Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
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- Liana E. Kafetzopoulou
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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- Kyriakos Efthymiadis
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, Brussels, Belgium
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- Kuiama Lewandowski
- Public Health England, National Infections Service, Porton Down, United Kingdom
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- Ant Crook
- Public Health England, National Infections Service, Porton Down, United Kingdom
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- Dan Carter
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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- Jane Osborne
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
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- Emma Aarons
- Rare and Imported Pathogens Laboratory, Public Health England, Porton Down, United Kingdom
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- Roger Hewson
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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- Julian A. Hiscox
- Institute of Infection and Global Health, University of Liverpool, United Kingdom
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- Miles W. Carroll
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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- Richard Vipond
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
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- Steven T. Pullan
- NIHR Health Protection Research Unit in Emerging and Zoonotic Infections, Liverpool, United Kingdom
説明
<jats:sec> <jats:title>Background</jats:title> <jats:p>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. </jats:p> </jats:sec> <jats:sec> <jats:title>Aim</jats:title> <jats:p>To investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples.</jats:p> </jats:sec> <jats:sec> <jats:title>Methods</jats:title> <jats:p>We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION on clinical samples which were real-time reverse transcription-PCR (qRT-PCR) positive for chikungunya (CHIKV) or dengue virus (DENV), two of the most important arboviruses. A total of 26 samples with a range of representative clinical Ct values were included in the study.</jats:p> </jats:sec> <jats:sec> <jats:title>Results</jats:title> <jats:p>Direct metagenomic sequencing of nucleic acid extracts from serum or plasma without viral enrichment allowed for virus identification, subtype determination and elucidated complete or near-complete genomes adequate for phylogenetic analysis. One PCR-positive CHIKV sample was also found to be coinfected with DENV. </jats:p> </jats:sec> <jats:sec> <jats:title>Conclusions</jats:title> <jats:p>This work demonstrates that metagenomic whole genome sequencing is feasible for the majority of CHIKV and DENV PCR-positive patient serum or plasma samples. Additionally, it explores the use of Nanopore metagenomic sequencing for DENV and CHIKV, which can likely be applied to other RNA viruses, highlighting the applicability of this approach to front-line public health and potential portable applications using the MinION.</jats:p> </jats:sec>
収録刊行物
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- Eurosurveillance
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Eurosurveillance 23 (50), 1800228-, 2018-12-13
European Centre for Disease Control and Prevention (ECDC)