Misclassifications in human papillomavirus databases.

Amino Acid Sequence Base Sequence Classification Databases, Nucleic Acid Humans Papillomaviridae / classification
Chimera HPVChimera Human papillomavirus International HPV Reference center

Journal

Virology
ISSN: 1096-0341
Titre abrégé: Virology
Pays: United States
ID NLM: 0110674

Informations de publication

Date de publication:
06 2021
Historique:
received: 12 12 2020
revised: 23 02 2021
accepted: 04 03 2021
pubmed: 18 3 2021
medline: 29 12 2021
entrez: 17 3 2021
Statut: ppublish

Résumé

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.

Identifiants

DOI: 10.1016/j.virol.2021.03.002 PMID: 33730650
pubmed: 33730650
pii: S0042-6822(21)00060-X
doi: 10.1016/j.virol.2021.03.002
pii:
doi:

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

57-66

Informations de copyright

Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.

Auteurs

Laila Sara Arroyo Mühr (LS)

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

Carina Eklund (C)

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

Joakim Dillner (J)

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.

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Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence d'acides aminés › Misclassifications in human papillomavirus databases.
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Misclassifications in human papillomavirus databases.
questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Classification › Misclassifications in human papillomavirus databases.
questionsmedicales.fr › Sciences de l'information › Mémorisation et recherche des informations › Bases de données comme sujet › Bases de données factuelles › Bases de données génétiques › Bases de données d'acides nucléiques › Misclassifications in human papillomavirus databases.
questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Misclassifications in human papillomavirus databases.
questionsmedicales.fr › Virus › Virus oncogènes › Virus tumoraux à ADN › Papillomaviridae › Misclassifications in human papillomavirus databases.