Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples.

Liana E Kafetzopoulou, Kyriakos Efthymiadis, Kuiama Lewandowski, Ant Crook, Dan Carter, Jane Osborne, Emma Aarons, Roger Hewson, Julian A Hiscox, Miles W Carroll, Richard Vipond, Steven T Pullan

Onderzoeksoutput: Articlepeer review

60 Citaten (Scopus)

Samenvatting

The recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION to study the feasibility of whole genome sequencing from clinical samples containing chikungunya or dengue virus, two of the most important arboviruses. Direct metagenomic sequencing of nucleic acid extracts from serum and plasma without viral enrichment allowed for virus and coinfection identification, subtype determination and in the majority of cases elucidated complete or near-complete genomes adequate for phylogenetic analysis. This work demonstrates that metagenomic whole genome sequencing is feasible for over 90% and 80% of chikungunya and dengue virus PCR-positive patient samples respectively. It confirms the feasibility of field metagenomic sequencing for these and likely other RNA viruses, highlighting the applicability of this approach to front-line public health.
Originele taal-2English
Artikelnummer1800228
Pagina's (van-tot)18-30
TijdschriftEurosurveillance
Volume23
Nummer van het tijdschrift50
DOI's
StatusPublished - 2018

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