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. 2022 Jun;94(6):2824-2832.
doi: 10.1002/jmv.27605. Epub 2022 Jan 28.

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

François Coutlée  1   2   3   4 , Alexandra de Pokomandy  5   6 , Ann N Burchell  7   8 , Mariam El-Zein  4 , Marie-Hélène Mayrand  2   3 , Sophie Rodrigues-Coutlée  1 , Deborah Money  9 , Émilie Comète  1 , Elisabeth McClymont  9 , Danielle Rouleau  2   3 , Eduardo L Franco  4
Affiliations

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

François Coutlée et al. J Med Virol. 2022 Jun.

Abstract

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< 0.001). In conclusion, HPV-28 compared favorably with LA-HPV, but was more frequently positive for HPV42 and HPV68.

Keywords: HPV; PCR; consensus PCR; genital cancer; genotyping.

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Conflict of interest statement

No potential conflict of interest was disclosed by the other authors.

Conflicts of interest:

ELF served as an occasional advisor for companies involved with HPV vaccines (Merck, GSK) and HPV diagnostics (Roche Diagnostics). MZ and ELF hold a patent related to the discovery “DNA methylation markers for early detection of cervical cancer”, registered at the Office of Innovation and Partnerships, McGill University, Montréal, Québec, Canada (October, 2018). FC received grants paid to the organization for research projects from Roche Diagnostics, Becton Dickinson and Merck Sharp and Dome, honorariums for presentations from Merck Sharp and Dome and Roche diagnostics, and has participated in an expert group by Merck Sharp and Dome.

Figures

Figure 1.
Figure 1.. Rate of detection of individual HPV genotypes in 410 anogenital samples, by assay
LAHPV : Linear array HPV genotyping assay; HPV-28: Anyplex II HPV-28. The 27 HPV genotypes detected with both assays were included. The difference between detection rates were statistically significant (p=0.001) for HPV42 and HPV68 (z-test of significance between proportions). The classification of HPV genotypes into high, low and unknown risk is defined in the methods section.
Figure 1.
Figure 1.. Rate of detection of individual HPV genotypes in 410 anogenital samples, by assay
LAHPV : Linear array HPV genotyping assay; HPV-28: Anyplex II HPV-28. The 27 HPV genotypes detected with both assays were included. The difference between detection rates were statistically significant (p=0.001) for HPV42 and HPV68 (z-test of significance between proportions). The classification of HPV genotypes into high, low and unknown risk is defined in the methods section.
Figure 2.
Figure 2.
Correlation between the number of genotypes detected per sample on 410 anogenital samples with LA-HPV and HPV-28 considering only the 27 genotypes detected with both assays. Figure 1. The dashed lines represent the 95% CI of the regression line. R2=0.82, p<0.01.
See this image and copyright information in PMC

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