Head‐to‐head comparison of genotyping of human papillomavirus by GP5+/6+‐PCR‐based reverse dot blot hybridization assay and SPF10‐PCR‐based line probe assay

Abstract

The SPF10‐PCR‐based line probe assay (LiPA‐25) for human papillomavirus (HPV) genotyping with high analytical sensitivity and specificity was widely used in HPV vaccine clinical trials and epidemiologic studies. In the study, we aimed to compare a novel GP5+/6+‐PCR‐based reverse dot blot hybridization assay (Yaneng‐23) with LiPA‐25. The performance of two assays was evaluated in 1735 cervical swab and 117 tissue samples, with a focus on 19 common HPV types (14 high‐risk: 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68/73; 5 low‐risk: 6, 11, 42, 43, and 53). A total of 1197 (69.0%) swab samples were identified as HPV‐positive by two assays. Of these, 878 (73.4%) samples displayed absolute agreement (concordant), 255 (21.3%) showed additional or fewer types (compatible), and the remaining 64 (5.3%) samples were discordant. Additionally, the two assays showed an excellent strength of agreement for 19 HPV‐combined detection (κ = 0.886) and 17 individual HPV types (all κ > 0.800), and displayed a good agreement for HPV39 (κ = 0.780) and 42 (κ = 0.699). Yaneng‐23 was more sensitive than LiPA‐25 for HPV58, 59, 68/73, 42, 43 and 53 (McNemar's test: all p < 0.05), while LiPA‐25 was more sensitive for HPV31, 39, 52, and 66 than Yaneng‐23 (all p < 0.05). In 113 HPV‐positive tissue specimens, the identification of genotypes was 82.3% identical and 17.7% compatible. The agreement between the tests for HPV45 (κ = 0.796) and 51 (κ = 0.742) was good, and for other types (all κ > 0.843) and 19 HPV‐combined detection (κ = 0.929) was perfect (all p > 0.05). In conclusion, Yaneng‐23 and LiPA‐25 are comparable. Yaneng‐23 could be used for the detection and genotyping of HPV in cervical samples for epidemiological and vaccine studies worldwide.

Evaluation of an E6/E7 PCR‐capillary electrophoresis fragment analysis in the genotyping of human papillomavirus in archival FFPE samples of oropharyngeal cancer

“…As for HPV58, 1 positive case was confirmed with SureX, but none with LiPA‐25. Previous studies with cervical samples have also found LiPA‐25 was less sensitive to HPV58 than other assays 29–31 …”

“…Previous studies with cervical samples have also found LiPA-25 was less sensitive to HPV58 than other assays. [29][30][31] T A B L E 5 Concordance of the human papillomaviruses results between LiPA-25, SureX, and p16 ink4a expression. HPV DNA and p16 ink4a detection are established markers for HPV-related OPSCC.…”

“…[16][17][18][19][20][21][22] Moreover, it has been used in a large international study to estimate fractions of head and neck cancers attributable to HPV. 23 The LiPA-25 system is based on the SPF10 polymerase chain reaction (PCR) primer set for amplifying a 65 bp fragment in the L1 region and the reverse hybridization assay (RHA) for specific detection of 25 HPV genotypes (i.e., HPV6,11,16,18,31,33,34,35,39,40,42,43,44,45,51,52,53,54,56,58,59, 66, 70, 74, and 68/73).…”

Pattern of multiple human papillomavirus infection and type competition: An analysis in healthy Chinese women aged 18–45 years

“…Third, the sensitivity for HPV58 by LiPA is relatively low, which may lead to inaccurate analysis of this type. 32 In addition, this is a cross-sectional study which cannot distinguish concurrently or sequentially acquired infections.…”