Comparison of whole-viral genome sequencing and PCR-based assay for anal HPV detection to inform clinical implementation

IF 1.7 4区医学 Q3 BIOCHEMICAL RESEARCH METHODS

Journal of virological methods Pub Date : 2026-06-01 Epub Date: 2026-02-13 DOI:10.1016/j.jviromet.2026.115366

Omar Harfouch , Derek MacMath , Poorani Subramanian , Rahwa Eyasu , Habib O. Ramadhani , Peiying Ye , Ashley Davis , Meredith Zoltick , Emade Ebah , Amay Shah , Amelia Cover , Phyllis Bijole , Rachel Silk , David Sternberg , Tina Liu , Grace Garrett , Miriam Jones , Randy Kier , Henry Masur , Shyamasundaran Kottilil , Andrea Lisco

{"title":"Comparison of whole-viral genome sequencing and PCR-based assay for anal HPV detection to inform clinical implementation","authors":"Omar Harfouch , Derek MacMath , Poorani Subramanian , Rahwa Eyasu , Habib O. Ramadhani , Peiying Ye , Ashley Davis , Meredith Zoltick , Emade Ebah , Amay Shah , Amelia Cover , Phyllis Bijole , Rachel Silk , David Sternberg , Tina Liu , Grace Garrett , Miriam Jones , Randy Kier , Henry Masur , Shyamasundaran Kottilil , Andrea Lisco","doi":"10.1016/j.jviromet.2026.115366","DOIUrl":null,"url":null,"abstract":"<div><div>To optimize anal cancer screening strategies, we compared two molecular platforms for anal high-risk Human Papillomavirus (HR-HPV) detection: whole-viral genome sequencing (WGS) and Cobas HPV-test-PCR (RC). Anal swabs from participants at high-risk for HPV acquisition were evaluated for cytological abnormalities and HR-HPV prevalence. Compared to WGS, RC had 51 % sensitivity and 98 % specificity for HPV16, 29 % and 92 % for HPV18, and 74 % and 93 % for non-16/18 HR-HPV. In a population with high prevalence of anal HR-HPV, RC had lower sensitivity in the detection of anal HR-HPV but was more robustly associated with abnormal anal cytology compared to WGS. In addition, WGS-based identification of HPV16 sub-lineages demonstrated that the composite A1, A2, A4, and C1 sub-lineages were associated with a higher risk of abnormal cytology compared to other HPV16 sub-lineages. WGS can further delineate the natural history of anal HR-HPV and their sub-lineages in populations at high-risk for HPV acquisition.</div></div>","PeriodicalId":17663,"journal":{"name":"Journal of virological methods","volume":"343 ","pages":"Article 115366"},"PeriodicalIF":1.7000,"publicationDate":"2026-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of virological methods","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0166093426000303","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2026/2/13 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}

引用次数: 0

Abstract

To optimize anal cancer screening strategies, we compared two molecular platforms for anal high-risk Human Papillomavirus (HR-HPV) detection: whole-viral genome sequencing (WGS) and Cobas HPV-test-PCR (RC). Anal swabs from participants at high-risk for HPV acquisition were evaluated for cytological abnormalities and HR-HPV prevalence. Compared to WGS, RC had 51 % sensitivity and 98 % specificity for HPV16, 29 % and 92 % for HPV18, and 74 % and 93 % for non-16/18 HR-HPV. In a population with high prevalence of anal HR-HPV, RC had lower sensitivity in the detection of anal HR-HPV but was more robustly associated with abnormal anal cytology compared to WGS. In addition, WGS-based identification of HPV16 sub-lineages demonstrated that the composite A1, A2, A4, and C1 sub-lineages were associated with a higher risk of abnormal cytology compared to other HPV16 sub-lineages. WGS can further delineate the natural history of anal HR-HPV and their sub-lineages in populations at high-risk for HPV acquisition.

查看原文本刊更多论文

全病毒基因组测序与pcr检测肛门HPV的比较，为临床实施提供依据。

为了优化肛门癌筛查策略，我们比较了肛门高危人乳头瘤病毒（HR-HPV）检测的两种分子平台：全病毒基因组测序（WGS）和Cobas hpv -测试- pcr （RC）。对HPV感染高风险参与者的肛门拭子进行细胞学异常和HR-HPV患病率评估。与WGS相比，RC对HPV16的敏感性为51%，特异性为98%，对HPV18的敏感性为29%，特异性为92%，对非16/18 HR-HPV的敏感性为74%，特异性为93%。在肛门HR-HPV患病率高的人群中，RC对肛门HR-HPV检测的敏感性较低，但与WGS相比，RC与肛门细胞学异常的相关性更强。此外，基于wgs的HPV16亚系鉴定表明，与其他HPV16亚系相比，复合的A1、A2、A4和C1亚系与更高的细胞学异常风险相关。WGS可以进一步描述肛门HR-HPV的自然历史及其在HPV感染高危人群中的亚系。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Journal of virological methods 医学-病毒学

CiteScore

5.80

自引率

0.00%

发文量

209

审稿时长

41 days

期刊介绍： The Journal of Virological Methods focuses on original, high quality research papers that describe novel and comprehensively tested methods which enhance human, animal, plant, bacterial or environmental virology and prions research and discovery. The methods may include, but not limited to, the study of: Viral components and morphology- Virus isolation, propagation and development of viral vectors- Viral pathogenesis, oncogenesis, vaccines and antivirals- Virus replication, host-pathogen interactions and responses- Virus transmission, prevention, control and treatment- Viral metagenomics and virome- Virus ecology, adaption and evolution- Applied virology such as nanotechnology- Viral diagnosis with novelty and comprehensive evaluation. We seek articles, systematic reviews, meta-analyses and laboratory protocols that include comprehensive technical details with statistical confirmations that provide validations against current best practice, international standards or quality assurance programs and which advance knowledge in virology leading to improved medical, veterinary or agricultural practices and management.