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. 2024 May;96(5):e29652.
doi: 10.1002/jmv.29652.

HPV genotyping in clinical samples using long-read single-molecule real-time sequencing

Christophe Pasquier  1 , Stéphanie Raymond  1 , Romain Carcenac  1 , Sofia Demmou  1 , Noémie Ranger  1 , Florence Nicot  1 , Jacques Izopet  1
Affiliations

HPV genotyping in clinical samples using long-read single-molecule real-time sequencing

Christophe Pasquier et al. J Med Virol. 2024 May.

Abstract

Human papillomavirus (HPV) genotyping is widely used, particularly in combination with high-risk (HR) HPV tests for cervical cancer screening. We developed a genotyping method using sequences of approximately 800 bp in the E6/E7 region obtained by PacBio single molecule real-time sequencing (SMRT) and evaluated its performance against MY09-11 L1 sequencing and after the APTIMA HPV genotyping assay. The levels of concordance of PacBio E6/E7 SMRT sequencing with MY09-11 L1 sequencing and APTIMA HPV genotyping were 100% and 90.8%, respectively. The sensitivity of PacBio E6/EA7 SMRT was slightly greater than that of L1 sequencing and, as expected, lower than that of HR-HPV tests. In the context of cervical cancer screening, PacBio E6/E7 SMRT is then best used after a positive HPV test. PacBio E6/E7 SMRT genotyping is an attractive alternative for HR and LR-HPV genotyping of clinical samples. PacBio SMRT sequencing provides unbiased genotyping and can detect multiple HPV infections and haplotypes within a genotype.

Keywords: HPV; SMRT sequencing; genotyping; papillomavirus.

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References

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