scholarly journals An Evidence-Based Approach to Plum Pox Virus Detection by DASI-ELISA and RT-PCR in Dormant Period

2008 ◽  
Vol 1 ◽  
pp. VRT.S495 ◽  
Author(s):  
Antonio Olmos ◽  
Edson Bertolini ◽  
Nieves Capote ◽  
Mariano Cambra
Keyword(s):  
Virus Detection ◽  
Screening Tests ◽  
Plum Pox Virus ◽  
Evidence Based ◽  
Rt Pcr ◽  
Likelihood Ratios ◽  
Dormant Period ◽  
Plant Materials ◽  
Calculation Of Parameters ◽  
Post Test

An evidence-based approach, such as those developed in clinical and veterinary medicine, was applied to the detection of Plum pox virus (PPV) during the dormant period. A standardized methodology was used for the calculation of parameters of the operational capacity of DASI-ELISA and RT-PCR in wintertime. These methods are routinely handled to test the sanitary status of plants in national or international trading and in those cases concerning export-import of plant materials. Diagnosis often has to be performed during the dormant period, when plant material is commercialized. Some guidelines to interpret diagnostic results of wintertime are provided in an attempt to minimize risks associated with the methods and over-reliance on the binary outcome of a single assay. In order to evaluate if a complementary test increased the confidence of PPV diagnosis when discordant results between DASI-ELISA and RT-PCR are obtained, NASBA-FH also was included. Likelihood ratios of each method were estimated based on the sensitivity and specificity obtained in wintertime. Subsequently, a Bayesian approach was performed to calculate post-test probability of PPV infection in spring. Results of evidence-based approach show that different PPV prevalences require different screening tests. Thus, at very low PPV prevalence levels DASI-ELISA should be used as the election method, whilst at the highest PPV prevalence levels RT-PCR should be performed. NASBA-FH could be used at medium prevalences to clarify discordances between DASI-ELISA and RT-PCR.

scholarly journals Virus Detection and Production of Virus Free Plant Materials from the Lily by Selecting Basal Filament Flower as Explants

2021 ◽  
pp. 94-103
Author(s):  
Yanjie Lv ◽  
Yajun Dou ◽  
Halizeremu Saidahemaiti ◽  
Xiangfeng He ◽  
Xiangxun Zhao ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Economic Value ◽  
Virus Detection ◽  
Pcr Detection ◽  
Economic Losses ◽  
Rt Pcr ◽  
Plant Materials ◽  
Lily Symptomless Virus ◽  
Virus Removal ◽  
Das Elisa

Lilium is a perennial bulbous flower of Lily family Liliaceae, with high ornamental and economic value. However, Lily is vulnerable to virus infection, which seriously affects the yield and quality of Lily, and poses a great threat to the production, sales, especially export of Lily, and has caused huge economic losses to the related industries. Therefore, the research on lily virus removal methods and virus detection technology has important practical significance to improve the ornamental value and economic value of lily. In this study, the filaments of four susceptible lily varieties,' Valdisole' (A),'Adoration'(LA),' Ice Cube'(OT) and ‘Zantriana’ (O), were used as explants. The filaments of lily were divided into three parts, namely, top, middle, and base. In this paper, the virus detection of tissue culture seedlings induced by lily filaments was carried out by using DAS-ELISA and RT-PCR, and the removal effects of Cucumber mosaic virus,(CMV) and lily symptomless virus (LSV), two common viruses in lily, were explored, and the two detection technologies were compared. The results showed that the success rate of tissue culture seedlings induced by filament base was the highest, and CMV virus could be basically removed. RT-PCR detection is more sensitive than DAS-ELISA detection, but RT-PCR detection requires higher test conditions and technology. Therefore, appropriate virus detection methods can be selected according to actual conditions and severity.

scholarly journals Modeling the Accuracy of Three Detection Methods of Grapevine leafroll-associated virus 3 During the Dormant Period Using a Bayesian Approach

2016 ◽  
Vol 106 (5) ◽  
pp. 510-518 ◽  
Author(s):  
Antonio Olmos ◽  
Edson Bertolini ◽  
Ana B. Ruiz-García ◽  
Carmen Martínez ◽  
Rosa Peiró ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Real Time ◽  
Latent Class ◽  
Latent Class Models ◽  
Rt Pcr ◽  
Likelihood Ratios ◽  
Dormant Period ◽  
Degree Of Confidence ◽  
Class Models ◽  
Das Elisa

Grapevine leafroll-associated virus 3 (GLRaV-3) has a worldwide distribution and is the most economically important virus that causes grapevine leafroll disease. Reliable, sensitive, and specific methods are required for the detection of the pathogen in order to assure the production of healthy plant material and control of the disease. Although different serological and nucleic acid-based methods have been developed for the detection of GLRaV-3, diagnostic parameters have not been established, and there is no gold standard method. Therefore, the main aim of this work was to determine the sensitivity, specificity, and likelihood ratios of three commonly used methods, including one serological test (double-antibody sandwich enzyme-linked immunosorbent assay [DAS-ELISA]) and two nucleic acid-based techniques (spot and conventional real-time reverse transcription-polymerase chain reaction [RT-PCR]). Latent class models using a Bayesian approach have been applied to determine diagnostic test parameters and to facilitate decision-making regarding diagnostic test selection. Statistical analysis has been based on the results of a total of 281 samples, which were collected during the dormant period from three different populations. The best-fit model out of the 49 implemented models revealed that DAS-ELISA was the most specific method (value = 0.99) and provided the highest degree of confidence in positive results. Conversely, conventional real-time RT-PCR was the most sensitive method (value = 0.98) and produced the highest degree of confidence in negative results. Furthermore, the estimation of likelihood ratios showed that in populations with low GLRaV-3 prevalence the most appropriate method could be DAS-ELISA, while conventional real-time RT-PCR could be the most appropriate method in medium or high prevalence populations. Combining both techniques significantly increases detection accuracy. The flexibility and power of Bayesian latent class models open new possibilities for the evaluation of diagnostic tests for plant viruses.

Evidence-based diagnostic accuracy measurement in urine cytology using likelihood ratios

2020 ◽  
Author(s):  
Nickolas Myles ◽  
Manon Auger ◽  
Yonca Kanber ◽  
Derin Caglar ◽  
Wassim Kassouf ◽  
...  
Keyword(s):  
Diagnostic Accuracy ◽  
Urine Cytology ◽  
Evidence Based ◽  
Likelihood Ratios ◽  
Accuracy Measurement

Comparison of high throughput sequencing to standard protocols for virus detection in berry crops

Plant Disease ◽  
2021 ◽  
Author(s):  
Dan Edward Veloso Villamor ◽  
Karen E Keller ◽  
Robert Martin ◽  
Ioannis Emmanouil Tzanetakis
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Wide Spectrum ◽  
Virus Detection ◽  
Rt Pcr ◽  
Host Interactions ◽  
Growing Seasons ◽  
Berry Crops ◽  
Sampling Times ◽  
Better Than

A comprehensive study comparing virus detection between high throughput sequencing (HTS) and standard protocols in 30 berry selections (12 Fragaria, 10 Vaccinium and 8 Rubus) with known virus profiles was completed. The study examined temporal detection of viruses at four sampling times encompassing two growing seasons. Within the standard protocols, RT-PCR proved better than biological indexing. Detection of known viruses by HTS and RT-PCR nearly mirrored each other. HTS provided superior detection compared to RT-PCR on a wide spectrum of virus variants and discovery of novel viruses. More importantly, in most cases where the two protocols showed parallel virus detection, 11 viruses in 16 berry selections were not consistently detected by both methods at all sampling points. Based on these data we propose a four sampling times/two-year testing requirement for berry and potentially other crops to ensure that no virus remains undetected independent of titer, distribution or other virus/virus or virus/host interactions.

scholarly journals Value and Diagnostic Efficacy of Fetal Morphology Assessment Using Ultrasound in A Poor-Resource Setting

Diagnostics ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 109 ◽  
Author(s):  
Ukweh ◽  
Ugbem ◽  
Okeke ◽  
Ekpo
Keyword(s):  
Predictive Value ◽  
Performance Metrics ◽  
Area Under The Curve ◽  
Youden Index ◽  
Likelihood Ratios ◽  
Diagnostic Efficacy ◽  
Predictive Values ◽  
Resource Setting ◽  
Post Test ◽  
Sensitivity Specificity

Background: Ultrasound is operator-dependent, and its value and efficacy in fetal morphology assessment in a low-resource setting is poorly understood. We assessed the value and efficacy of fetal morphology ultrasound assessment in a Nigerian setting. Materials and Methods: We surveyed fetal morphology ultrasound performed across five facilities and followed-up each fetus to ascertain the outcome. Fetuses were surveyed in the second trimester (18th–22nd weeks) using the International Society of Ultrasound in Obstetrics and Gynecology (ISUOG) guideline. Clinical and surgical reports were used as references to assess the diagnostic efficacy of ultrasound in livebirths, and autopsy reports to confirm anomalies in terminated pregnancies, spontaneous abortions, intrauterine fetal deaths, and still births. We calculated sensitivity, specificity, positive and negative predictive values, Area under the curve (AUC), Youden index, likelihood ratios, and post-test probabilities. Results: In total, 6520 fetuses of women aged 15–46 years (mean = 31.7 years) were surveyed. The overall sensitivity, specificity, and AUC were 77.1 (95% CI: 68–84.6), 99.5 (95% CI: 99.3–99.7), and 88.3 (95% CI: 83.7–92.2), respectively. Other performance metrics were: positive predictive value, 72.4 (95% CI: 64.7–79.0), negative predictive value, 99.6 (95% CI: 99.5–99.7), and Youden index (77.1%). Abnormality prevalence was 1.67% (95% CI: 1.37–2.01), and the positive and negative likelihood ratios were 254 (95% CI: 107.7–221.4) and 0.23 (95% CI: 0.16–0.33), respectively. The post-test probability for positive test was 72% (95% CI: 65–79). Conclusion: Fetal morphology assessment is valuable in a poor economics setting, however, the variation in the diagnostic efficacy across facilities and the limitations associated with the detection of circulatory system anomalies need to be addressed.

scholarly journals First Report of Plum pox virus (Sharka Disease) in Prunus persica in the United States

Plant Disease ◽  
2000 ◽  
Vol 84 (2) ◽  
pp. 202-202 ◽  
Author(s):  
L. Levy ◽  
V. Damsteegt ◽  
R. Welliver
Keyword(s):  
Prunus Persica ◽  
Virus Disease ◽  
Sandwich Elisa ◽  
Pcr Amplification ◽  
The United States ◽  
Enzyme Linked Immunosorbent Assay ◽  
Plum Pox Virus ◽  
Rt Pcr ◽  
Peach Fruit ◽  
First Report

Plum pox (Sharka) is the most important virus disease of Prunus in Europe and the Mediterranean region and is caused by Plum pox potyvirus (PPV). In September 1999, PPV-like symptoms were observed in peach fruit culls in a packinghouse in Pennsylvania. All symptomatic fruit originated from a single block of peach (P. persica cv. Encore) in Adams County. Trees in the block exhibited ring pattern symptoms on their leaves. A potyvirus was detected in symptomatic fruit using the Poty-Group enzyme-linked immunosorbent assay (ELISA) test from Agdia (Elkhart, IN). Reactions for symptomatic peach fruit and leaves also were positive using triple-antibody sandwich ELISA with the PPV polyclonal antibody from Bioreba (Carrboro, NC) for coating, the Poty-Group monoclonal antibody (MAb; Agdia) as the intermediate antibody, and double-antibody sandwich ELISA with PPV detection kits from Sanofi (Sanofi Diagnostics Pasteur, Marnes-La-Coquette, France) and Agdia and the REAL PPV kit (Durviz, Valencia, Spain) containing universal (5B) and strain typing (4DG5 and AL) PPV MAbs (1). PPV also was identified by immunocapture-reverse transcription-polymerase chain reaction (IC-RT-PCR) amplification and subsequent sequencing of the 220-bp 3′ noncoding region (2) (>99% sequence homology to PPV) and by IC-RT-PCR amplification of a 243-bp product in the coat protein (CP) gene (1). The virus was identified as PPV strain D based on serological typing with strainspecific MAbs and on PCR-restriction fragment length polymorphism of the CP IC-RT-PCR product with Rsa1 and Alu1 (1). This is the first report of PPV in North America. References: (1) T. Candresse et al. Phytopathology 88:198, 1998. (2) L. Levy and A. Hadidi. EPPO Bull. 24:595, 1994.

scholarly journals Diarrhea caused by rotavirus A, B, and C in suckling piglets from southern Brazil: molecular detection and histologic and immunohistochemical characterization

2018 ◽  
Vol 30 (3) ◽  
pp. 370-376 ◽  
Author(s):  
Paula R. Almeida ◽  
Elis Lorenzetti ◽  
Raquel S. Cruz ◽  
Tatiane T. Watanabe ◽  
Priscila Zlotowski ◽  
...  
Keyword(s):  
Virus Detection ◽  
Enteric Virus ◽  
Transmissible Gastroenteritis Virus ◽  
Southern Brazil ◽  
Rt Pcr ◽  
Viral Pathogen ◽  
Rotavirus A ◽  
Diarrhea Virus ◽  
Suckling Piglets ◽  
Transmissible Gastroenteritis

Rotavirus (RV) is an important viral pathogen causing diarrhea in piglets and other mammals worldwide. We describe 34 cases from 4 diarrheal outbreaks caused by RV in unvaccinated farrowing units in southern Brazil from 2011 to 2013. We performed autopsy, histologic examinations, bacterial culture, RV immunohistochemistry (IHC), and enteric virus detection through molecular assays for rotavirus A, B, and C, transmissible gastroenteritis virus, porcine epidemic diarrhea virus, sapovirus, norovirus, and kobuvirus. Histologically, villus atrophy (29 of 34) and epithelial vacuolation (27 of 34) occurred in all 4 outbreaks. Cell debris in the lamina propria occurred in 20 cases, mostly from outbreaks A (8 of 11), C (4 of 6), and D (7 of 11). IHC was positive for RV in 21 of 34 samples. RT-PCR was positive for RV in 20 of 30 samples; RV-C was the most frequently detected RV ( n = 17). Kobuvirus was detected in 11 samples, and, in 3 of them, there was single detection of this enteric virus.

Reactive Lymphoid Hyperplasia or Tubercular Lymphadenitis: Can Real-Time PCR on Fine-Needle Aspirates Help Physicians in Concluding the Diagnosis?

2018 ◽  
Vol 62 (3) ◽  
pp. 204-208 ◽  
Author(s):  
Vivek Gupta ◽  
Arvind Bhake
Keyword(s):  
Lymph Node ◽  
Lymph Nodes ◽  
Real Time ◽  
Predictive Value ◽  
Lymphoid Hyperplasia ◽  
Reactive Lymphoid Hyperplasia ◽  
Rt Pcr ◽  
Likelihood Ratios ◽  
Diagnostic Challenge ◽  
Cross Sectional

Background: Enlarged lymph nodes in adult patients often present a diagnostic challenge. In the absence of granuloma or necrosis, the cytology/tissue findings are misleading and relate the enlarged lymph nodes to reactive lymphoid hyperplasia (RLH), because granuloma formation is an immunological response that usually takes 14–100 days to develop. This study assesses the role of real-time (RT)-PCR in the diagnosis of the Mycobacterium complex (MTBC) in lymph node aspirates compared with culture in cases of RLH. Methods: A cross-sectional study was conducted on 112 patients, aged 15–74 years, with a diagnosis of RLH on cytology. RT-PCR for MTBC detection and culture on Löwenstein-Jensen medium for tubercular bacilli was done on lymph node aspirates. Comparative values with reference to culture were calculated. The χ2 value, positive predictive value (PPV), negative predictive value (NPV), and likelihood ratios (LR) were calculated. Results: Out of 112 RLH cases, 35 (31%) were positive on both RT-PCR and culture. RT-PCR was positive in 43 cases and culture was positive in 44 cases. The χ2 test was found to be highly significant. PPV, NPV, positive LR, and negative LR were 81.4%, 87%, 6.76, and 0.23, respectively. Conclusion: RT-PCR for MTBC proves to be useful in arriving at a conclusive diagnosis in patients with a cytological diagnosis of RLH.

Secondary Prevention 1: Cancers and Principles of Screening

2010 ◽  
pp. 141-157
Author(s):  
Martha P. Millman ◽  
Paul J. Limburg
Keyword(s):  
United States ◽  
Cause Of Death ◽  
Cancer Survival ◽  
Task Force ◽  
The United States ◽  
Screening Tests ◽  
Evidence Based ◽  
Level Of Education ◽  
Screening Strategies ◽  
Evidence Based Guidelines

Screening tests are used to differentiate between persons with and without the condition of interest in a defined population. Screening strategies, or mass screening, is applied relatively indiscriminately to a population. Cancer is the second-leading overall cause of death in the United States; however, it is the leading cause of death for those under 85. Cancer risk is associated with environmental risk factors. Racial disparities in cancer incidence and death persist in the United States; level of education also appears to affect cancer survival. The United States Preventive Services Task Force has established evidence-based guidelines for screening, counseling, and chemoprevention.

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