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Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour

Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus

MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
Authors to whom correspondence should be addressed.
Current address: University of Groningen, GELIFES—Groningen Institute for Evolutionary Life Sciences, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
Current address: Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany and German Centre for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Riems, 20359 Hamburg, Germany.
Viruses 2019, 11(9), 865;
Received: 27 August 2019 / Revised: 11 September 2019 / Accepted: 14 September 2019 / Published: 17 September 2019
(This article belongs to the Special Issue Viromics: Approaches, Advances, and Applications)
Biting midges (Culicoides species) are vectors of arboviruses and were responsible for the emergence and spread of Schmallenberg virus (SBV) in Europe in 2011 and are likely to be involved in the emergence of other arboviruses in Europe. Improved surveillance and better understanding of risks require a better understanding of the circulating viral diversity in these biting insects. In this study, we expand the sequence space of RNA viruses by identifying a number of novel RNA viruses from Culicoides impunctatus (biting midge) using a meta-transcriptomic approach. A novel metaviromic pipeline called MetaViC was developed specifically to identify novel virus sequence signatures from high throughput sequencing (HTS) datasets in the absence of a known host genome. MetaViC is a protein centric pipeline that looks for specific protein signatures in the reads and contigs generated as part of the pipeline. Several novel viruses, including an alphanodavirus with both segments, a novel relative of the Hubei sobemo-like virus 49, two rhabdo-like viruses and a chuvirus, were identified in the Scottish midge samples. The newly identified viruses were found to be phylogenetically distinct to those previous known. These findings expand our current knowledge of viral diversity in arthropods and especially in these understudied disease vectors. View Full-Text
Keywords: metaviromics; RNA viruses; Culicoides impunctatus metaviromics; RNA viruses; Culicoides impunctatus
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MDPI and ACS Style

Modha, S.; Hughes, J.; Bianco, G.; Ferguson, H.M.; Helm, B.; Tong, L.; Wilkie, G.S.; Kohl, A.; Schnettler, E. Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus. Viruses 2019, 11, 865.

AMA Style

Modha S, Hughes J, Bianco G, Ferguson HM, Helm B, Tong L, Wilkie GS, Kohl A, Schnettler E. Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus. Viruses. 2019; 11(9):865.

Chicago/Turabian Style

Modha, Sejal, Joseph Hughes, Giovanni Bianco, Heather M. Ferguson, Barbara Helm, Lily Tong, Gavin S. Wilkie, Alain Kohl, and Esther Schnettler. 2019. "Metaviromics Reveals Unknown Viral Diversity in the Biting Midge Culicoides impunctatus" Viruses 11, no. 9: 865.

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