Towards high quality real-time whole genome sequencing during outbreaks using Usutu virus as example.
Infect Genet Evol
; 73: 49-54, 2019 09.
Article
in En
| MEDLINE
| ID: mdl-31014969
ABSTRACT
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.
Key words
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Bird Diseases
/
Genome, Viral
/
Flavivirus Infections
/
Strigiformes
/
Genomics
/
Flavivirus
Type of study:
Guideline
Limits:
Animals
Language:
En
Journal:
Infect Genet Evol
Journal subject:
BIOLOGIA
/
DOENCAS TRANSMISSIVEIS
/
GENETICA
Year:
2019
Document type:
Article
Affiliation country:
Netherlands