas 4800 HPV assay on 4,334 women aged 20–64 years attending routine, population-based organized cervical cancer screening during 2009/2010. After 36 months, they were invited to participate in the second screening round (2012–2014) and later followed-up through centralized national cervical cancer screening registry. In women 30 and older, the clinical sensitivity for cervical intraepithelial neoplasia grade 2+ (CIN2+) was 100.0% (95% CI, 88.2–100.0%) for Alinity and 100.0% (95% CI, 88.2–100.0%) for cobas, and for CIN3+ 100.0% (95% CI, 78.9–100.0%) for both assays. The clinical specificity for ≤ CIN1 in women 30 and older was 92.4% (95% CI, 91.4–93.3%) and 92.9% (95% CI, 91.9–93.7%), respectively. The assays demonstrated excellent overall agreement for hrHPV detection (97.9%) and genotype-specific agreement for HPV16 (99.6%), HPV18 (99.8%), and other hrHPV (98.1%). Overall positive agreement and positive agreements for HPV16, HPV18, and other hrHPV genotypes were 84.3%, 89.1%, 73.2%, and 82.3%. Based on a 5-year CIN3+ risk, slightly more HPV-positive women would require referral to immediate colposcopy after testing with Alinity vs. cobas (4.1% vs. 3.8%; p = 0.470), but significantly fewer Alinity-tested women would need a 6- to 12-month follow-up visit compared with those tested with cobas (5.0% vs. 8.6%; p < 0.0001). Alinity and cobas have comparable clinical performance and showed excellent overall and genotype-specific agreement. The Alinity's extended genotyping ability could help predict the 5-year CIN3+ risk and cost-saving management of HPV-screen-positive women.