Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example.
Arboviruses
Nanopore
Sequencing
USUV
Journal
Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases
ISSN: 1567-7257
Titre abrégé: Infect Genet Evol
Pays: Netherlands
ID NLM: 101084138
Informations de publication
Date de publication:
09 2019
09 2019
Historique:
received:
17
03
2019
revised:
17
04
2019
accepted:
18
04
2019
pubmed:
25
4
2019
medline:
27
3
2020
entrez:
25
4
2019
Statut:
ppublish
Résumé
Recently, protocols for amplicon based whole genome sequencing using Nanopore technology have been described for Ebola virus, Zika virus, yellow fever virus and West Nile virus. However, there is some debate regarding reliability of sequencing using this technology, which is important for applications beyond diagnosis such as linking lineages to outbreaks, tracking transmission pathways and pockets of circulation, or mapping specific markers. To our knowledge, no in depth analyses of the required read coverage to compensate for the error profile in Nanopore sequencing have been described. Here, we describe the validation of a protocol for whole genome sequencing of USUV using Nanopore sequencing by direct comparison to Illumina sequencing. To that point we selected brain tissue samples with high viral loads, typical for birds which died from USUV infection. We conclude that the low-cost MinION Nanopore sequencing platform can be used for characterization and tracking of Usutu virus outbreaks.
Identifiants
pubmed: 31014969
pii: S1567-1348(19)30056-5
doi: 10.1016/j.meegid.2019.04.015
pii:
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
49-54Informations de copyright
Copyright © 2019. Published by Elsevier B.V.