Human papillomavirus genotype concordance between Anyplex II HPV28 and linear array HPV genotyping test in anogenital samples

Anyplex II HPV‐28 (HPV‐28) can detect individually 28 HPV genotypes. We assessed the agreement between linear array HPV genotyping (LA‐HPV) and HPV‐28 for detection of 27 HPV genotypes in 410 stored anogenital samples (75 anal samples, 335 physician‐collected cervical samples) collected over 5 years from 410 individuals (13 men, 397 women), including 202 HIV‐seropositive individuals. HPV DNA was detected in 393 (95.9%, 95% confidence interval [CI]: 93.4–97.4) and 382 (93.2%, 95% CI: 90.3–95.3) samples with HPV‐28 and LA‐HPV (p = 0.13), respectively, for a good agreement of 96.3% (κ = 0.65). Of the 10503 HPV typing results, 10195 (780 positive, 9577 negative) were concordant, for an agreement of 97.1% (95% CI: 96.7–97.4) and an excellent of κ = 0.82 (95% CI: 0.80–0.84). The mean type‐specific concordance for 27 genotypes was 97.0%, 95% CI: 95.8–98.5 (κ = 0.86 ± 0.07, 95% CI: 0.83–0.88). Excellent agreement was obtained individually for all high‐risk genotypes (κ = 0.81–0.97) and for most other genotypes except for types 42, 44, 54, 68, and 69. The mean number of types per sample in discordant samples detected with LA‐HPV (3.0, 95% CI: 2.7–3.4) was greater than in concordant samples (1.4, 95% CI: 1.3–1.5; p