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 toward HPV-45 and -59. Therefore, anogenital samples from the PASSYON study were retrospectively analyzed with type-specific (TS) HPV-45 and -59 real-time quantitative PCR (qPCR) assays. The SPF₁₀ method missed 51.1% of HPV-45 and 76.1% of HPV-59 infections that were detected by the TS qPCR assays. The 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 SPF₁₀-detected HPV-59 variants, but variants bearing the A6562G single-nucleotide polymorphism (SNP) in the SPF₁₀ target region were more likely to be missed (P = 0.0392). HPV cooccurrence 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 nonvaccinated women than vaccinated women, likely due to a stronger masking effect by increased HPV cooccurrence in the former group. Consequently, 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 HPV-45, the relative increase in detection in nonvaccinated women compared vaccinated women was more similar, resulting in comparable VE estimates. In conclusion, this study shows that HPV-45 and -59 detection with the SPF₁₀ method is dependent on factors including VCn, HPV cooccurrence, and vaccination, thereby showing that knowledge of the limitations of the HPV detection method used is of great importance.

中文翻译：

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与特定类型的qPCR分析相比，使用SPF10-DEIA-LiPA25（版本1）平台缺失HPV-45和-59阳性的证据，以及对疫苗有效性估计的影响。

人乳头瘤病毒（HPV）流行病学和疫苗研究需要高度敏感的HPV检测系统。广泛使用的广谱SPF ₁₀ -DEIA-LiPA ₂₅（SPF ₁₀方法）对HPV-45和-59的敏感性降低。因此，使用类型特异性（TS）HPV-45和-59实时定量PCR（qPCR）分析对PASSYON研究中的肛门生殖器样本进行了回顾性分析。通过TS qPCR分析检测到的SPF ₁₀方法漏掉了51.1％的HPV-45和76.1％的HPV-59感染。SPF ₁₀缺失的HPV-45和-59的病毒拷贝数（VCn）明显低于SPF ₁₀缺失的HPV-45和-59（P对于两种HPV类型，均<0.0001）。Sanger测序显示在SPF ₁₀缺失和SPF ₁₀检测到的HPV-59变体之间没有系统发育差异，但是在SPF ₁₀目标区域中带有A6562G单核苷酸多态性（SNP）的变体更容易被遗漏（P = 0.0392） 。HPV的同时出现对使用SPF ₁₀方法检测HPV-45和-59的检测概率有轻微影响。此外，用SPF ₁₀方法检测HPV-59在未接种疫苗的女性中比在接种疫苗的女性中受阻更大，这可能是由于前一组中增加的HPV并发掩盖作用更强。因此，SPF ₁₀该方法导致针对HPV-59的强阴性疫苗效力（VE）为–84.6％，而基于TS qPCR的VE为3.1％。对于HPV-45，与未接种疫苗的妇女相比，未接种疫苗的妇女的检出率相对增加更为相似，因此VE估算值可比。总之，这项研究表明，使用SPF ₁₀方法检测HPV-45和-59取决于VCn，HPV共存和接种疫苗等因素，因此表明了解所用HPV检测方法的局限性非常重要。