Negative Xpert HPV Test (Cepheid) With Late Amplification Signals - Is There a Clinical Significance? - (the PaPCR Study)

Sep 22, 2026

Cervical cancer is the fourth most common cancer among women worldwide, and limited access to screening and vaccination increases prevalence in low-resource settings. Xpert HPV (Cepheid) NAATs rapidly detect high-risk HPV genotypes, yet weak and late amplification signals (cycle threshold ≥ 38) are reported negative and their clinical meaning is unclear. Comparing such cases with cytology in 6846 samples, retesting using in-house PCR/ LiPA and cytological assessment evaluated clinical risk. Overall follow-up supported that review of history and cytology triage can prevent missing at-risk patients.

LanguageEnglish

CategoryHealthcare

FormatPDF

Pages10

Reading Time25 min

AccessFree to download

Introduction

Screening and HPV persistence

Abstract

Study objective

Methods

Results

Conclusions

Journal of Medical Virology RESEARCH ARTICLE Negative Xpert HPV Test (Cepheid) With Late Amplification Signals: Is There a Clinical Significance?(the PaPCR Study) Valentin Lemoine1,2 | Romain Legros1,3 | Sylvain Rosec4 | Camille Salaun1 | Adissa Tran‐Minoui1 | Léa Pilorgé1 | Sophie Vallet1,3 | Anne Le Gourrierec5 | Pierre Alemany6 | Pascale Marcorelles6 | Christopher Payan1,3 1Department of Infectious Agents, Laboratory of Virology, Brest University Hospital, Brest, Bretagne, France | 2Present address: Laboratory of Bacteriology and Hospital Hygiene, University Hospital of Rennes, Rennes, France | 3Génétique, Génomique fonctionnelle et Biotechnologies (UMR 1078), Inserm, Université de Bretagne Occidentale, Brest, Bretagne, France | 4Clinical Investigation Center (CIC 1412), Brest University Hospital, Brest, Bretagne, France | 5Gynecology unit, Brest University Hospital, Brest, Bretagne, France | 6Laboratory of Pathology and Cytology, Brest University Hospital, Brest, Bretagne, France Correspondence: Valentin Lemoine ([valentin.lemoine@chu-rennes.fr](valentin.lemoine@chu-rennes.fr)) Received: 30 January 2026 | Revised: 22 March 2026 | Accepted: 30 March 2026 Keywords: cancer | genotyping | HPV | human papillomavirus | PCR | sexually transmitted infections ABSTRACT Cervical cancer is the fourth most common cancer among women worldwide, with higher prevalence in low‐resource countries due to limited access to screening and HPV vaccination. Nucleic acid amplification tests (NAATs) such as Xpert HPV (Cepheid), enable rapid detection of high‐risk HPV (HR‐HPV) genotypes. However, the clinical significance of weak and late amplification signals (cycle threshold ≥ 38), interpreted as negative, remains unclear. In this study, a comparison with cytological results aimed to assess their significance. Out of 6846 cervical samples analyzed at Brest University Hospital (Jan. 2022–June 2024), 45 showed late amplification and were reported negative by Xpert. These samples were retested using an in‐house HPV pangenotypic PCR followed by genotyping (LiPA) and were assessed by cytology. Of the 44 available cytology results, 65.9% were normal, 15.9% showed low‐grade squamous intraepithelial lesions (LSIL), and 18.2% were atypical squamous cells of undetermined significance (ASC‐US) . No high‐grade squamous intraepithelial lesions (HSIL) were found at initial cytology. Among the 42 samples available for in‐house PCR, 59.5% tested positive for HPV, and 11.9% were confirmed as HR‐HPV genotypes (types 52, 56, 35). Additionally, among patients with available HPV history, 73.3% had a previous positive test. In 91% of these cases, the genotype suspected during the late amplification was concordant with the previous infection. During the 1‐year follow‐up, one patient initially classified as LSIL developed a histologically confirmed HSIL (CIN2) and needed treatment by conization, whereas 3 others were found to have low‐grade CIN1 cell lesions. Overall, for 15 out of 45 patients with weak HPV PCR signal and abnormal cytology (33.3%), clinicians chose to recommend a closer 1‐year follow‐up and not at 5 years as recommended for HPV negative patients. In conclusion, cytological triage and a review of patient history remain crucial to avoid missing at‐risk patients, especially in settings where HPV‐negative women are re‐screened only 5 years later. A multicenter study using Xpert HPV and other automated platforms is recommended to strengthen these findings and further explore potential correlations between viral load and clinical severity. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. © 2026 The Author(s) . Journal of Medical Virology published by Wiley Periodicals LLC. Journal of Medical Virology, 2026; 98:e70915 1 of 10 [https://doi.org/10.1002/jmv.70915](https://doi.org/10

FAQs

What does a late amplification signal mean in Xpert HPV testing?

Late amplification signals with cycle threshold values ≥ 38 are interpreted as negative by Xpert HPV. Their clinical significance remains uncertain without further review and retesting.

How were Xpert-negative late amplification cases evaluated in the study?

Late amplification cases were retested using an in-house HPV pangenotypic PCR followed by genotyping (LiPA), and the results were assessed alongside cytology.

What follow-up findings suggested clinical risk despite an initial negative result?

During a 1-year follow-up, one patient initially classified as LSIL developed histologically confirmed HSIL (CIN2), and three others were found to have low-grade CIN1 lesions, supporting closer monitoring in selected cases.

Sep 22, 2026

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