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Updated: Nov 12, 2025

RNAscope for In situ Detection of Transcriptionally Active Human Papillomavirus in Head and Neck Squamous Cell Carcinoma

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Published on: March 11, 2014

Misclassifications in human papillomavirus databases.

Laila Sara Arroyo Mühr¹, Carina Eklund¹, Joakim Dillner²

¹International HPV Reference Center, Department of Laboratory Medicine, Karolinska Institutet, SE-141 86 Stockholm, Sweden.

|March 17, 2021

Summary

This study evaluated human papillomavirus (HPV) sequence quality in GenBank, finding numerous taxonomy errors and chimeric sequences. Improving data quality is crucial for advancing HPV research.

Keywords:

Chimera HPVChimera Human papillomavirus International HPV Reference center

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Area of Science:

Virology
Bioinformatics
Genomics

Background:

GenBank is a critical repository for genetic sequences, including those of human papillomavirus (HPV).
Ensuring the accuracy of HPV sequence data is vital for research into viral evolution, pathogenesis, and vaccine development.
Previous assessments of large sequence databases have identified data quality issues, necessitating specific evaluations for important viral families like HPV.

Purpose of the Study:

To assess the quality of human papillomavirus (HPV) nucleotide sequences deposited in GenBank.
To identify and quantify instances of chimeric sequences, misassembled contigs, and taxonomic errors within the HPV sequence data.
To evaluate the potential impact of these data quality issues on the broader field of HPV research.

Main Methods:

Utilized an open-source script, HPVChimera_Gb, to analyze 25,638 HPV-related nucleotide sequences in GenBank.
Compared analyzed sequences against a curated set of 221 numbered HPV types and 220 complete HPV sequences.
Performed manual verification of sequences flagged for potential errors, including chimeric sequences and taxonomy/naming discrepancies.

Main Results:

Identified 110 sequences with taxonomy/naming errors and 1318 possibly chimeric sequences.
Manual analysis confirmed 114 sequences as chimeras and 13 with taxonomy/naming errors, with many previously flagged as 'unverified' by GenBank.
The analysis suggests the existence of approximately 800 unique putative HPV types when comparing correct sequences.

Conclusions:

The GenBank repository contains a significant number of human papillomavirus (HPV) sequences with quality issues, including chimeric sequences and taxonomic errors.
Systematic efforts to identify and rectify these errors are essential for improving the reliability and orderliness of HPV research.
Enhancing data quality in GenBank will facilitate more accurate studies on HPV diversity, epidemiology, and control strategies.