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Article

Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics

1
Department of Plant Pathology, University of California-Davis, Davis, CA 95616, USA
2
Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA
3
Department of Computer Science, University of California-Davis, Davis, CA 95616, USA
4
Department of Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
These authors contributed equally to this work.
Academic Editor: Nuredin Habili
Viruses 2021, 13(6), 1130; https://doi.org/10.3390/v13061130
Received: 24 March 2021 / Revised: 7 June 2021 / Accepted: 10 June 2021 / Published: 11 June 2021
Development of High-Throughput Sequencing (HTS), also known as next generation sequencing, revolutionized diagnostic research of plant viruses. HTS outperforms bioassays and molecular diagnostic assays that are used to screen domestic and quarantine grapevine materials in data throughput, cost, scalability, and detection of novel and highly variant virus species. However, before HTS-based assays can be routinely used for plant virus diagnostics, performance specifications need to be developed and assessed. In this study, we selected 18 virus-infected grapevines as a test panel for measuring performance characteristics of an HTS-based diagnostic assay. Total nucleic acid (TNA) was extracted from petioles and dormant canes of individual samples and constructed libraries were run on Illumina NextSeq 500 instrument using a 75-bp single-end read platform. Sensitivity was 98% measured over 264 distinct virus and viroid infections with a false discovery rate (FDR) of approximately 1 in 5 positives. The results also showed that combining a spring petiole test with a fall cane test increased sensitivity to 100% for this TNA HTS assay. To evaluate extraction methodology, these results were compared to parallel dsRNA extractions. In addition, in a more detailed dilution study, the TNA HTS assay described here consistently performed well down to a dilution of 5%. In that range, sensitivity was 98% with a corresponding FDR of approximately 1 in 5. Repeatability and reproducibility were assessed at 99% and 93%, respectively. The protocol, criteria, and performance levels described here may help to standardize HTS for quality assurance and accreditation purposes in plant quarantine or certification programs. View Full-Text
Keywords: high-throughput sequencing; grapevine virus; validation; performance assessment; sensitivity; specificity; reproducibility; repeatability high-throughput sequencing; grapevine virus; validation; performance assessment; sensitivity; specificity; reproducibility; repeatability
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MDPI and ACS Style

Soltani, N.; Stevens, K.A.; Klaassen, V.; Hwang, M.-S.; Golino, D.A.; Al Rwahnih, M. Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics. Viruses 2021, 13, 1130. https://doi.org/10.3390/v13061130

AMA Style

Soltani N, Stevens KA, Klaassen V, Hwang M-S, Golino DA, Al Rwahnih M. Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics. Viruses. 2021; 13(6):1130. https://doi.org/10.3390/v13061130

Chicago/Turabian Style

Soltani, Nourolah, Kristian A. Stevens, Vicki Klaassen, Min-Sook Hwang, Deborah A. Golino, and Maher Al Rwahnih. 2021. "Quality Assessment and Validation of High-Throughput Sequencing for Grapevine Virus Diagnostics" Viruses 13, no. 6: 1130. https://doi.org/10.3390/v13061130

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