We report the first identification of novel viruses, and sequence of an entire viral genome, by a single step of high-throughput parallel sequencing of small RNAs from diseased, as well as symptomless plants. Contigs were assembled from sequenced total siRNA from plants using small sequence assembly software and could positively identify RNA, ssDNA and dsDNA reverse transcribing viruses and in one case spanned the entire genome. The results present a novel approach which cannot only identify known viral pathogens, occurring at extremely low titers, but also novel viruses, without the necessity of any prior knowledge.

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Accurate detection of viruses in plants and animals is critical for agriculture production and human health. Deep sequencing and assembly of virus-derived small interfering RNAs has proven to be a highly efficient approach for virus discovery. Here we present VirusDetect, a bioinformatics pipeline that can efficiently analyze large-scale small RNA (sRNA) datasets for both known and novel virus identification. VirusDetect performs both reference-guided assemblies through aligning sRNA sequences to a curated virus reference database and de novo assemblies of sRNA sequences with automated parameter optimization and the option of host sRNA subtraction. The assembled contigs are compared to a curated and classified reference virus database for known and novel virus identification, and evaluated for their sRNA size profiles to identify novel viruses. Extensive evaluations using plant and insect sRNA datasets suggest that VirusDetect is highly sensitive and efficient in identifying known and novel viruses. VirusDetect is freely available at http://bioinfo.bti.cornell.edu/tool/VirusDetect/.

Co-infection of Sweet potato chlorotic stunt virus (SPCSV, genus Crinivirus) with Sweet potato feathery mottle virus (SPFMV, genus Potyvirus) results in sweet potato virus disease (SPVD), a synergistic disease that is widely distributed in the sweet potato (Ipomoea batatas) growing regions of the world. Since both SPCSV and SPFMV are common and often detected as part of multiple co-infections of severely diseased plants, the occurrence of synergistic interactions with other viruses was investigated. Data from this study show that SPCSV, but not SPFMV, can cause synergistic diseases in sweet potato with all viruses tested, including members of the genus Potyvirus (Sweet potato latent virus, Sweet potato mild speckling virus), Ipomovirus (Sweet potato mild mottle virus), Cucumovirus (Cucumber mosaic virus), and putative members of the genus Carlavirus (Sweet potato chlorotic fleck virus and C-6 virus). The synergism was expressed as an increase in the severity of symptoms, virus accumulation, viral movement in plants, and as an effect on yield of storage roots. The presence of a third different virus in plants affected with SPVD increased the severity of symptoms even further compared with SPVD alone. There was a positive correlation between increase in virus accumulation and symptom expression in double and triple SPCSV-associated co-infections. The epidemiological implications of the results are discussed.

Sweetpotato virus disease (SPVD), the most important disease affecting sweetpotato (Ipomoea batatas (L.) Lam), is caused by the synergistic interaction of the aphid-transmitted Sweetpotato feathery mottle virus (SPFMV) and whitefly-transmitted Sweetpotato chlorotic stunt virus (SPCSV). In this study, SPVD was the main disease in the Cañete Valley, the major sweetpotato-producing area in Peru. Studies on virus incidence showed that SPCSV and SPFMV were the most frequently identified viruses in Cañete Valley. Symptoms of different severity were associated with isolates of both viruses involved in the SPVD. Over 80% of plants infected with both SPFMV and SPCSV showed the symptoms (leaf reduction and deformation, vein clearing or mosaic, and stunting) typically attributed to SPVD elsewhere. SPFMV did not significantly affect the yield of the sweetpotato cultivars Jonathan and Costanero, but infection of these cultivars by SPCSV was associated with significant yield reduction. Double infection by the two viruses resulted in SPVD and greater yield reduction than for either alone. These results demonstrate that SPFMV and SPCSV interact synergistically and that the severity of SPVD symptoms also depends on the particular isolate of each virus.