Development of a High-Throughput Crop Virus Diagnostic Service Using Viral Enrichment and RNA Sequencing

Detection of viruses is a critical priority to mitigate spread of diseases that threaten plant healthfruit yield and quality and the US horticulture industry's economic bottom-line. NuPhY's USDASBIR Phase II work will optimize our viral enrichment and high-throughput sequencing (HTS)- based diagnostic platform for broad-spectrum virus screening in horticultrual crops.The proposed work aligns with the program goals because it entails translation of NuPhY's cutting- edge scientific expertise in crop virus diagnostics to a commercializable innovation that willprovide a much-needed diagnostic service to the horticulture indutry.Previously we established that our platform provides superior crop virus detection capacity incomparison with industry standard methods. Now we will optimize the platform with regards toboth turnaround time and cost. Our first objective will develop protocols for performing viralenrichment library preparations and sequencing in-house while comparing the results tocost/turnaround for sequencing outsourced to the WSU genomics core. For our second objectivewe will establish sequencing multiplexing capacity which will inform how sequencing runs areorganized when client sample volume is high.By the end of the Phase II effort and with thesupport and expertise of our subaward collaborator we anticipate successful establishment ofefficient protocols for our entire pipeline—from sample acquisition to sequencing to data analysisand results reporting—in the NuPhY lab. Our strong existing ties and history of serving thehorticulture industry will ensure seamless transition of our innovation from the benchtop to thefield. Once commercialized our virus screening platform will help growers and nursery managersto pre-emptively mitigate billions of dollars in losses that are incurred each year as a result of viralpathogens.