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Background Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America. Results Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize. Conclusions Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.

Background Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available. Methods In this study, soybean fields were scouted for virus-like disease symptoms during the 2016–2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes. Results Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common. Conclusions Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.

Tobacco streak virus (TSV) has an extensive plant host range, but until recently has not been a common problem in North American soybean. TSV is associated with bud blight and yield loss due to reduced plant height and density, and delayed seed development and plant maturity. TSV has been reported in recent years in Illinois, Iowa, Kansas, and Wisconsin, as well as Ontario, Canada. Presence of the virus was confirmed by ELISA. In an Iowa field with high incidence, regression analysis indicated a significant positive relationship between incidence and seed moisture. TSV is seed and pollen transmitted, as well as being spread by thrips. Increasingly variable weather creating favorable conditions for thrips may be facilitating the rise of TSV. The combination of increased incidence of TSV with associated potential for yield loss and few known management methods brings attention to the need for further research. Accepted for publication 14 April 2016. Published 26 April 2016.

Soybean vein necrosis virus (SVNV), a tospovirus and one of the most widespread soybean viruses in North America, is primarily transmitted by soybean thrips (Neohydatothrips variabilis). Although soybean is not considered the primary plant host for SVNV, there is a dearth of knowledge about alternative host plants for SVNV. We therefore investigated whether commonly present specialty and cover crops in Iowa can serve as alternative hosts for SVNV. Seventeen cover crops and seven specialty crops were tested using mechanical and thrips inoculations. Clear symptoms of SVNV and systemic infection in buckwheat and clear local infection with possible systemic infection on melon were shown. Additionally, we compared soybean thrips feeding on 18 cover crops and determined that they preferred alfalfa, buckwheat, crimson clover, and red clover. Our results suggested that alternative host crops may harbor SVNV and be a possible source of inoculum for soybean.