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ARS Home » Southeast Area » Fort Pierce, Florida » U.S. Horticultural Research Laboratory » Subtropical Plant Pathology Research » Research » Publications at this Location » Publication #292209
Title: The use of latent class analysis to estimate the sensitivities and specificities of diagnostic tests for Squash vein yellowing virus in cucurbit species when there is no gold standard

Author
item Turechek, William
item Webster, Craig
item Duan, Jingyi
item ROBERTS, PAM - University Of Florida
item Kousik, Chandrasekar - Shaker
item Adkins, Scott

Submitted to: Phytopathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/27/2013
Publication Date: 12/1/2013
Publication URL: http://dx.doi.org/10.1094/PHYTO-03-13-0071-R
Citation: Turechek, W., Webster, C.G., Duan, J., Roberts, P., Kousik, C.S., Adkins, S.T. 2013. The use of latent class analysis to estimate the sensitivities and specificities of diagnostic tests for Squash vein yellowing virus in cucurbit species when there is no gold standard. Phytopathology. 103(12):1243-1251. https://doi.org/10.1094/PHYTO-03-13-0071-R.
DOI: https://doi.org/10.1094/PHYTO-03-13-0071-R

Interpretive Summary: Squash vein yellowing virus (SqVYV) is the causal agent of viral watermelon vine decline, one of the most serious diseases in watermelon (Citrullus lanatus L.) production in the southeastern United States. Current diagnostic methods for identification of SqVYV-infected plants or tissues are based on the polymerase chain reaction (RT-PCR), tissue blot nucleic acid hybridization assays (TB), and expression of visual symptoms. A quantitative assessment of the performance of these diagnostic tests is lacking, which may lead to an incorrect interpretation of results. In this study, latent class analysis was used to determine whether their performances varied among the type of plant tissue being tested (crown vs. vine tissue), where plant samples were taken relative to the position of the crown (i.e., distance from the crown), host (i.e., genus), and habitat (field-grown versus greenhouse-grown plants). Results showed that RT-PCR was the superior test of the three tests. TB was better at identifying infected plants than symptoms, althought the visual assessment of symptoms was a better indicator of non-infection than TB. With respect to the grouping variables, crown tissue was better to test than vine tissue for detecting infection. Test performance also varied with habitat and genus, but not with distance from the crown. The results given here provide quantitative measurements of test performance for a range of conditions, and provide the information needed to interpret test results when tests are used in combination for a diagnosis.

Technical Abstract: Squash vein yellowing virus (SqVYV) is the causal agent of viral watermelon vine decline, one of the most serious diseases in watermelon (Citrullus lanatus L.) production in the southeastern United States. Current diagnostic methods for identification of SqVYV-infected plants or tissues are based on the polymerase chain reaction (RT-PCR), tissue blot nucleic acid hybridization assays (TB), and expression of visual symptoms. A quantitative assessment of the performance of these diagnostic tests is lacking, which may lead to an incorrect interpretation of results. In this study, latent class analysis was used to estimate the sensitivities and specificities of RT-PCR, TB, and visual assessment of symptoms as diagnostic tests for SqVYV and to determine whether their performances varied among the type of plant tissue being tested (crown vs. vine tissue), where plant samples were taken relative to the position of the crown (i.e., distance from the crown), host (i.e., genus), and habitat (field-grown versus greenhouse-grown plants). Results showed that RT-PCR had the highest sensitivity (0.94) and specificity (0.98) of the three tests. TB had better sensitivity than symptoms for detection of SqVYV infection (0.70 vs. 0.32), while the visual assessment of symptoms was more specific than TB and thus a better indicator of non-infection (0.98 vs. 0.65). With respect to the grouping variables, RT-PCR and TB had better sensitivity but poorer specificity for diagnosing SqVYV infection in crown tissue than it did in vine tissue, whereas symptoms had very poor sensitivity but excellent specificity in both tissues for all cucurbits analyzed in this study. Test performance also varied with habitat and genus, but not with distance from the crown. The results given here provide quantitative measurements of test performance for a range of conditions, and provide the information needed to interpret test results when tests are used in parallel or serial combination for a diagnosis.