Development of a High-Throughput Crop Virus Diagnostic Service Using Viral Enrichment and RNA Sequencing
Award last edited on: 1/11/2023

Sponsored Program
Awarding Agency
Total Award Amount
Award Phase
Solicitation Topic Code
Principal Investigator
Seanna Hewitt

Company Information

Qualterra Inc (AKA: NuPhY Inc)

1610 Ne Eastgate Boulevard Suite 850
Pullman, WA 99163
   (509) 336-2249
Location: Single
Congr. District: 05
County: Whitman

Phase I

Contract Number: 2021-01573
Start Date: 3/22/2021    Completed: 2/28/2022
Phase I year
Phase I Amount
Global economic impact of pathogenic plant viruses is valued at $60 billion. In the US for appleand cherry alone these losses total up to $678 million annually. Detection of viruses is a criticalpriority to mitigate spread of diseases that threaten horticultural crop health fruit yield andquality. The current methods for virus diagnostics are low-throughput and limited to detection ofindividual viruses with established sequence information. In contrast double-stranded RNAsequencing (dsRNAseq) is capable of screening large numbers of samples for all viruses in asingle workflow. NuPhY's USDA SBIR Phase I application will evaluate the feasibility ofusing a dsRNAseq-based platform for broad-spectrum high-throughput virus screening inhorticultural crops.During Phase I we aim to develop an accurate rapid cost-effective dsRNAseq-based system ofbroad-spectrum tree fruit virus detection. The first objective will establish virus detection limits(sensitivity) of dsRNAseq in infected cherry tissues and determine the optimal tissue type forsequencing-based analysis using Little Cherry Virus as a case study. The second objective willoptimize the high-throughput dsRNAseq workflow and establish a customized data analysispipleline through testing of infected and healthy tissues from cherry apple and pear trees.NuPhY's proposed work aligns with the USDA SBIR program goals because it entails theinnovation optimization and provision of an agriculturally-related manufacturing technologythat can quickly be deployed as a service to US tree fruit growers and nursery managers.Ultimately our technological solution will pre-emptively mitigate economic losses associatedwith viral pathogens while enhancing efficiency and sustainability within US horticultureindustries.

Phase II

Contract Number: 2022-04868
Start Date: 8/31/2022    Completed: 8/31/2024
Phase II year
Phase II Amount
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.