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. 2022 Mar 21;17(1):9.
doi: 10.1186/s13027-022-00420-8.

A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

Zhihai Ma  1 , Baback Gharizadeh  1 , Xingsheng Cai  2 , Mengzhen Li  2 , María Dolores Fellner  3 , Jorge Alejandro Basiletti  3 , Rita Mariel Correa  3 , María Celeste Colucci  3 , Gabriela Baldoni  4 , Martín Vacchino  4 , Patricia Galarza  4 , María Alejandra Picconi  3 , Chunlin Wang  5
Affiliations

A comprehensive HPV-STI NGS assay for detection of 29 HPV types and 14 non-HPV sexually transmitted infections

Zhihai Ma et al. Infect Agent Cancer. .

Abstract

Background: Sexually transmitted infections (STIs) are prevalent throughout the world and impose a significant burden on individual health and public health systems. Missed diagnosis and late treatment of STIs can lead to serious complications such as infertility and cervical cancer. Although sexually transmitted co-infections are common, most commercial assays target one or a few STIs. The HPV-STI ChapterDx Next Generation Sequencing (NGS) assay detects and quantifies 29 HPVs and 14 other STIs in a single-tube and single-step PCR reaction and can be applied to tens to thousands of samples in a single sequencing run.

Methods: A cohort of 274 samples, previously analyzed by conventional cytology/histology and Roche cobas HPV Test, were analyzed by ChapterDx HPV-STI NGS assay for detection of 43 HPV and STI. A set of 43 synthetic control DNA fragments for 43 HPV and STI were developed to evaluate the limit of detection, specificity, and sensitivity of ChapterDx HPV-STI NGS assay.

Results: The assay was evaluated in this study, and the limit of detection was 100% at 50 copies for all targets, and 100%, 96%, 88% at 20 copies for 34, 8, and 1 target, respectively. The performance of this assay has been compared to Roche cobas HPV test, showing an overall agreement of 97.5% for hr-HPV, and 98.5% for both, HPV16 and HPV18. The assay also detected all HPV-infected CIN2/3 with 100% agreement with Roche cobas HPV results. Moreover, several co-infections with non-HPV STIs, such as C. trachomatis, T. vaginalis, M. genitalium, and HSV2 were identified.

Conclusions: The ChapterDx HPV-STI NGS assay is a user-friendly, easy to automate and cost-efficient assay, which provides accurate and comprehensive results for a wide spectrum of HPVs and STIs.

Keywords: Cervical cancer; Chlamydia trachomatis; HPV genotyping; Human papillomavirus (HPV); Neisseria gonorrhoeae; Next generation sequencing (NGS); Sexually transmitted disease (STD); Sexually transmitted infections (STI); Treponema pallidum; Trichomonas vaginalis.

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Conflict of interest statement

ZM, BG, and CW are shareholders and employees of Chapter Diagnostics. A patent has been issued for the technology. The INEI-ANLIS Malbrán investigators declare no competing interests; they did not receive any financial contribution from Chapter Diagnostics.

Figures

Fig. 1
Fig. 1
A schematic illustration of ChapterDx HPV-STI NGS workflow
See this image and copyright information in PMC

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