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

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

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Evaluation Study

MeSH terms

  • DNA, Viral / genetics
  • Early Detection of Cancer / methods
  • Female
  • Genotype*
  • Genotyping Techniques* / methods
  • High-Throughput Nucleotide Sequencing / methods
  • Humans
  • Oncogene Proteins, Viral / genetics
  • Papillomaviridae* / classification
  • Papillomaviridae* / genetics
  • Papillomaviridae* / isolation & purification
  • Papillomavirus Infections* / diagnosis
  • Papillomavirus Infections* / virology
  • Sensitivity and Specificity
  • Sequence Analysis, DNA / methods
  • Uterine Cervical Neoplasms / diagnosis
  • Uterine Cervical Neoplasms / virology

Substances

  • Oncogene Proteins, Viral
  • DNA, Viral