Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts
Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts Shelley Cook1*☯, Betty Y.-W. Chung2☯, David Bass1, Gregory Moureau3, Shuoya Tang2, Erica McAlister1, C. Lorna Culverwell1, Edvard Glücksman4, Hui Wang5, T. David K. Brown6, Ernest A. Gould3,5, Ralph E. Harbach1, Xavier de Lamballerie3, Andrew E. Firth6* 1 Department of Life Sciences, Natural History Museum, London, United Kingdom, 2 Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom, 3 UMR_D 190 "Emergence des Pathologies Virales" (Aix-Marseille Univ. IRD French Institute of Research for Development EHESP French School of Public Health), Marseille, France, 4 Department of General Botany, University Duisburg-Essen, Essen, Germany, 5 Centre for Ecology & Hydrology, Wallingford, Oxfordshire, United Kingdom, 6 Department of Pathology, University of Cambridge, Cambridge, United Kingdom Abstract We investigated whether small RNA (sRNA) sequenced from field-collected mosquitoes and chironomids (Diptera) can be used as a proxy signature of viral prevalence within a range of species and viral groups, using sRNAs sequenced from wild-caught specimens, to inform total RNA deep sequencing of samples of particular interest. Using this strategy, we sequenced from adult Anopheles maculipennis s.l. mosquitoes the apparently nearly complete genome of one previously undescribed virus related to chronic bee paralysis virus, and, from a pool of Ochlerotatus caspius and Oc. detritus mosquitoes, a nearly complete entomobirnavirus genome. We also reconstructed long sequences (1503-6557 nt) related to at least nine other viruses. Crucially, several of the sequences detected were reconstructed from host organisms highly divergent from those in which related viruses have been previously isolated or discovered.
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