Cross comparison of AmpFire HPV genotyping assay and Roche human papillomavirus (HPV) linear array for HPV genotyping of anal swab samples

J Virol Methods. 2021 Jun:292:114113. doi: 10.1016/j.jviromet.2021.114113. Epub 2021 Feb 27.

Abstract

Although anal cancers represent just 0.5 % of all new cancer cases in U.S., rates have increased markedly, with highest rates in HIV-infected MSM. American Cancer Society estimates there will be ∼9090 new cases and ∼1420 deaths in 2021. We compared Roche Linear Array HPV Genotyping (Roche) and AmpFire HPV Genotyping (AmpFire) assays for concordance and agreement to detect 15 hr-HPV types from 151 anal specimens. Within run precision of AmpFire was assessed on 50 anal specimens. Specimens with Roche Combo-positive and HPV33, HPV35 and/or HPV58-positive results were further tested using HPV52-specific TaqMan assay. AmpFire generated valid results on 149/151 (98.7 %) specimens; 135/149 (90.6 %) and 134/149 (89.9 %) had detectable HR-HPV DNA by AmpFire or Roche, respectively. Overall concordance was 89.8 % (2007/2235, κ = 0.65). HPV16 showed highest overall concordance at 93.3 % (139/149, κ = 0.84). HPV68 had lowest overall concordance at 77.2 % (115/149, κ = 0.28). Kappa values were interpreted as being moderate or good for all other HR-HPV types. Within run precision generated 744/750 concordant results; R2 value = 0.97 (p < 0.0001) (Mantel Test). In conclusion, AmpFire and Roche demonstrated good inter-assay agreement for detecting most HR-HPV types from anal samples, with AmpFire detecting a broader range of HPV68 subtypes and detecting HPV52 without the need for confirmatory testing.

Keywords: Anal specimens; Genotyping; HPV.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Alphapapillomavirus* / genetics
  • DNA, Viral / genetics
  • Genotype
  • Homosexuality, Male
  • Humans
  • Male
  • Papillomaviridae / genetics
  • Papillomavirus Infections* / diagnosis
  • Sexual and Gender Minorities*

Substances

  • DNA, Viral