Development of the TypeSeq Assay for Detection of 51 Human Papillomavirus Genotypes by Next-Generation Sequencing

Journal of Clinical Microbiology
Sarah WagnerNicolas Wentzensen

Abstract

We have developed a new human papillomavirus (HPV) genotyping assay for detection of 51 HPV genotypes by next-generation sequencing (NGS). The TypeSeq assay consists of 3 PCR steps that equalize viral load and each type's amplicon copies prior to genotyping by NGS, thereby maximizing multiple-type sensitivity with minimal sequencing reads. The analytical sensitivity of the TypeSeq assay is 10 copies per reaction for 49 of the 51 types, including 13 high-risk (HR) types. We tested 863 clinical cervical specimens previously evaluated with the Roche Linear Array HPV genotyping test (LA). TypeSeq achieved 94.4% positive agreement with LA for detection of any HR type. Positive agreement was 91.4% and 85.5% for HPV16 and HPV18, respectively. Low-risk (LR) types ranged from 40.0% positive agreement (HPV83) to 90.9% (HPV69). Our unique approach to HPV amplification achieved a multiple-type sensitivity comparable to that of LA, with 83.9% and 84.2% of specimens positive for multiple HPV types by TypeSeq or LA, respectively. A total of 48.2% of specimens showed perfect agreement for all 37 types common to both assays. The simplicity of our open-source TypeSeq assay allows for high-throughput yet scalable processing, with a single technic...Continue Reading

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Citations

Feb 25, 2020·Journal of the National Cancer Institute·Sabrina H TsangUNKNOWN Costa Rica HPV Vaccine Trial (CVT) Group
Feb 25, 2020·Journal of the National Cancer Institute·Aimée R KreimerUNKNOWN Costa Rica HPV Vaccine Trial (CVT) Group
Aug 8, 2020·The Tohoku Journal of Experimental Medicine·Iwao KukimotoUNKNOWN MINT Study II Group
May 8, 2020·Diagnostic Pathology·Wai Sing ChanBone Siu Fai Tang
Sep 2, 2020·Scientific Reports·Matthew J InkmanJin Zhang
Nov 27, 2020·BMC Infectious Diseases·Andrea Molina-PinedaAdriana Aguilar-Lemarroy
Dec 17, 2020·The Journal of Infectious Diseases·Mónica S SierraUNKNOWN Costa Rica Human Papillomavirus Vaccine Trial (CVT) Group
Jan 31, 2021·Viruses·Mangalathu S RajeevanElizabeth R Unger

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