Misclassifications in human papillomavirus databases

Laila Sara Arroyo Mühr; Carina Eklund; Joakim Dillner

doi:10.1016/j.virol.2021.03.002

Misclassifications in human papillomavirus databases

Virology. 2021 Jun:558:57-66. doi: 10.1016/j.virol.2021.03.002. Epub 2021 Mar 11.

Authors

Laila Sara Arroyo Mühr¹, Carina Eklund², Joakim Dillner³

Affiliations

¹ International HPV Reference Center, Department of Laboratory Medicine, Karolinska Institutet, SE-141 86 Stockholm, Sweden. Electronic address: Sara.arroyo.muhr@ki.se.
² International HPV Reference Center, Department of Laboratory Medicine, Karolinska Institutet, SE-141 86 Stockholm, Sweden.
³ International HPV Reference Center, Department of Laboratory Medicine, Karolinska Institutet, SE-141 86 Stockholm, Sweden; International HPV Reference Center, Karolinska University Laboratory, Karolinska University Hospital, SE-141 86 Stockholm, Sweden.

PMID: 33730650
DOI: 10.1016/j.virol.2021.03.002

Abstract

We assessed the quality of human papillomavirus (HPV) sequences in GenBank by analyzing the possible presence of chimeras, "wrong-assembled" contigs and errors in taxonomy using an open-source script (HPVChimera_Gb) that compared 25 638 HPV-related nucleotide sequences in GenBank with the 221 numbered HPV types and another 220 complete HPV sequences. There were 110 sequences with taxonomy/naming errors (sequences reported as another HPV type than the one they corresponded to) and 1318 possibly chimeric sequences. Manual analysis found plausible explanations for most of them (e.g. sequence covering an integration site) but 114 sequences appeared to be chimeras (96/114 were already flagged as "unverified" by GenBank) and 13 had taxonomy/naming errors. When comparing all correct HPV sequences in GenBank, there appeared to exist about 800 unique putative HPV types. Systematic and regular work towards eliminating chimeric sequences and taxonomy/naming errors could increase the quality and order in HPV research.

Keywords: Chimera; HPVChimera; Human papillomavirus; International HPV Reference center.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Amino Acid Sequence
Base Sequence
Classification
Databases, Nucleic Acid*
Humans
Papillomaviridae / classification*
Papillomaviridae / genetics*