Comparative evaluation of HPV genotyping: A study on the performance concordance between Anyplex II HPV28 detection and Linear Array genotyping tests in nationwide studies in Brazil
Open accessAbstract
Background: Advances in laboratory techniques for HPV diagnosis necessitate a thorough assessment of the efficiency, replicability, sensitivity, and specificity of those methods. This study aims to validate and compare HPV detection/genotyping using the Anyplex™ II HPV28 Detection assay (Seegene) assay and the Linear Array HPV Genotyping test (Roche Diagnostics) on genital samples for use in epidemiological studies. Methods: From 6,388 penile and cervical DNA samples collected in the POP-Brazil, 1,745 were randomly selected to be included in this study. The samples were submitted to HPV detection and genotyping following the manufacturers’ protocols. DNA was genotyped using the Anyplex™ II HPV28 Detection kit (Seegene), and the results were compared to those obtained using the Linear Array HPV Genotyping test (Roche Diagnostics). Concordance of HPV genotyping results was assessed by the percentage agreement and Cohen’s kappa score (κ). Results: The agreement between the two methodologies was deemed good for HPV detection (κ = 0.78). Notably, Anyplex™ II HPV28 demonstrated enhanced capability in detecting a broader spectrum of genotypes compared to Linear Array. Conclusion: Anyplex™ II HPV28 exhibited comparable results to the Linear Array assay in clinical specimens, showcasing its potential suitability for a diverse array of research applications requiring the detection and genotyping of HPV. The study supports the utility of Anyplex™ II HPV28 as an effective tool for HPV screening in epidemiological studies, emphasizing its robust performance in comparison to established diagnostic tests.
AI snapshot
Written from the paper’s full text.
TL;DR
In 1,709 genital DNA samples from POP-Brazil, Anyplex™ II HPV28 and Linear Array showed good overall agreement for HPV detection (κ = 0.78) and high-risk HPV (κ = 0.76), with Anyplex detecting more genotypes overall. Anyplex had high sensitivity versus Linear Array (97% overall, 96% HR-HPV) but lower specificity (82% overall, 76% HR-HPV), supporting its use as a replacement for the discontinued Linear Array in epidemiological studies.
Key findings
- Overall HPV agreement between Anyplex™ II HPV28 and Linear Array was 95.85%, with κ = 0.78; HR-HPV κ was 0.76. Anyplex detected 22 of 26 individually analyzed types more frequently, while Linear Array detected HPV 59, 61, 52, and 6 more often.
- Using Linear Array as gold standard, Anyplex sensitivity was 97% (95% CI 96–98) for overall HPV and 96% (95% CI 95–97) for HR-HPV; specificity was 82% (95% CI 75–87) for overall HPV and 76% (95% CI 72–80) for HR-HPV. Type-specific HR-HPV sensitivity ranged from 98% for HPV56 to 71% for HPV52; low-risk sensitivity ranged from 99% for HPV42 to 25% for HPV6.
- Most HPV types had excellent κ (≥0.8), including HPV16 and HPV18; nine genotypes had good κ, HPV40, HPV42, and HPV68 had moderate κ, and HPV6 had fair κ (0.31). Highest individual agreement was HPV69 (99.12%), HPV26 (98.71%), and HPV11 (98.64%); lowest was HPV6 (88.37%), HPV42 (90.73%), and HPV52 (91.19%).
- Anyplex false-positive rates were 2.34% for overall HPV and 2.57% for HR-HPV. HPV52 had the most false-negative results (62 samples, 3.64%), while HPV6 had the most false-positive results (162 samples, 9.56%).
Methods
- Cross-sectional comparison using 1,745 randomly selected penile and cervical DNA samples from the 6,388 collected in POP-Brazil, a nationwide study of adults aged 16–25 recruited September 2016–November 2017; 1,709 samples were suitable for analysis.
- Samples were tested with Anyplex™ II HPV28 Detection (Seegene) and Linear Array HPV Genotyping test (Roche Diagnostics) following manufacturers’ protocols; samples were considered adequate when internal control signal was observed.
- Concordance was assessed by percentage agreement and Cohen’s kappa, with sensitivity and specificity calculated using Linear Array as gold standard; McNemar test assessed discordance; analyses used SAS version 9.4.
Limitations
- The paper states that Linear Array has cross-reactivity of the HPV52 probe with HPV33, 35, and 58, requiring an additional PCR test, and notes that defrosting samples could degrade genetic material but reportedly does not significantly impact assay sensitivity.
- No formal limitations section is present; evident from the text, the study is restricted to genital samples from Brazilian young adults aged 16–25, so generalizability to other populations or sample types is unclear.
- Also evident: the assays have different genotype coverage, and 36 samples were inadequate due to absent internal control amplification in Anyplex while 18 had insufficient volume, limiting the final analyzed sample to 1,709.
Model-written summary. Check it against the paper before relying on it.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
8 of 25 cited sources checked · 4 supported · 0 flagged · accuracy not yet measured
- Premisecitation
In several studies that compared HPV genotyping methodologies, AnyplexTM II HPV28 demonstrated good agreement with other HPV assays, including LA.
“In several studies that compared HPV genotyping methodologies, Anyplex™ II HPV28 demonstrated good agreement with other HPV assays, including LA.”
Quote in the paperSubstantial claim1 of 4 sources checked- cites [8] F Marcuccilli, 2015, Performance evaluation of AnyplexTM II HPV28 detection kit in a routine diagnostic setting: Comparison with the HPV Sign® Genotyping Test, Journal of Virological Methods source
- cites [28] MJ Kwon, 2014, Comparison of the Anyplex II HPV28 assay with the Hybrid Capture 2 assay for the detection of HPV infection, Journal of Clinical Virology source
- cites [29] GL Larsson, 2015, Evaluation of HPV Genotyping Assays for Archival Clinical Samples, The Journal of Molecular Diagnostics source
The Discussion (page not supplied) says all four methods showed good agreement for the specified HPV genotypes, and the Detection of Genotypes Specified by Reference Protocol section reports 97% agreement for Anyplex II HPV28 against the reference protocol. But this study did not compare Anyplex directly with LA (Roche Linear Array); it mentions LA only as an assay against which primers had previously been validated. The cited paper is also one study, not evidence by itself for 'several studies.' (LLM, conf=0.88)
Experimental — accuracy not yet measured - cites [30] A Latsuzbaia, 2016, Analytical performance evaluation of Anyplex II HPV28 and Euroarray HPV for genotyping of cervical samples, Diagn Microbiol Infect Dis source
- Premisecitation
The Linear Array HPV Genotyping test was discontinued in December 2019.
“However, the LA was discontinued in December 2019, which made it necessary to evaluate new available methodologies [16, 17].”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [16] V Dalstein, 2009, Analytical evaluation of the Papillo Check test, a new commercial DNA chip for detection and genotyping of human papillomavirus, J Virol Methods source
- cites [17] M Demarco, 2018, Validation of a Human Papillomavirus (HPV) DNA Cervical Screening Test That Provides Expanded HPV Typing., J Clin Microbiol source
The Materials and Methods section says LA was used for testing in 2014–2015, and the Results compare LA with Onclarity. Neither section addresses whether LA was discontinued in December 2019; searches for that date and for discontinuation found no supporting passage in this 2018 paper. (LLM, conf=0.78)
Experimental — accuracy not yet measured
- Interpretationcitation
AnyplexTM II HPV28's good agreement with other HPV assays is likely due to its highly sensitive multiplexed detection approach.
“This is likely due to its highly sensitive multiplexed detection approach [8, 28–30].”
Quote in the paperNot a substantial claim1 of 4 sources checked- cites [8] F Marcuccilli, 2015, Performance evaluation of AnyplexTM II HPV28 detection kit in a routine diagnostic setting: Comparison with the HPV Sign® Genotyping Test, Journal of Virological Methods source
- cites [28] MJ Kwon, 2014, Comparison of the Anyplex II HPV28 assay with the Hybrid Capture 2 assay for the detection of HPV infection, Journal of Clinical Virology source
- cites [29] GL Larsson, 2015, Evaluation of HPV Genotyping Assays for Archival Clinical Samples, The Journal of Molecular Diagnostics source
The paper reports good agreement for Anyplex II HPV28 in the Discussion and describes its technology as allowing a “very sensitive multiplexed detection approach” in the assay description. It does not explicitly attribute the agreement to that approach; the proposed causal link is an inference. (LLM, conf=0.79)
Experimental — accuracy not yet measured - cites [30] A Latsuzbaia, 2016, Analytical performance evaluation of Anyplex II HPV28 and Euroarray HPV for genotyping of cervical samples, Diagn Microbiol Infect Dis source
- Findingown data
Specificity was 76% (95% CI, 72%-80%) for HR-HPV.
“Specificity was 82% (95% CI, 75%–87%) for overall HPV and 76% (95% CI, 72%– 80%) for HR-HPV.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingnone given
Anyplex II HPV28 demonstrated enhanced capability in detecting a broader spectrum of genotypes compared to Linear Array.
“Notably, Anyplex™ II HPV28 demonstrated enhanced capability in detecting a broader spectrum of genotypes compared to Linear Array.”
Quote in the paperSubstantial claim
- Findingown data
Cohen's kappa score (κ) for most of the HPV types identified by the two tests was considered excellent (≥0.8), including the most prevalent HR-HPV types, HPV 16 and 18.
“Cohen’s kappa score (κ) for most of the HPV types identified by the two tests was considered excellent (≥0.8), including the most prevalent HR-HPV types, HPV 16 and 18.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The false-positive rate for high-risk HPV genotyping with AnyplexTM II HPV28, using Linear Array as the gold standard, was 2.57%.
“the false-positive rate for general HPV and high-risk HPV genotyping Anyplex™ II HPV28 were 2.34% and 2.57%, respectively.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The lowest individual genotype agreement percentages were observed for HPV6 (88.37%), HPV42 (90.73%), and HPV52 (91.19%).
“On the other hand, the lowest percentages were observed for HPV6 (88.37%), HPV42 (90.73%), and HPV52 (91.19%) (Fig 1).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
HPV6 showed the highest number of false-positive results (162 samples, 9.56%).
“Conversely, HPV6 showed the highest number of false-positive results (162 samples, 9.56%).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The false-positive rate for general HPV genotyping with AnyplexTM II HPV28, using Linear Array as the gold standard, was 2.34%.
“the false-positive rate for general HPV and high-risk HPV genotyping Anyplex™ II HPV28 were 2.34% and 2.57%, respectively.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
LA exhibited higher detectability for HPV types 59, 61, 52, and 6.
“Among the 26 types analyzed individually, Anyplex™ II HPV28 detected 22 types more frequently, while LA exhibited higher detectability for HPV types 59, 61, 52, and 6.”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The agreement between Anyplex II HPV28 and Linear Array for HPV detection was good (κ = 0.78).
“The agreement between the two methodologies was deemed good for HPV detection (κ = 0.78).”
Quote in the paperSubstantial claim - Findingown data
The κ scores for three other types (HPV40, 42, and 68) were considered moderate.
“The κ scores for three other types (HPV40, 42, and 68) were considered moderate”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
In the LR-HPV types, the sensitivity varied from 99% (95% CI, 95%-100%) for HPV42 to 25% (95% CI, 20%-32%) for HPV6.
“In the LR-HPV types, the sensitivity varied from 99% (95% CI, 95%–100%) for HPV42 to 25% (95% CI, 20%–32%) for HPV6.”
Quote in the paperNot a substantial claim - Findingown data
Among the 26 types analyzed individually, AnyplexTM II HPV28 detected 22 types more frequently.
“Among the 26 types analyzed individually, Anyplex™ II HPV28 detected 22 types more frequently, while LA exhibited higher detectability for HPV types 59, 61, 52, and 6.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The κ score for HPV6 was considered fair.
“and only that of the HPV6 type was considered fair (Table 3).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
Specificity was 82% (95% CI, 75%-87%) for overall HPV.
“Specificity was 82% (95% CI, 75%–87%) for overall HPV and 76% (95% CI, 72%– 80%) for HR-HPV.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
Nine genotypes were considered to have good κ scores.
“Besides that, nine genotypes were considered to have good κ scores.”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
HPV52 was the type that presented more false-negative results (62 samples, 3.64%).
“Considering the percentage agreement in relation to genotype detection, HPV52 was the type that presented more false-negative results (62 samples, 3.64%).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
Considering type-specific HR-HPV, the sensitivity varied between 98% for HPV56 and 71% for HPV52.
“Considering type-specific HR-HPV, the sensitivity varied between 98% for HPV56 and 71% for HPV52.”
Quote in the paperNot a substantial claim - Findingown data
The overall sensitivity for AnyplexTM II HPV28, using Linear Array as the gold standard, was 97% (95% CI, 96%-98%).
“The overall sensitivity and high-risk HPV sensitivity for Anyplex™ II HPV28, using Linear Array as the gold standard, exhibited similar values of 97% (95% CI, 96%–98%) and 96% (95% CI, 95%–97%), respectively.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
The overall HPV agreement between the two techniques was 95.85%.
“The overall HPV agreement between the two techniques was 95.85% (Table 2).”
Quote in the paperSubstantial claim - Findingown data
The high-risk HPV sensitivity for AnyplexTM II HPV28, using Linear Array as the gold standard, was 96% (95% CI, 95%-97%).
“The overall sensitivity and high-risk HPV sensitivity for Anyplex™ II HPV28, using Linear Array as the gold standard, exhibited similar values of 97% (95% CI, 96%–98%) and 96% (95% CI, 95%–97%), respectively.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
Both the Linear Array (LA) and AnyplexTM II HPV28 assays exhibited robust agreement in HPV detection from genital samples.
“The study findings reveal that both the Linear Array (LA) and Anyplex™ II HPV28 assays exhibited robust agreement in HPV detection and in high-risk typing from genital samples.”
Quote in the paperSubstantial claim - Findingown data
The Kappa score for HPV52 detection between LA and AnyplexTM II HPV28 was 0.68.
“In our study, LA detected more cases of HPV52 than Anyplex™ II HPV28, with a substantial Kappa score of 0.68.”
Quote in the paperSubstantial claim - Findingown data
Our study revealed that AnyplexTM II HPV28 exhibits a lower detection sensitivity for the low-risk genotype, HPV6.
“Our study revealed that Anyplex™ II HPV28 exhibits a lower detection sensitivity for the low-risk genotype, HPV6.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Findingown data
In this study, LA detected more cases of HPV52 than AnyplexTM II HPV28.
“In our study, LA detected more cases of HPV52 than Anyplex™ II HPV28, with a substantial Kappa score of 0.68.”
Quote in the paperSubstantial claim - Findingown data
Both the Linear Array (LA) and AnyplexTM II HPV28 assays exhibited robust agreement in high-risk HPV typing from genital samples.
“The study findings reveal that both the Linear Array (LA) and Anyplex™ II HPV28 assays exhibited robust agreement in HPV detection and in high-risk typing from genital samples.”
Quote in the paperSubstantial claim - Interpretationown data
AnyplexTM II HPV28 has demonstrated acceptable reproducibility in detecting the HPV genotypes covered by the assays.
“AnyplexTM II HPV28 has demonstrated acceptable reproducibility in detecting the HPV genotypes covered by the assays.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
- Interpretationown data
Anyplex II HPV28 has robust performance in comparison to established diagnostic tests.
“The study supports the utility of Anyplex™ II HPV28 as an effective tool for HPV screening in epidemiological studies, emphasizing its robust performance in comparison to established diagnostic tests.”
Quote in the paperSubstantial claim - Interpretationown data
Anyplex II HPV28 is potentially suitable for a diverse array of research applications requiring HPV detection and genotyping.
“Anyplex™ II HPV28 exhibited comparable results to the Linear Array assay in clinical specimens, showcasing its potential suitability for a diverse array of research applications requiring the detection and genotyping of HPV.”
Quote in the paperSubstantial claim - Interpretationown data
Anyplex II HPV28 exhibited comparable results to the Linear Array assay in clinical specimens.
“Anyplex™ II HPV28 exhibited comparable results to the Linear Array assay in clinical specimens, showcasing its potential suitability for a diverse array of research applications requiring the detection and genotyping of HPV.”
Quote in the paperSubstantial claim - Study design and conductown data
Thirty-six samples provided inadequate results due to the absence of internal control amplification in the AnyplexTM II HPV28 assay.
“Thirty-six samples provided inadequate results due to the absence of internal control amplification in the Anyplex™ II HPV28 assay”
Quote in the paperNot a substantial claim - Interpretationown data
Anyplex II HPV28 is an effective tool for HPV screening in epidemiological studies.
“The study supports the utility of Anyplex™ II HPV28 as an effective tool for HPV screening in epidemiological studies, emphasizing its robust performance in comparison to established diagnostic tests.”
Quote in the paperSubstantial claim- Rests on an assumption: The 1,745 randomly selected samples are representative of the POP-Brazil population and of populations used in epidemiological studies of HPV.
- Rests on an assumption: A good kappa agreement (κ = 0.78) between Anyplex II HPV28 and Linear Array is sufficient for Anyplex II HPV28 to be considered an effective tool for HPV screening in epidemiological studies.
- Study design and conductnone given
Among the 6,388 penile and cervical DNA samples collected in the POP-Brazil study, 1,745 were randomly selected for this investigation.
“Among the 6,388 penile and cervical DNA samples collected in the POP-Brazil study, 1,745 were randomly selected for this investigation.”
Quote in the paperSubstantial claim - Interpretationreasoning
AnyplexTM II HPV28 is a viable alternative to other commercially available HPV diagnostic tests.
“Its notable concordance with the Linear Array suggests its reliability, positioning it as a viable alternative to other commercially available HPV diagnostic tests.”
Quote in the paperSubstantial claim - Premisecitation
The inclusion of additional HPV types 35, 39, 51, 56, 58, 59, 66, or 68 resulted in a minimal increase in prevalence, accounting for only 12 of the 808 cases (1.5% for all eight types collectively).
“The inclusion of additional HPV types, specifically 35, 39, 51, 56, 58, 59, 66, or 68, which are also encompassed in currently employed HPV tests, resulted in a minimal increase in prevalence, accounting for only 12 of the 808 cases (1.5% for all eight types collectively).”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [31] K Sundström, 2021, How Many Human Papillomavirus Types Do We Need to Screen For?, J Infect Dis source
- Interpretationreasoning
The notable concordance of AnyplexTM II HPV28 with Linear Array suggests its reliability.
“Its notable concordance with the Linear Array suggests its reliability, positioning it as a viable alternative to other commercially available HPV diagnostic tests.”
Quote in the paperSubstantial claim - Interpretationreasoning
The additional PCR test required to confirm HPV52 status increases the complexity and cost of the LA method.
“This requires the use of an additional PCR test to confirm the status of HPV52, increasing the complexity and cost of the method.”
Quote in the paperSubstantial claim - Interpretationreasoning
The Seegene assay demonstrated excellent performance as an HPV screening tool in epidemiological studies.
“The Seegene assay, in particular, demonstrated excellent performance as an HPV screening tool in epidemiological studies.”
Quote in the paperSubstantial claim - Interpretationreasoning
The cross-reactivity of the LA HPV52 probe requires an additional PCR test to confirm HPV52 status.
“This requires the use of an additional PCR test to confirm the status of HPV52, increasing the complexity and cost of the method.”
Quote in the paperSubstantial claim- Rests on an assumption: The HPV52 probe of the LA assay cross-reacts with HPV33, HPV35, and HPV58.
- Interpretationreasoning
The results underscore the potential of the AnyplexTM II HPV28 assay for effective and accurate HPV screening in diverse research applications.
“These results underscore the potential of the Anyplex™ II HPV28 assay for effective and accurate HPV screening in diverse research applications.”
Quote in the paperSubstantial claim
- Classified as probably not a substantial claim. 16
- May combine two claims. 9
Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
PremisecitationThe POP-Brazil study was a nationwide, cross-sectional study designed to estimate the prevalence of type-specific HPV in young adults aged 16 to 25, from both sexes, and to serve as a baseline to assess the impact of the Brazilian national vaccination program.
“Study participants were recruited between September 2016 and November 2017 by the POP Brazil study, a nationwide, cross-sectional study designed to estimate the prevalence of type-specific HPV in young adults aged between 16 and 25, from both sexes and to serve as a baseline to assess the impact of the Brazilian national vaccination program [24].”
Quote in the paperNot a substantial claim1 of 1 sources checked- cites [24] POP-Brazil Study Group, 2020, Prevalence of HPV infection among sexually active adolescents and young adults in Brazil: The POP-Brazil Study., Scientific Reports source
Classified as probably not a substantial claim. May combine two claims.
PremisecitationThe Linear Array HPV Genotyping test was considered the gold standard for many years and was used in research on HPV epidemiology, cervical cancer screening, and vaccine surveillance.
“The Linear Array® HPV Genotyping test (Roche Diagnostics) (LA) was considered the gold standard for many years and was also used in research on HPV epidemiology, cervical cancer screening, and vaccine surveillance [12, 13].”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [12] I Kukimoto, 2020, Human Papillomavirus (HPV) Genotyping Assay Suitable for Monitoring the Impact of the 9-Valent HPV Vaccine., Tohoku J Exp Med source
- cites [13] SM Garland, 2018, Final analysis of a study assessing genital human papillomavirus genoprevalence in young Australian women, following eight years of a national vaccination program, Vaccine source
Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).
PremisecitationThe consideration of screening for all 14 HPV types could potentially lead to a suboptimal balance between the associated harms and benefits.
“Moreover, the consideration of screening for all 14 HPV types could potentially lead to a suboptimal balance between the associated harms and benefits [31, 33].”
Quote in the paperNot a substantial claim1 of 2 sources checkedProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationDefrosting samples does not significantly impact the sensitivity of the assays.
“However, it is worth mentioning that this does not significantly impact the sensitivity of the assays [34, 35].”
Quote in the paperNot a substantial claim1 of 2 sources checked- cites [34] MP Stevens, 2008, Development and validation of a real-time PCR assay specifically detecting human papillomavirus 52 using the Roche LightCycler 480 system, J Virol Methods source
- cites [35] F Coutlée, 2007, Confirmatory Real-Time PCR Assay for Human Papillomavirus (HPV) Type 52 Infection in Anogenital Specimens Screened for HPV Infection with the Linear Array HPV Genotyping Test, Journal of Clinical Microbiology source
The Clinical specimens and Performance of RT-52 passages (indexed as Abstract; page unavailable) describe sample processing and assay sensitivity, but do not compare sensitivity before and after defrosting. Searches for freeze–thaw and thawed specimens found no passage addressing that effect. (LLM, conf=0.75)
Experimental — accuracy not yet measured
May combine two claims.
PremisecitationAnyplexTM II demonstrated similar sensitivity to LA for most high-risk genotypes, with slightly lower sensitivity observed for HPV51 or 52.
“Additionally, the authors reported that Anyplex™ II demonstrated similar sensitivity to LA for most high-risk genotypes, with slightly lower sensitivity observed for HPV51 or 52 [14, 32].”
Quote in the paperSubstantial claim1 of 2 sources checked- cites [14] AM Cornall, 2017, HPV genotype-specific concordance between EuroArray HPV, Anyplex II HPV28 and Linear Array HPV Genotyping test in Australian cervical samples., Papillomavirus Research source
- cites [32] AM Cornall, 2017, Anyplex II HPV28 detection and Anyplex II HPV HR detection assays are highly concordant with other commercial assays for detection of high-risk HPV genotypes in women with high grade cervical abnormalities, Eur J Clin Microbiol Infect Dis source
May combine two claims.
Findingown dataThe individual genotype agreement exhibited the highest percentage for HPV69 (99.12%), followed by HPV26 (98.71%) and HPV11 (98.64%).
“The individual genotype agreement exhibited the highest percentage for HPV69 (99.12%), followed by HPV26 (98.71%) and HPV11 (98.64%).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
May combine two claims.
Findingown dataConsidering type-specific specificity, the majority was above 95%, the lowest value being observed for HPV42 (90%; 95% CI, 89%-92%).
“Considering type-specific specificity, the majority was above 95%, the lowest value being observed for HPV42 (90%; 95% CI, 89%–92%) (Table 3).”
Quote in the paperNot a substantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
Classified as probably not a substantial claim.
Study design and conductnone givenSamples were considered adequate when the internal control signal was observed, according to Anyplex II HPV28 and LA manufacturer's instructions.
“We consider the samples as adequate when the internal control signal was observed, according to Anyplex™ II HPV28 and LA manufacturer’s instructions.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe study was approved by the ethics review committees of all participating centers.
“This study was approved by the ethics review committees of all participating centers.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenBoth FMUSP and the Clinical Epidemiology Laboratory of UFCSPA performed the HPV DNA typing proficiency study from Equalis, an external quality assessment for laboratories that perform HPV typing, organized by the Global HPV LabNet, for both HPV DNA assays included in the manuscript.
“Both FMUSP and Clinical Epidemiology Laboratory of UFCSPA performed the HPV DNA typing proficiency study from Equalis, an external quality assessment for laboratories that perform HPV typing, organized by the Global HPV LabNet, to both HPV DNA assays included in this manuscript.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductnone givenThe study follows the ethical recommendations of Resolutions 347/05, 441/11, and 466/12 of the National Health Council.
“The study follows the ethical recommendations of Resolutions 347/05, 441/11, and 466/12 of the National Health Council.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataOf 1,745 samples processed, 1,709 were suitable for analysis.
“Of the 1,745 samples processed, 1,709 were suitable for analysis.”
Quote in the paperNot a substantial claimMay combine two claims.
Interpretationown dataBoth tests exhibited comparable agreement and sensitivity, effectively detecting and identifying HPV types with no significant differences.
“Both tests exhibited comparable agreement and sensitivity, effectively detecting and identifying HPV types with no significant differences.”
Quote in the paperSubstantial claim- Rests on an assumption: LA is the gold standard methodology for HPV genotyping.
Classified as probably not a substantial claim.
Study design and conductreasoningThe draw was made so that HPV types with the lowest occurrence were not under-sampled, resulting in an equivalent number of samples for each type.
“Since each HPV type has a different occurrence rate, the draw was made so that the types with the lowest occurrence were not under sampled, resulting in an equivalent number of samples for each type.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductown dataEighteen samples did not have sufficient volume to be processed.
“18 samples did not have a sufficient volume to be processed.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenRecruited individuals agreed voluntarily to participate and signed an informed consent form.
“Recruited individuals agreed voluntarily to participate and signed an informed consent form.”
Quote in the paperNot a substantial claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationThe Linear Array assay is capable of detecting 37 HPV genotypes.
“This assay is capable of detecting 37 genotypes and consists of a PCR followed by in situ hybridization and subsequent reading on a nylon strip coated with HPV type-specific and human beta-globin-specific oligonucleotide probes [15].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [15] L Xu, 2018, Assessment of the Roche Linear Array HPV Genotyping Test within the VALGENT framework., J Clin Virol source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationA Swedish study revealed that HPV types 16, 18, 31, 33, 45, or 52 were detected in 689 out of 808 screen-detected invasive cervical cancers (ICC), constituting 85.3% of cases.
“Notably, a Swedish study revealed that HPV types 16, 18, 31, 33, 45, or 52 were detected in 689 out of 808 screen-detected invasive cervical cancers (ICC), constituting 85.3% of cases [31].”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [31] K Sundström, 2021, How Many Human Papillomavirus Types Do We Need to Screen For?, J Infect Dis source
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationCornall and colleagues (2017b) evaluated the HPV genotyping performance of two genotyping assays, AnyplexTM II HPV28 and EuroArray HPV, in comparison with LA.
“Cornall and colleagues (2017b) evaluated the HPV genotyping performance of two genotyping assays, AnyplexTM II HPV28 (Seegene) and EuroArray HPV (EuroImmun), in comparison with LA.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Cornall and colleagues (2017b)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
Classified as probably not a substantial claim.
PremisecitationBoth comprehensive global meta-analyses and extensive long-term cohort studies have consistently identified variations in the oncogenic potential among different HPV types.
“However, both comprehensive global meta-analyses and extensive long-term cohort studies have consistently identified variations in the oncogenic potential among different HPV types.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [31] K Sundström, 2021, How Many Human Papillomavirus Types Do We Need to Screen For?, J Infect Dis source
May combine two claims.
PremisecitationThe agreement between LA and the other two assays was nearly perfect for most genotypes (κ = 0.81−1.00), including all high-risk genotypes (κ = 0.81-0.98).
“The agreement between LA and the other two assays was nearly perfect for most genotypes (κ = 0.81−1.00), including all high-risk genotypes (κ = 0.81–0.98).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites Cornall and colleagues (2017b)
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
The paper relies on this without support.
The 1,745 randomly selected samples are representative of the POP-Brazil population and of populations used in epidemiological studies of HPV.
“Among the 6,388 penile and cervical DNA samples collected in the POP-Brazil study, 1,745 were randomly selected for this investigation.”
The paper relies on this without support.
A good kappa agreement (κ = 0.78) between Anyplex II HPV28 and Linear Array is sufficient for Anyplex II HPV28 to be considered an effective tool for HPV screening in epidemiological studies.
“The study supports the utility of Anyplex™ II HPV28 as an effective tool for HPV screening in epidemiological studies, emphasizing its robust performance in comparison to established diagnostic tests.”
The paper relies on this without support.
LA is the gold standard methodology for HPV genotyping.
“LA, the gold standard methodology for HPV genotyping, has been widely used in clinical diagnosis and epidemiological research.”
The paper relies on this without support.
LA has been discontinued.
“However, since LA has been discontinued, the assessment of genotype prevalence over time presents a new challenge, while maintaining the necessary confidence to compare populations across different time periods.”
The paper relies on this without support.
The HPV52 probe of the LA assay cross-reacts with HPV33, HPV35, and HPV58.
“The LA assay has a limitation in comparison with Anyplex™ II HPV28, which is the cross-reactivity of the HPV52 probe with HPV33, 35, and 58.”
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.
High-risk specificity does not match Table 2
MajorUsing Linear Array as the reference, Table 2 yields high-risk specificity of 350/(350 + 44) = 88.8%, rather than 76%.
“Specificity was 82% (95% CI, 75%–87%) for overall HPV and 76% (95% CI, 72%– 80%) for HR-HPV.”
“| HR-HPV | Positive | 1207 (70.63%) | 44 (2.57%) | | HR-HPV | Negative | 108 (6.32%) | 350 (20.48%) |”
High-risk Anyplex positive count differs between tables
MajorTable 2 gives 1,207 + 44 = 1,251 high-risk Anyplex-positive samples, whereas Table 3 reports 1,315.
“| HR-HPV | 1,280 [72.93 (70.85–75.01)] | 1,315 [76.91 (74.90–78.90)] | 76 (73–80) | 96 (95–97) | 76 (72–80) |”
“| HR-HPV | Positive | 1207 (70.63%) | 44 (2.57%) |”
High-risk Linear Array positive count differs between tables
MajorTable 2 gives 1,207 + 108 = 1,315 high-risk Linear Array-positive samples, whereas Table 3 reports 1,280.
“| HR-HPV | 1,280 [72.93 (70.85–75.01)] | 1,315 [76.91 (74.90–78.90)] | 76 (73–80) | 96 (95–97) | 76 (72–80) |”
“| HR-HPV | Positive | 1207 (70.63%) | 44 (2.57%) | | HR-HPV | Negative | 108 (6.32%) | 350 (20.48%) |”
Overall Linear Array positive count differs between tables
MajorTable 2 gives 1,497 + 31 = 1,528 Linear Array-positive samples, whereas Table 3 reports 1,577.
“| Overall HPV | 1,577 [89.86 (88.44–91.27)] | 1,529 [89.41 (87.96–0.87)] | 78 (72–83) | 97 (96–98) | 82 (75–87) |”
“| Overall HPV | Positive | 1497 (87.60%) | 40 (2.34) | | Overall HPV | Negative | 31 (1.81%) | 141 (8.25%) |”
Overall specificity does not match Table 2
MajorUsing Linear Array as the reference, Table 2 yields overall specificity of 141/(141 + 40) = 77.9%, rather than 82%.
“Specificity was 82% (95% CI, 75%–87%) for overall HPV and 76% (95% CI, 72%– 80%) for HR-HPV.”
“| Overall HPV | Positive | 1497 (87.60%) | 40 (2.34) | | Overall HPV | Negative | 31 (1.81%) | 141 (8.25%) |”
HPV6 genotype totals disagree between tables
MajorTable 4 gives 90 Linear Array-positive and 217 Anyplex-positive HPV6 samples. Table 3 instead gives 225 and 90, respectively.
“| HPV6 | Positive | 55 (3.24%) | 162 (9.56%) | | HPV6 | Negative | 35 (2.06%) | 1443 (85.13%) |”
“| 6 | 225 [12.8 (11.2–14.4)] | 90 [5.3 (4.2–6.4)] | 31 (24–38) | 25 (20–32) | 98 (97–98) |”
Overall Anyplex positive count differs between tables
MajorTable 2 gives 1,497 + 40 = 1,537 Anyplex-positive samples, whereas Table 3 reports 1,529.
“| Overall HPV | 1,577 [89.86 (88.44–91.27)] | 1,529 [89.41 (87.96–0.87)] | 78 (72–83) | 97 (96–98) | 82 (75–87) |”
“| Overall HPV | Positive | 1497 (87.60%) | 40 (2.34) |”
High-risk sensitivity does not match Table 2
MinorUsing Linear Array as the reference, Table 2 yields high-risk sensitivity of 1,207/(1,207 + 108) = 91.8%, rather than the reported 96%.
“The overall sensitivity and high-risk HPV sensitivity for Anyplex™ II HPV28, using Linear Array as the gold standard, exhibited similar values of 97% (95% CI, 96%–98%) and 96% (95% CI, 95%–97%), respectively.”
“| HR-HPV | Positive | 1207 (70.63%) | 44 (2.57%) | | HR-HPV | Negative | 108 (6.32%) | 350 (20.48%) |”
Overall sensitivity does not match Table 2
MinorUsing Linear Array as the reference, Table 2 yields sensitivity of 1,497/(1,497 + 31) = 98.0%, rather than the reported 97%.
“The overall sensitivity and high-risk HPV sensitivity for Anyplex™ II HPV28, using Linear Array as the gold standard, exhibited similar values of 97% (95% CI, 96%–98%) and 96% (95% CI, 95%–97%), respectively.”
“| Overall HPV | Positive | 1497 (87.60%) | 40 (2.34) | | Overall HPV | Negative | 31 (1.81%) | 141 (8.25%) |”
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“HPV is also accountable for a substantial proportion of cancers and precancerous lesions, not only in the head and neck but also in the genital regions, including penile, vulvar and anal cancers [5, 6].”
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“Samples from men were self-collected from the entire surface of the scrotum, glans penis/coronal sulcus, and penile shaft using a saline-wetted Dacron swab [25, 26].”
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“Both proficiency panels are composed of a series of validated and traceable samples of international standards in terms of generating acceptable results [23].”
BackgroundGlobal Proficiency Study of Human Papillomavirus Genotyping
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“Simultaneously, the WHO global reference laboratory offers, each year, the “Global HPV DNA Proficiency Study” to certify laboratories as proficient in the genotyping of the main HPV types [22].”
MethodHartwig, S., Baldauf, J., Dominiak-Felden, G., Simondon, F., Alemany, L., de Sanjosé, S., & Castellsagué, X. (2015) · Papillomavirus Research · doi:10.1016/j.pvr.2015.06.003 · Cited by 94 · see citing works
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“In epidemiology, HPV assays are mainly used to determine the prevalence of HPV types distributed in the study population [9, 10].”
MethodWendland, E. M., Villa, L. L., Unger, E. R., Domingues, C. M., Benzaken, A. S., POP-Brazil Study Group, Maranhão, A. G. K., Kops, N. L., Bessel, M., Caierão, J., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-61582-2 · Cited by 72 · cited 2× · see citing works
“…2016 and November 2017 by the POP Brazil study, a nationwide, cross-sectional study designed to estimate the prevalence of type-specific HPV in young adults aged between 16 and 25, from both sexes and to serve as a base-line to assess the impact of the Brazilian national vaccination program [24].”
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“However, it is worth mentioning that this does not significantly impact the sensitivity of the assays [34, 35].”
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Evaluation of HPV Genotyping Assays for Archival Clinical Samples
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Assessment of the Roche Linear Array HPV Genotyping Test within the VALGENT framework
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“This assay is capable of detecting 37 genotypes and consists of a PCR followed by in situ hybridization and subsequent reading on a nylon strip coated with HPV type-specific and human beta-globin-specific oligo-nucleotide probes [15].”
MethodHow Many Human Papillomavirus Types Do We Need to Screen For?
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Human papillomavirus genotype-specific risks for cervical intraepithelial lesions
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“Moreover, the consideration of screening for all 14 HPV types could potentially lead to a suboptimal balance between the associated harms and benefits [31, 33].”
BackgroundEvaluation of the Clinical Performance of the HPV-Risk Assay Using the VALGENT-3 Panel
Polman, N. J., Oštrbenk, A., Xu, L., Snijders, P. J. F., Meijer, C. J. L. M., Poljak, M., Heideman, D. A. M., & Arbyn, M. (2017) · Journal of Clinical Microbiology · doi:10.1128/jcm.01282-17 · Cited by 33 · cited 1× · see citing works
“This protocol accounts with an established panel of cervical samples with abnormalities in cytology analyzed by different laboratories and methods to generate accuracy and concordance statistics [20, 21].”
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“However, the LA was discontinued in December 2019, which made it necessary to evaluate new available methodologies [16, 17].”
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Validation of EUROArray HPV test using the VALGENT framework
Viti, J., Poljak, M., Oštrbenk, A., Bhatia, R., Boada, E. A., Cornall, A. M., Cuschieri, K. S., Garland, S. M., Xu, L., & Arbyn, M. (2018) · Journal of Clinical Virology · doi:10.1016/j.jcv.2018.09.005 · Cited by 23 · see citing works
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“Additionally, the authors reported that Anyplex ™ II demonstrated similar sensitivity to LA for most high-risk genotypes, with slightly lower sensitivity observed for HPV51 or 52 [14, 32].”
Cornall, A. M., Poljak, M., Garland, S. M., Phillips, S., Machalek, D. A., Tan, J. H., Quinn, M. A., & Tabrizi, S. N. (2017) · Papillomavirus Research · doi:10.1016/j.pvr.2017.10.002 · Cited by 22 · cited 2× · see citing works
“Additionally, the authors reported that Anyplex ™ II demonstrated similar sensitivity to LA for most high-risk genotypes, with slightly lower sensitivity observed for HPV51 or 52 [14, 32].”
MethodXu, L., Oštrbenk, A., Poljak, M., & Arbyn, M. (2020) · Journal of Clinical Microbiology · doi:10.1128/jcm.00234-20 · Cited by 16 · cited 1× · see citing works
“Nowadays, more than 250 assays are available to detect and/or genotype HPV [11].”
BackgroundMarcuccilli, F., Farchi, F., Mirandola, W., Ciccozzi, M., Paba, P., Bonanno, E., Perno, C. F., & Ciotti, M. (2015) · Journal of Virological Methods · doi:10.1016/j.jviromet.2015.02.018 · Cited by 15 · cited 2× · see citing works
“HPV genotype testing represents an important tool for studying the carcinogenic potential of HPV types and is used widely to screen for and follow-up persistent infections that could lead to cervical cancer [7, 8].”
BackgroundMethodSarıer, M., Sepin, N., Emek, M., et al. (2023) · Journal of Infection and Chemotherapy · doi:10.1016/j.jiac.2023.01.017 · Cited by 14 · cited 1× · see citing works
“Samples from men were self-collected from the entire surface of the scrotum, glans penis/coronal sulcus, and penile shaft using a saline-wetted Dacron swab [25, 26].”
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Bhatia, R., Boada, E. A., Bonde, J. H., Quint, W. G. V., Christiansen, I. K., Xu, L., Ejegod, D. M., Moncur, S., Cuschieri, K. S., & Arbyn, M. (2021) · Journal of Virological Methods · doi:10.1016/j.jviromet.2021.114161 · Cited by 5 · cited 1× · see citing works
“Over the years, several new diagnostic methodologies that seek greater efficiency have been implemented and have gained prominence in the market, which currently has more than 250 commercial tests for HPV diagnosis that vary in methodologies, genotype coverage, feasibility, and costs [12, 18].”
Background
Flagged first, then by citations
Cited by
Sorted by citations
Godoy, L. R., El-Zein, M., Padalko, E. Y., Verberckmoes, B., Eenooghe, B. V., Vermandere, H., Dias, S., Gama, A., Vega, B., Neira, V. A., et al. (2025) · Journal of Clinical Microbiology · doi:10.1128/jcm.00200-25 · Cited by 5 · see citing works
“Although Anyplex is commonly described as targeting the L1 region (21, 22), recent evidence from a similar test developed by the same company (Allplex HPV28) suggests that amplification may also involve sequences from the E6/E7 regions (23).”
Performance Analysis of Human Papillomavirus Viruses Genotype Detection Kit Using ZIP Nucleic Acid
Kim, J.-H., So, S. M., Park, K., et al. (2025) · Journal of Experimental & Biomedical Sciences/Biomedical Science Letters · doi:10.15616/bsl.2025.31.2.187
Curici, A., Tsaneva, D., Nedelcheva, G., et al. (2026) · Microorganisms · doi:10.3390/microorganisms14081794
“Numerous studies have reported substantial concordance between these assays in detecting HPV positivity and specific genotypes, as evidenced by Cohen’s kappa statistics indicating good to excellent agreement (e.g., κ values generally >0.6) [44].”
Influential
- Authors
- Bandeira, I. C., Comerlato, J., Bessel, M., Fernandes, B. V., Mota, G., Villa, L. L., de Souza, F. M. A., Pereira, G. F. M., & Wendland, E. M.
- Affiliations
- Hospital Moinhos de Vento (BR)
- Instituto do Câncer do Estado de São Paulo (BR)
- Universidade Federal de Ciências da Saúde de Porto Alegre (BR)
- Corresponding author
- Wendland, Eliana Marcia
- ORCID
- Venue
- PLOS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2024-06-11
- Volume
- 19
- Issue
- 6
- Pages
- e0305122
- ISSN
- 1932-6203 (ISSN-L)
- PMC
- PMC11166333
- OpenAlex
- W4399527665
- Semantic Scholar
- d3dbdcbf170bd11369e6604bbbacfd6f523d1701
- Cited by
- 3
- References
- 35
- Citations by year
- 2026: 1 · 2025: 2
- FWCI
- 0.78
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS ONE (publishedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (submittedVersion, cc-by)
- Funders
- Program for Supporting the Institutional Development of the Public Health System
- Topics
- Health Sciences › Medicine › Epidemiology › Cervical Cancer and HPV Research
- Life Sciences › Immunology and Microbiology › Microbiology › Reproductive tract infections research
- Health Sciences › Medicine › Surgery › Genital Health and Disease
- Keywords
- human papillomavirus, HPV genotyping, assay concordance, HPV testing, cervical HPV, diagnostic test validation
- MeSH terms
- Adult, Brazil, DNA, Viral, Female, Genotype, Humans, Male, Middle Aged, Sensitivity and Specificity, Papillomaviridae, Papillomavirus Infections, Alphapapillomavirus, Genotyping Techniques
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