Evidence for missing HPV-45 and -59 positives with the SPF-DEIA-LiPA (version 1) platform compared to the type-specific qPCR assays and the impact on vaccine effectiveness estimates.

Abstract

Human papillomavirus (HPV) epidemiological and vaccine studies require highly sensitive HPV detection systems. The widely used broad-spectrum SPF10-DEIA-LiPA25 (SPF10 method) has reduced sensitivity towards HPV-45 and -59. Therefore, anogenital samples from the PASSYON study were retrospectively analyzed with type-specific (TS) HPV-45 and -59 qPCR assays. The SPF10 method missed 51.1% of HPV-45 and 76.1% of HPV-59 infections, detected by the TS qPCR assays. Viral copy number (VCn) of SPF10 missed HPV-45 and -59 was significantly lower than SPF10 detected HPV-45 and -59 (p<0.0001 for both HPV types). Sanger sequencing showed no phylogenetic distinction between SPF10 missed and detected HPV-59 variants, but variants bearing the A6562G SNP in the SPF10 target region were more likely to be missed (p=0.0392). HPV co-occurrence slightly influenced the detection probability of HPV-45 and -59 with the SPF10 method. Moreover, HPV-59 detection with the SPF10 method was hampered more in non-vaccinated women than vaccinated women, likely due a stronger masking effect by increased HPV co-occurrence in the former group. Consequentially, the SPF10 method led to a strong negative vaccine effectiveness (VE) of -84.6% against HPV-59 while the VE based on TS qPCR was 3.1%. For HPV45, the relative increase in detection in non-vaccinated women compared vaccinated women was more similar, resulting in comparable VE estimates. In conclusion, this study shows that HPV-45 and -59 detection with SPF10 method is dependent on factors including VCn, HPV co-occurrence, and vaccination, thereby showing that knowledge of the limitations of the HPV detection method used is of great importance.