A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies

Blouin, Arnaud G., Ross, Howard A., Hobson-Peters, Jody, O'Brien, Caitlin, Warren, Ben and MacDiarmid, Robin (2016) A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies. Molecular Ecology Resources, 16 5: 1255-1263. doi:10.1111/1755-0998.12525


Author Blouin, Arnaud G.
Ross, Howard A.
Hobson-Peters, Jody
O'Brien, Caitlin
Warren, Ben
MacDiarmid, Robin
Title A new virus discovered by immunocapture of double-stranded RNA, a rapid method for virus enrichment in metagenomic studies
Journal name Molecular Ecology Resources   Check publisher's open access policy
ISSN 1755-0998
1755-098X
Publication date 2016-03-15
Year available 2016
Sub-type Article (original research)
DOI 10.1111/1755-0998.12525
Open Access Status Not Open Access
Volume 16
Issue 5
Start page 1255
End page 1263
Total pages 9
Place of publication Chichester, West Sussex, United Kingdom
Publisher Blackwell Publishing
Collection year 2017
Language eng
Formatted abstract
Next-generation sequencing technologies enable the rapid identification of viral infection of diseased organisms. However, despite a consistent decrease in sequencing costs, it is difficult to justify their use in large-scale surveys without a virus sequence enrichment technique. As the majority of plant viruses have an RNA genome, a common approach is to extract the double-stranded RNA (dsRNA) replicative form, to enrich the replicating virus genetic material over the host background. The traditional dsRNA extraction is time-consuming and labour-intensive. We present an alternative method to enrich dsRNA from plant extracts using anti-dsRNA monoclonal antibodies in a pull-down assay. The extracted dsRNA can be amplified by reverse transcriptase-polymerase chain reaction and sequenced by next-generation sequencing. In our study, we have selected three distinct plant hosts: Maori potato (Solanum tuberosum), rengarenga (Arthropodium cirratum) and broadleaved dock (Rumex obtusifolius) representing a cultivated crop, a New Zealand-native ornamental plant and a weed, respectively. Of the sequence data obtained, 31-74% of the reads were of viral origin, and we identified five viruses including Potato virus Y and Potato virus S in potato; Turnip mosaic virus in rengarenga (a new host record); and in the dock sample Cherry leaf roll virus and a novel virus belonging to the genus Macluravirus. We believe that this new assay represents a significant opportunity to upscale virus ecology studies from environmental, primary industry and/or medical samples.
Keyword NGS
Antibodies
dsRNA
Metagenomics
Plant virus
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Article (original research)
Collections: HERDC Pre-Audit
School of Chemistry and Molecular Biosciences
 
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Created: Fri, 01 Apr 2016, 13:37:14 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences