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Cited by 9Cervical Cancer and HPV ResearchReproductive tract infections researchWomen's cancer prevention and management

Comparative evaluation of Allplex HPV28 and Anyplex II HPV28 assays for high-risk HPV genotyping in cervical samples

Open access
Mafi, Sarah, Theuillon, Flavie, Meyer, Sylvain, Woillard, Jean-Baptiste, Dupont, Marine, Rogez, Sylvie, Alain, Sophie, Hantz, Sébastien·2025·PLOS ONE
DOI 10.1371/journal.pone.0320978PMC PMC11960881
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Abstract

Background/Objectives: Human papillomavirus (HPV) genotyping is essential for cervical cancer screening and prevention. The Allplex TM HPV28 real-time PCR kit, using different chemistry and results analysis compared with its predecessor, the Anyplex TM II HPV28 kit, has recently been launched. This study aims to compare the Allplex TM HPV28 and Anyplex TM II HPV28 assays in detecting and genotyping the 13 high-risk (HR)-HPV types. Study design: Between 2022 and 2023, 459 cervical samples from women undergoing cervical cancer screening were selected. These samples were analysed by liquid-based cytology and tested by both kits concurrently. Results: Allplex TM HPV28 Ct values correlated well with Anyplex TM II HPV28 signal intensity scores. No significant differences between assays were observed in overall and genotype-specific HR-HPV prevalence determined in all samples and according to cytological results. In addition, no significant differences were identified between assays in the detection of single and multiple HR-HPV infections. Most of the discordant results corresponded to samples showing weak HR-HPV signals and multiple HR-HPV types. Conclusions: Our results demonstrate that the Allplex TM HPV28 kit can be used for HPV genotyping, with results overall similar to those obtained with the Anyplex TM II HPV28 kit and the addition of Ct values for patient follow-up. The clinical implications of the potentially reduced sensitivity of the Allplex TM HPV28 kit in detecting HPV31 (p = 0.07) and HPV39 (p = 0.08) warrant further investigation in subsequent studies.

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Written from the paper’s full text.

TL;DR

This study compared the Allplex HPV28 and Anyplex II HPV28 assays for detecting and genotyping the 13 high-risk HPV types in 459 cervical samples. It found high overall agreement (95.0%, K = 0.87) and no significant differences in overall or genotype-specific HR-HPV prevalence, though trends toward reduced Allplex HPV28 sensitivity for HPV31 and HPV39 warrant further investigation.

Key findings

  • Overall HR-HPV DNA was detected in 72.8% (334/459) of samples with Allplex HPV28 and 72.5% (333/459) with Anyplex II HPV28; overall agreement was 95.0% (436/459), positive percent agreement 96.7% (322/333), negative percent agreement 90.5% (114/126), K = 0.87, p = 1.00.
  • Allplex HPV28 Ct values correlated with Anyplex II HPV28 signal intensity scores: median Ct [IQR] was 38.0 [36.8–39.6] for +, 31.1 [28.6–33.7] for ++, and 23.8 [21.1–25.4] for +++ (p < 0.0001, Kruskal-Wallis).
  • Single and multiple HR-HPV infections were detected in 48.1% (221/459) and 24.6% (113/459) by Allplex HPV28, versus 47.1% (216/459) and 25.5% (117/459) by Anyplex II HPV28, with no significant differences (p > 0.05). Genotype-specific agreement ranged from 96.7% to 99.6%; agreement was almost perfect except HPV58 (substantial, K = 0.80). Discordant results occurred in 81 cases: 39 Allplex+/Anyplex− and 42 Allplex−/Anyplex+; trends favored Allplex for HPV51/HPV52 and Anyplex for HPV31/HPV39, but none reached significance (p = 0.07 and p = 0.08, respectively).
  • By cytology, HR-HPV was detected in 65.5% of NILM, 83.0% of ASCUS, 100% of ASCH, and 100% of HSIL samples with both assays; in LSIL, 81.9% with Allplex versus 80.6% with Anyplex, with no significant differences.

Methods

  • Between 2022 and 2023, 459 cervical samples from women undergoing cervical cancer screening at Limoges University Hospital, France, were selected based on Anyplex II HPV28 results to include at least 20 positive samples per HR-HPV type; liquid-based cytology results were available for 453/459 samples.
  • DNA was extracted from 800 µL using the EMAG system; the same thawed extract was tested concurrently with both Allplex HPV28 and Anyplex II HPV28. Primer set A detected 13 HR-HPV types (16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68); HPV66 was excluded from analysis.
  • Statistical analysis included Kruskal-Wallis for Ct versus signal intensity, prevalence estimates overall and by cytology, agreement measures (overall, positive, negative, Cohen’s kappa), McNemar tests for paired detection differences, and chi-squared tests for infection status and discordance; significance was p < 0.05.

Limitations

  • Stated by the authors: selection of HR-HPV-positive samples introduced bias and overestimated HR-HPV prevalence (>70%); the study population had >50% ASCUS among abnormal cytology and only 1.7% HSIL, limiting subgroup power; no cervical cancer smears were included; 37.5% abnormal cytology may increase positive agreement; and no reproducibility studies were conducted for Allplex HPV28.
  • Evident from the text: no clinical cut-offs were applied for either assay, and Allplex HPV28 used an absolute Ct ≤ 43 rather than genotype-specific cut-offs, which may affect detection of low viral loads. Primer/probe locations are proprietary, so the mechanism of discordance cannot be confirmed.

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Crossref · 10.1371/journal.pone.0320978

Cites

31 of 31 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

23 of 41 cited sources checked · 14 supported · 0 flagged · accuracy not yet measured

  • Premisecitation

    A study by Oštrbenk Valenčak A. et al. reported a high overall agreement between the Allplex HPV HR and Anyplex II HPV HR assays (96.3% concordance, K = 0.88).

    “In another study conducted by Oštrbenk Valenčak A. et al., a high overall agreement was reported between the Allplex™ HPV HR and the Anyplex™ II HPV HR assays (96.3% concordance, K = 0.88).”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] A Oštrbenk Valenčak, 2024, Allplex HPV HR Detection assay fulfils all clinical performance and reproducibility validation requirements for primary cervical cancer screening, Journal of Clinical Virology source
  • Premisecitation

    A previous study by Bell M. et al. demonstrated a high concordance between the Allplex HPV28 and Anyplex II HPV28 assays in mocked self-samples (100% concordance, K = 1.00, analysis performed on the 14 HPV types included in set A).

    “Our results are in line with a previous study conducted by Bell M. et al., demonstrating a high concordance between the AllplexTM HPV28 and AnyplexTM II HPV28 assays in mocked self-samples (100% concordance, K = 1.00, analysis performed on the 14 HPV types included in set A) [19].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [19] M Bell, 2023, Comparison between the Roche Cobas 4800 Human Papillomavirus (HPV), Abbott RealTime High-Risk HPV, Seegene Anyplex II HPV28, and Novel Seegene Allplex HPV28 Assays for High-Risk HPV Detection and Genotyping in Mocked Self-Samples, Microbiology Spectrum source

      The Results section, ‘Concordance for detecting any hrHPV genotype’ (page unavailable), reports 100% agreement and κ = 1.00 between Anyplex and Allplex in mocked self-samples. However, the Methods section, ‘Data analysis’ (page unavailable), says the comparison grouped high-risk genotypes other than HPV16 and HPV18; the paper does not identify this as a ‘set A’ analysis of 14 individual types. The Results also note discrepancies for individual genotypes 51, 52, and 59. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
  • Interpretationcitation

    This relatively high frequency of cytological abnormalities, compared to unselected screening samples, may contribute to increase the positive agreement between assays.

    “This relatively high frequency of cytological abnormalities, compared to unselected screening samples, may contribute to increase the positive agreement between assays.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [32] M Rebolj, 2014, Disagreement between human papillomavirus assays: an unexpected challenge for the choice of an assay in primary cervical screening, PLoS One source
  • Premisecitation

    Women with cytological abnormalities may exhibit, on average, higher viral loads than the minimum detectable threshold required for a positive result.

    “As suggested by Rebolj M. et al., women with cytological abnormalities may exhibit, on average, higher viral loads than the minimum detectable threshold required for a positive result [32].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [32] M Rebolj, 2014, Disagreement between human papillomavirus assays: an unexpected challenge for the choice of an assay in primary cervical screening, PLoS One source
  • Premisecitation

    Samples with relatively low viral loads might be more susceptible to the established cut-off on any assay before these assays yield a positive result.

    “In contrast, samples with relatively low viral loads might be more susceptible to the established cut-off on any assay before these assays yield a positive result [32].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [32] M Rebolj, 2014, Disagreement between human papillomavirus assays: an unexpected challenge for the choice of an assay in primary cervical screening, PLoS One source
  • Classified as probably not a substantial claim. 23
  • May combine two claims. 33

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Other studies have not found a correlation between increased HR-HPV viral load and the severity and progression of cervical lesions.

    “while others have not found such a correlation [15,16].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [15] AT Lorincz, 2002, Viral load of human papillomavirus and risk of CIN3 or cervical cancer, Lancet source
    • cites [16] S Andersson, 2005, Type distribution, viral load and integration status of high-risk human papillomaviruses in pre-stages of cervical cancer (CIN), Br J Cancer source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The prognostic significance of HR-HPV viral load in cervical cancer remains controversial.

    “The prognostic significance of HR-HPV viral load in cervical cancer remains controversial.”
    Quote in the paperNot a substantial claim3 of 4 sources checked
    • cites [13] Y Liu, 2021, Significance of the viral load of high-risk HPV in the diagnosis and prediction of cervical lesions: a retrospective study, BMC Womens Health source

      The Background and Discussion state that the significance of HR-HPV viral load for detecting and predicting cervical lesions remains controversial, and the Discussion describes conflicting findings concerning cervical cancer risk. They do not establish that its prognostic significance for patients who already have cervical cancer—for example, predicting their outcomes—is controversial. (LLM, conf=0.82)

      Experimental — accuracy not yet measured
    • cites [14] V Dalstein, 2003, Persistence and load of high-risk HPV are predictors for development of high-grade cervical lesions: A longitudinal French cohort study, International Journal of Cancer source

      The Discussion reports conflicting findings on whether HR-HPV load predicts development of high-grade cervical lesions, supporting the claim that its prognostic value is debated. The paper studies progression to CIN2/3+, not prognosis in patients with cervical cancer, so the claim extends beyond its evidence. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [15] AT Lorincz, 2002, Viral load of human papillomavirus and risk of CIN3 or cervical cancer, Lancet source
    • cites [16] S Andersson, 2005, Type distribution, viral load and integration status of high-risk human papillomaviruses in pre-stages of cervical cancer (CIN), Br J Cancer source

  • Classified as probably not a substantial claim.

    Premisecitation

    Previous studies have reported an association between increased HR-HPV viral load and the severity and progression of cervical lesions.

    “Previous studies have reported an association between increased HR-HPV viral load and the severity and progression of cervical lesions [13,14]”
    Quote in the paperSubstantial claim2 of 2 sources checked
    • cites [13] Y Liu, 2021, Significance of the viral load of high-risk HPV in the diagnosis and prediction of cervical lesions: a retrospective study, BMC Womens Health source

      The Discussion (page not available) reports that higher high-risk HPV viral load was associated with more advanced cervical lesions, and the Background describes previous studies reporting associations with lesion severity. The paper does not establish that higher viral load is associated with lesions progressing over time; its methods compare biopsy-defined lesion grades rather than tracking progression. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [14] V Dalstein, 2003, Persistence and load of high-risk HPV are predictors for development of high-grade cervical lesions: A longitudinal French cohort study, International Journal of Cancer source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Recent data report a slightly higher detection rate of multiple HPV infections using the Anyplex II HPV28 assay compared with the Allplex HPV28 assay.

    “This observation aligns with recent data reporting a slightly higher detection rate of multiple HPV infections using the AnyplexTM II HPV28 assay compared with the AllplexTM HPV28 assay [19].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [19] M Bell, 2023, Comparison between the Roche Cobas 4800 Human Papillomavirus (HPV), Abbott RealTime High-Risk HPV, Seegene Anyplex II HPV28, and Novel Seegene Allplex HPV28 Assays for High-Risk HPV Detection and Genotyping in Mocked Self-Samples, Microbiology Spectrum source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Other studies have suggested a significantly increased risk of cervical carcinogenesis among women with multiple HPV infections compared with women with single infections.

    “Other studies have suggested a significantly increased risk of cervical carcinogenesis among women with multiple HPV infections compared with women with single infections [7–9].”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [7] KH Fife, 2001, Detection of multiple human papillomavirus types in the lower genital tract correlates with cervical dysplasia, J Med Virol source
    • cites [8] Y van der Graaf, 2002, Human Papillomavirus and the Long-term Risk of Cervical Neoplasia, American Journal of Epidemiology source
    • cites [9] H Trottier, 2006, Human Papillomavirus Infections with Multiple Types and Risk of Cervical Neoplasia, Cancer Epidemiology, Biomarkers & Prevention source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    In some studies, multiple HPV infections were not associated with an increased risk of cervical cancer in women with cytological abnormalities.

    “In some studies, multiple HPV infections were not associated with an increased risk of cervical cancer in women with cytological abnormalities [24–26].”
    Quote in the paperNot a substantial claim1 of 3 sources checked
    • cites [24] N Muñoz, 2003, Epidemiologic classification of human papillomavirus types associated with cervical cancer, N Engl J Med source

      In “Risk Associated with HPV” (page unavailable), the paper reports that the cervical-cancer odds ratio for multiple HPV infection was not significantly different from that for single infection (0.7; 95% CI, 0.4–1.0). The study compared women with histologically confirmed squamous-cell cervical cancer with controls; it does not establish this finding specifically for women with cytological abnormalities. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [25] R Herrero, 2000, Population-Based Study of Human Papillomavirus Infection and Cervical Neoplasia in Rural Costa Rica, JNCI: Journal of the National Cancer Institute source
    • cites [26] F Gargiulo, 2007, Prevalence and distribution of single and multiple HPV infections in cytologically abnormal cervical samples from Italian women, Virus Res source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The role of multiple HPV infections in the progression of cervical disease is still controversial.

    “The role of multiple HPV infections in the progression of cervical disease is still controversial.”
    Quote in the paperNot a substantial claim2 of 6 sources checked
    • cites [24] N Muñoz, 2003, Epidemiologic classification of human papillomavirus types associated with cervical cancer, N Engl J Med source

      The “risk associated with HPV” section examines multiple infections and reports no significantly greater cervical-cancer risk than with a single type. It does not assess progression of cervical disease or say that the role of multiple infections remains controversial (page unavailable in our copy). (LLM, conf=0.78)

      Experimental — accuracy not yet measured
    • cites [25] R Herrero, 2000, Population-Based Study of Human Papillomavirus Infection and Cervical Neoplasia in Rural Costa Rica, JNCI: Journal of the National Cancer Institute source
    • cites [26] F Gargiulo, 2007, Prevalence and distribution of single and multiple HPV infections in cytologically abnormal cervical samples from Italian women, Virus Res source
    • cites [7] KH Fife, 2001, Detection of multiple human papillomavirus types in the lower genital tract correlates with cervical dysplasia, J Med Virol source
    • cites [8] Y van der Graaf, 2002, Human Papillomavirus and the Long-term Risk of Cervical Neoplasia, American Journal of Epidemiology source
    • cites [9] H Trottier, 2006, Human Papillomavirus Infections with Multiple Types and Risk of Cervical Neoplasia, Cancer Epidemiology, Biomarkers & Prevention source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationcitation

    Strict cut-offs may potentially miss low-level infections, even though such infections are not necessarily clinically significant.

    “This highlights the importance of carefully evaluating the cut-offs used for cervical cancer screening and HPV infection monitoring, as strict cut-offs may potentially miss low-level infections, even though such infections are not necessarily clinically significant [14].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [14] V Dalstein, 2003, Persistence and load of high-risk HPV are predictors for development of high-grade cervical lesions: A longitudinal French cohort study, International Journal of Cancer source

      The Methods passage (page unavailable) defines HPV positivity using an HCII ratio of at least 1, but the paper does not test whether stricter cut-offs miss low-level infections. The Discussion reports that low-load infections were more likely to clear, supporting the qualified point that they are not necessarily clinically significant; it also cautions that low load does not exclude progressive disease. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    DPO systems for multiplex detection may generate less competition.

    “Nevertheless, the DPO systems for multiplex detection may generate less competition [23].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [23] F Coutlée, 2022, Human Papillomavirus genotype concordance between Anyplex II HPV28 and Linear array HPV genotyping test in anogenital samples, Journal of medical virology source

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Co-amplification of β-globin with HPV DNA or the presence of multiple HPV types can result in competition for assay reagents and hamper assay performance.

    “As previously reported with consensus PCR assays, the co-amplification of β-globin with HPV DNA or the presence of multiple HPV types can result in competition for assay reagents and hamper assay performance [21,22].”
    Quote in the paperNot a substantial claim2 of 2 sources checked
    • cites [21] F Coutlée, 1999, Nonisotopic detection and typing of human papillomavirus DNA in genital samples by the line blot assay. The Canadian Women’s HIV study group, J Clin Microbiol source

      The Results (page not available) report reduced HPV detection sensitivity with β-globin co-amplification and improved detection when it was avoided. The Discussion (page not available) says the line blot assay was less sensitive especially in samples with multiple HPV types. The paper does not establish competition for assay reagents as the mechanism for either effect. (LLM, conf=0.86)

      Experimental — accuracy not yet measured
    • cites [22] SD Vernon, 2000, Comparison of Human Papillomavirus Detection and Typing by Cycle Sequencing, Line Blotting, and Hybrid Capture, Journal of Clinical Microbiology source

      The Discussion says co-amplification of HPV and β-globin could explain reduced amplification efficiency and that samples with multiple HPV types may yield preferential amplification and inaccurate results. It does not identify competition for assay reagents as the mechanism, so that part of the claim is unsupported by our copy. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    Oštrbenk Valenčak A. et al. reported a statistically significant difference in overall genotype detection (p < 0.0001) and for three specific genotypes: HPV31, HPV51, and HPV68 - in favor of the Anyplex II HPV HR assay, with p-values of 0.002, 0.02, and 0.008, respectively (using the clinically validated Ct cut-offs).

    “In contrast, Oštrbenk Valenčak A. et al. reported a statistically significant difference in overall genotype detection (p < 0.0001) and for three specific genotypes: HPV31, HPV51, and HPV68 - in favor of the Anyplex™ II HPV HR assay, with p-values of 0.002, 0.02, and 0.008, respectively (using the clinically validated Ct cut-offs) [20].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] A Oštrbenk Valenčak, 2024, Allplex HPV HR Detection assay fulfils all clinical performance and reproducibility validation requirements for primary cervical cancer screening, Journal of Clinical Virology source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The study by Oštrbenk Valenčak A. et al. concluded that the Allplex HPV HR assay meets all validation criteria outlined in the international guidelines for HPV testing in primary cervical cancer screening for women aged 30 years and older.

    “This finding aligns with the study performed by Oštrbenk Valenčak A. et al., which concluded that the Allplex™ HPV HR assay meets all validation criteria outlined in the international guidelines for HPV testing in primary cervical cancer screening for women aged 30 years and older [20].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] A Oštrbenk Valenčak, 2024, Allplex HPV HR Detection assay fulfils all clinical performance and reproducibility validation requirements for primary cervical cancer screening, Journal of Clinical Virology source

  • May combine two claims.

    Interpretationcitation

    Viral loads in unselected screening samples are likely to be more heterogeneous, encompassing a range from recent transient infections to high-level persistent infections, allowing samples with lower viral loads to have a more significant influence on the frequency of disagreement between the assays.

    “Therefore, viral loads in unselected screening samples are likely to be more heterogeneous, encompassing a range from recent transient infections to high-level persistent infections, allowing samples with lower viral loads to have a more significant influence on the frequency of disagreement between the assays [32].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [32] M Rebolj, 2014, Disagreement between human papillomavirus assays: an unexpected challenge for the choice of an assay in primary cervical screening, PLoS One source

  • May combine two claims.

    Findingown data

    Allplex HPV28 exhibited a trend toward higher detection of HPV51 (4 cases detected only with Allplex vs 0 with Anyplex, p = 0.13) and HPV52 (5 vs 1, p = 0.22).

    “Of note, the AllplexTM HPV28 assay exhibited a trend toward higher detection of HPV51 (4 cases detected only with the AllplexTM HPV28 versus 0 cases detected with the AnyplexTM II HPV28, p = 0.13), and HPV52 (5 cases detected only with the AllplexTM HPV28 versus 1 case detected only with the AnyplexTM II HPV28, p = 0.22).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In samples with NILM, ASCUS, ASCH, and HSIL cytology, HR-HPV DNA was detected with both assays at rates of 65.5% (184/281), 83.0% (73/88), 100% (9/9), and 100% (3/3), respectively, with no significant difference between assays (p > 0.05).

    “Considering all 13 HR-HPV types, HPV DNA was detected in 65.5% (184/281) of NILM samples, 83.0% (73/88) of ASCUS samples, 100% (9/9) of ASCH samples, and 100% (3/3) of HSIL samples with both assays (p > 0.05, McNemar’s test for paired data) (Table 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    IC signal intensities were predominantly categorized as ++ or +++ in both Allplex-/Anyplex+ samples and non-discordant samples, with no significant differences between the groups.

    “Similarly, the IC signal intensities were predominantly categorized as ++ or +++ in both Allplex-/Anyplex+ samples and non-discordant samples, with no significant differences between the groups.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Median Allplex HPV28 Ct values were 38.0 [36.8-39.6] for Anyplex signal intensity +, 31.1 [28.6-33.7] for ++, and 23.8 [21.1-25.4] for +++.

    “AllplexTM HPV28 Ct values correlated well with AnyplexTM II HPV28 signal intensity scores, with median Ct values [interquartile range] of 38.0 [36.8-39.6], 31.1 [28.6-33.7], and 23.8 [21.1-25.4] corresponding to + , ++, and +++ signal intensity scores, respectively (Fig 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Overall HR-HPV DNA prevalence was 72.8% (334/459) with Allplex HPV28 and 72.5% (333/459) with Anyplex II HPV28.

    “Considering all 13 HR-HPV types, HPV DNA was detected in 72.8% (334/459) and 72.5% (333/459) of samples with the AllplexTM HPV28 and AnyplexTM II HPV28 assays, respectively (Table 1).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Positive and negative percent agreements for genotype-specific detection were at least 75.9% and 97.8%, respectively.

    “Positive and negative percent agreements were at least 75.9% and 97.8%, respectively.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    For the 13 HR-HPV types, discordant results were observed in 81 cases; 39 (48.1%) were positive only with Allplex HPV28 and 42 (51.9%) were positive only with Anyplex II HPV28.

    “For the 13 HR-HPV types, discordant results were observed in 81 cases (some discordances involving different types were found in identical samples): 39 cases (48.1%) were positive only with AllplexTM HPV28 (Allplex+/Anyplex-), while 42 (51.9%) were positive only with AnyplexTM II HPV28 (Allplex-/Anyplex+).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In LSIL samples, HR-HPV DNA was detected in 81.9% (59/72) with Allplex HPV28 and 80.6% (58/72) with Anyplex II HPV28, with no significant difference (p > 0.05).

    “In the LSIL group, HPV DNA was detected in 81.9% (59/72) and 80.6% (58/72) of samples with the AllplexTM HPV28 and AnyplexTM II HPV28 assays, respectively (p > 0.05, McNemar’s test for paired data) (Table 3).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Based on Anyplex II HPV28, single and multiple HR-HPV infections were detected in 47.1% (216/459) and 25.5% (117/459) of samples, respectively.

    “Based on the results of the AnyplexTM II HPV28 assay, single and multiple HR-HPV infections were detected in 47.1% (216/459) and 25.5% (117/459) of samples, respectively.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Based on Allplex HPV28, single and multiple HR-HPV infections were detected in 48.1% (221/459) and 24.6% (113/459) of samples, respectively.

    “Based on the results of the AllplexTM HPV28 assay, single and multiple HR-HPV infections were detected in 48.1% (221/459) and 24.6% (113/459) of samples, respectively (Table 2).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Cohen's kappa for overall HR-HPV detection agreement between assays was 0.87, indicating almost perfect agreement.

    “The kappa value (K) was 0.87, indicating an almost perfect agreement between assays.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Anyplex II HPV28 exhibited a trend toward higher detection of HPV31 (5 cases detected only with Anyplex vs 0 with Allplex, p = 0.07) and HPV39 (7 vs 1, p = 0.08).

    “Conversely, the AnyplexTM II HPV28 assay showed a trend toward higher detection of HPV31 (5 cases detected only with the AnyplexTM II HPV28 versus 0 cases detected with the AllplexTM HPV28, p = 0.07) and HPV39 (7 cases detected only with the AnyplexTM II HPV28 versus 1 case detected only with the AllplexTM HPV28, p = 0.08).”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    Genotype-specific agreement was almost perfect for all HR-HPV types except HPV58, which showed substantial agreement.

    “Genotype-specific agreement was almost perfect, except for HPV58 (substantial).”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Analysis of discordant results showed no significant difference in the detection of overall or individual HR-HPV type.

    “Analysis of discordant results showed no significant difference in the detection of overall or individual HR-HPV type.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    In our study, there was a trend toward higher detection of HPV51 and HPV52 with the Allplex HPV28 assay compared to the Anyplex II HPV28 assay, although this difference did not reach statistical significance.

    “In our study, we observed a trend toward higher detection of HPV51 and HPV52 with the AllplexTM HPV28 assay compared to the AnyplexTM II HPV28 assay (using the absolute cut-off of Ct ≤ 43 for all targeted HPV genotypes), although this difference did not reach statistical significance.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    In our study, there was a trend toward higher detection of HPV31 and HPV39 with the Anyplex II HPV28 assay compared to the Allplex HPV28 assay, although this difference did not reach statistical significance.

    “Conversely, the AnyplexTM II HPV28 assay showed a trend toward higher detection of HPV31 and HPV39 compared to the AllplexTM HPV28 assay (using the same absolute cut-off), but this also did not reach statistical significance.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    The proportion of multiple infections was not significantly different between the Allplex HPV28 and Anyplex II HPV28 assays, although a slightly higher number of multiple infections was detected with the Anyplex II HPV28 assay.

    “The proportion of multiple infections was not significantly different between the AllplexTM HPV28 and AnyplexTM II HPV28 assays, although a slightly higher number of multiple infections was detected with the AnyplexTM II HPV28 assay.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    HPV18 was the second (Allplex HPV28 assay) or third (Anyplex II HPV28 assay) most frequent carcinogenic HPV type according to our results, whereas it ranked fourth among the ten most frequent carcinogenic types according to French epidemiology.

    “HPV18 was the second (AllplexTM HPV28 assay) or third (AnyplexTM II HPV28 assay) most frequent carcinogenic HPV type according to our results, whereas it ranked fourth among the ten most frequent carcinogenic types (after HPV16, 51 and 52) according to French epidemiology [31].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] L Bruni

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The human β-globin gene was co-amplified as an endogenous internal control with the L1 gene of targeted HPV types.

    “The human β-globin gene (endogenous internal control, IC) was co-amplified with the L1 gene of targeted HPV types within the clinical specimens.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductreasoning

    Rigorous internal method validation was conducted in the laboratory prior to using the EMAG extraction system, which does not appear in the instructions for use.

    “Given that this extraction system does not appear in the instructions for use (IFU), rigorous internal method validation was conducted in our laboratory prior to its use.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Interpretationown data

    The Allplex HPV28 kit can be used for HPV genotyping, with results overall similar to those obtained with the Anyplex II HPV28 kit and the addition of Ct values for patient follow-up.

    “Our results demonstrate that the AllplexTM HPV28 kit can be used for HPV genotyping, with results overall similar to those obtained with the AnyplexTM II HPV28 kit and the addition of Ct values for patient follow-up.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Allplex HPV28 Ct values and Anyplex II HPV28 signal intensity scores provide comparable measures of HR-HPV viral load.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    There were no invalid results among the 459 samples analysed.

    “There were no invalid results among the 459 samples analysed.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductreasoning

    The samples selected based on Anyplex II HPV28 results were subsequently tested again at the same time using the same thawed extract with both kits to avoid storage-related discrepancies.

    “The samples selected based on the results of the AnyplexTM II HPV28 assay were subsequently tested again at the same time (using the same thawed extract) with both the AnyplexTM II HPV28 and AllplexTM HPV28 kits to avoid any storage-related discrepancies.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    HPV quantification may be relevant to monitor as a potential prognostic marker of residual lesions after treatment.

    “Although there is no clear evidence of the value of HPV quantification in cervical cancer screening, it may be relevant to monitor HPV quantification as a potential prognostic marker of residual lesions after treatment [17,18].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [17] JY Park, 2008, The association of pre-conization high-risk HPV load and the persistence of HPV infection and persistence/recurrence of cervical intraepithelial neoplasia after conization, Gynecol Oncol source
    • cites [18] L Chen, 2020, HR-HPV viral load quality detection provide more accurate prediction for residual lesions after treatment: a prospective cohort study in patients with high-grade squamous lesions or worse, Med Oncol source

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The Allplex HPV28 assay may be useful because it provides signal strength information through Ct values.

    “In this context, the AllplexTM HPV28 assay, which provides signal strength information through Ct values, may be useful.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductreasoning

    Our study, performed on a smaller sample size (N = 459) compared to the dataset used in the summary report on HPV and related diseases in France, is therefore less representative of the broader French population.

    “In addition, our study, performed on a smaller sample size (N = 459) compared to the dataset used in the summary report on HPV and related diseases in France [31], is therefore less representative of the broader French population.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] L Bruni

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Study design and conductown data

    The high prevalence of HR-HPV infections and the presence of multiple HR-HPV infections in our population enabled us to increase the statistical power of our analysis for each HR-HPV type (at least 20 positive samples per HR-HPV type).

    “Nevertheless, the high prevalence of HR-HPV infections and the presence of multiple HR-HPV infections in our population enabled us to increase the statistical power of our analysis for each HR-HPV type (at least 20 positive samples per HR-HPV type).”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    According to a French summary report, HPV16, 51, 56, 31, 52, and 39 were the six most frequent genotypes in women with NILM.

    “According to this report, HPV16, 51, 56, 31, 52, and 39 were the six most frequent genotypes in women with NILM [31].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] L Bruni

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Premisecitation

    According to French data, HPV16, 31, 33, 52, 51 were the most frequent in the HSIL group, and HPV56 was not found among the ten most frequent HPV carcinogenic types.

    “According to French data, HPV16, 31, 33, 52, 51 were the most frequent in the HSIL group, and HPV56 was not found among the ten most frequent HPV carcinogenic types [31].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] L Bruni

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    This high proportion of ASCUS is consistent with the current French cervical cancer screening strategy but does not reflect the general population.

    “This high proportion of ASCUS is consistent with the current French cervical cancer screening strategy but does not reflect the general population.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Study design and conductnone given

    Samples were tested simultaneously by both assays, using the same DNA extract stored at -20°C.

    “Samples were tested simultaneously by both assays, using the same DNA extract stored at -20°C.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Study design and conductnone given

    The selection of HR-HPV-positive samples may have introduced a bias and explains the relatively low number of HR-HPV-negative samples.

    “Firstly, the selection of HR-HPV-positive samples may have introduced a bias and explains the relatively low number of HR-HPV-negative samples.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Interpretationreasoning

    Our results are broadly consistent with French data, except for HPV51 and HPV56.

    “Our results are therefore broadly consistent with these French data, except for HPV51 and HPV56.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    The use of this new assay may be of great value for cervical cancer screening and HPV infections monitoring.

    “Therefore, the use of this new assay may be of great value for cervical cancer screening and HPV infections monitoring.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    We did not conduct reproducibility studies on the Allplex HPV28 assay, which constitutes a limitation in the evaluation of this new assay.

    “Fourthly, we did not conduct reproducibility studies on the AllplexTM HPV28 assay, which constitutes a limitation in the evaluation of this new assay.”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    HPV31 and HPV39 are the third (prevalence of 3.8%) and tenth (prevalence of 0.8%) most frequent carcinogenic genotypes among women with cervical cancer in France, respectively.

    “HPV31 and HPV39 are the third (prevalence of 3.8%) and tenth (prevalence of 0.8%) most frequent carcinogenic genotypes among women with cervical cancer in France, respectively [31].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [31] L Bruni

      Couldn’t be matched to a paper in Crossref, so it can’t be checked.

  • May combine two claims.

    Interpretationown data

    The Allplex HPV28 assay can be used for HR-HPV detection and genotyping, with results overall similar to those obtained with the Anyplex II HPV28 kit and the addition of Ct values for patient follow-up.

    “In conclusion, our results demonstrate that the AllplexTM HPV28 assay can be used for HR-HPV detection and genotyping, with results overall similar to those obtained with the well-known AnyplexTM II HPV28 kit and the addition of Ct values for patient follow-up.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: The Anyplex II HPV28 assay is a valid comparator for HR-HPV detection and genotyping.
50 of 50

  • The paper relies on this without support.

    The Allplex HPV28 kit uses different chemistry and results analysis compared with the Anyplex II HPV28 kit.

    “The AllplexTM HPV28 real-time PCR kit, using different chemistry and results analysis compared with its predecessor, the AnyplexTM II HPV28 kit, has recently been launched.”

  • The paper relies on this without support.

    Allplex HPV28 Ct values and Anyplex II HPV28 signal intensity scores provide comparable measures of HR-HPV viral load.

    “AllplexTM HPV28 Ct values correlated well with AnyplexTM II HPV28 signal intensity scores, with median Ct values [interquartile range] of 38.0 [36.8-39.6], 31.1 [28.6-33.7], and 23.8 [21.1-25.4] corresponding to + , ++, and +++ signal intensity scores, respectively (Fig 3).”

  • The paper relies on this without support.

    Internal control Ct values and signal intensities are valid measures of sample DNA quality.

    “The mean IC Ct values were almost identical between Allplex+/Anyplex- samples and non-discordant samples (25.27 versus 25.20, respectively).”
    “These findings support that sample DNA quality was comparable between discordant and non-discordant samples.”

  • The paper relies on this without support.

    Ct values > 35 indicate weak HR-HPV signals.

    “Among Allplex+/Anyplex- cases, 97.4% (38/39) had Ct values > 35 (Fig 6A).”
    “Most of our discordant results corresponded to samples with weak HR-HPV signals, suggesting differences in sensitivity between assays according to HR-HPV types.”

  • The paper relies on this without support.

    Signal intensity score (+) indicates weak HR-HPV signal.

    “Among Allplex-/Anyplex+ cases, 85.7% (36/42) were detected at the lowest signal intensity (+), and 14.3% (6/42) at the intermediate signal intensity (++).”
    “Most of our discordant results corresponded to samples with weak HR-HPV signals, suggesting differences in sensitivity between assays according to HR-HPV types.”

  • The paper relies on this without support.

    The Anyplex II HPV28 assay is a valid comparator for HR-HPV detection and genotyping.

    “In the present study, a new multiplex real-time PCR kit, the AllplexTM HPV28 assay, was compared with the AnyplexTM II HPV28 assay for the detection and genotyping of the 13 HR-HPV types.”
    “with results overall similar to those obtained with the well-known AnyplexTM II HPV28 kit”
6 of 6

Statistics recomputed

Every reported test result, recomputed from its test statistic and degrees of freedom. A result shows as not adding up only once an independent check has confirmed it.

  • Consistentχ²(1) = 0.047reported p = .83 · recomputed p = .828

    “χ2 (1) = 0.047, p = .83”

1 of 1

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • PPA and NPA are given conflicting definitions

    Minor

    The Table 4 note defines PPA and NPA as predictive values, while the methods say the study calculated positive and negative percent agreement. These are different measures, so the table labels are internally inconsistent.

1 of 1

Cites

Flagged first, then by citations

Research works printed but not linked: 2

  1. E Meites, Human papillomavirus. Chapter 11. In: Pink Book: Communicable Disease Control: A Guide for Public Health. Centers for Disease Control and Prevention; 2024 [Internet]. [cited October 22, 2024]
  2. L Bruni, ICO/IARC Information Centre on HPV and Cancer (HPV Information Centre). Human Papillomavirus and Related Diseases in France. Summary Report 10 March 2023. Accessed September 23, 2023. [Internet]. [cited 2023 Sep 23]

Cited by

Sorted by citations

Related

Authors
Mafi, S., Theuillon, F., Meyer, S., Woillard, J.-B., Dupont, M., Rogez, S., Alain, S., & Hantz, S.
Affiliations
  • Inserm (FR)
  • Centre Hospitalier Universitaire de Limoges (FR)
Corresponding author
  • Mafi, Sarah
  • Hantz, Sébastien
ORCID
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2025-04-01
Volume
20
Issue
4
Pages
e0320978
ISSN
1932-6203 (ISSN-L)
DOI
10.1371/journal.pone.0320978
PMC
PMC11960881
OpenAlex
W4409049396
Semantic Scholar
19ed779f8811f7d91efa29284cfd6034023b3106
Cited by
9
References
31
Citations by year
2026: 6 · 2025: 3
FWCI
5.46
Type
journal article
Language
en
Open access
Licence
Locations
  • PLoS ONE (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
Seegene
Topics
  • Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
  • Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Women's cancer prevention and management
Keywords
high-risk HPV genotyping, HPV 31, HPV39, cervical cancer screening, liquid-based cytology, assay comparison, multiple HPV infection, HPV prevalence
MeSH terms
Adult, Uterine Cervical Neoplasms, Cervix Uteri, DNA, Viral, Female, Genotype, Humans, Middle Aged, Reagent Kits, Diagnostic, Papillomaviridae, Papillomavirus Infections, Alphapapillomavirus, Early Detection of Cancer, Genotyping Techniques, Real-Time Polymerase Chain Reaction

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-16.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-16.

Cited sources are checked by gpt-6-sol.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

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