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Abstract

Background

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.

Aim

To investigate the feasibility of metagenomic sequencing for recovering whole genome sequences of chikungunya and dengue viruses from clinical samples.

Methods

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.

Results

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.

Conclusions

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.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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/content/10.2807/1560-7917.ES.2018.23.50.1800228
2018-12-13
2024-11-21
http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2018.23.50.1800228
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Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Liana+E.+Kafetzopoulou&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kafetzopoulou Liana E.</a>, <a href="/search?value1=Kyriakos+Efthymiadis&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Efthymiadis Kyriakos</a>, <a href="/search?value1=Kuiama+Lewandowski&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lewandowski Kuiama</a>, <a href="/search?value1=Ant+Crook&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Crook Ant</a>, <a href="/search?value1=Dan+Carter&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Carter Dan</a>, <a href="/search?value1=Jane+Osborne&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Osborne Jane</a>, <a href="/search?value1=Emma+Aarons&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Aarons Emma</a>, <a href="/search?value1=Roger+Hewson&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hewson Roger</a>, <a href="/search?value1=Julian+A.+Hiscox&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hiscox Julian A.</a>, <a href="/search?value1=Miles+W.+Carroll&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Carroll Miles W.</a>, <a href="/search?value1=Richard+Vipond&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Vipond Richard</a>, <a href="/search?value1=Steven+T.+Pullan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pullan Steven T.</a></span>. Assessment of metagenomic Nanopore and Illumina sequencing for recovering whole genome sequences of chikungunya and dengue viruses directly from clinical samples. <a href="/content/ecdc">Euro Surveill.</a> 2018;23(50):pii=1800228. <a href="https://doi.org/10.2807/1560-7917.ES.2018.23.50.1800228" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2018.23.50.1800228</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 27 Apr 2018;&nbsp;&nbsp; <span class="generated">Accepted</span>: 23 Oct 2018 </span> </p>
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