Rapid HPV genotype detection

16 April 2025

A team led by the late Prof Piotr Bała, as part of the HEAP – Human Exposome Assessment Platform project funded by Horizon 2020, has developed a novel tool for rapid HPV viral sequence detection.

The paper entitled “HPV-KITE: sequence analysis software for rapid HPV genotype detection”, whose first author is Dr Marek Nowicki from ICM UW, has just been published in the prestigious journal Briefings in Bioinformatics.

Detecting HPV gene sequences is a major challenge due to the large number of closely related HPV genotypes, the presence of significant amounts of non-viral DNA in samples and the high variability and rapid mutation of viruses.

Dr Nowicki and co-authors have developed HPV-KITE, a tool that enables the detection of HPV genotypes from virtually any next-generation sequencing data. The method is based on k-mer analysis and uses the Tversky index, which allows for high scalability.

  • HPV-KITE was evaluated on three previously analyzed HPV data sets, comprising a total of 1430 samples.
  • The tool outperformed standard sequence mapping and k-mer classification methods in terms of speed and scalability, with comparable detection accuracy.
  • Very fast processing times were achieved through shingling and parallelization.
  • The analysis demonstrated optimal performance when running on multiple nodes.
  • HPV-KITE is a fast, accurate, and scalable DNA/RNA classification tool that can be successfully adapted to detect a variety of viruses and microorganisms, not only HPV.

Publication link

HPV-KITE: sequence analysis software for rapid HPV genotype detection
Briefings in Bioinformatics, Volume 26, Issue 2, March 2025, bbaf155,

https://doi.org/10.1093/bib/bbaf155

The Human Exposome Assessment Platform project was co-financed by the European Union under the Horizon 2020 program (grant 874662) and by the Minister of Education and Science’s project called “Premia na Horyzoncie 2” (497700/PnH 2/2020).

Funding information: https://icm.edu.pl/heap-human-exposome-assessment-platform/

Project website: https://heap-exposome.eu/