scholarly journals Diagnostics of Grapevine fanleaf virus

Biljni lekar ◽  
2021 ◽  
Vol 49 (1) ◽  
pp. 54-64
Author(s):  
Đina Konstantin ◽  
Goran Barać ◽  
Renata Iličić ◽  
Ferenc Bagi
Keyword(s):  
Visual Inspection ◽  
Virus Detection ◽  
Plant Viruses ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Economic Losses ◽  
Rt Pcr ◽  
Grapevine Fanleaf Virus ◽  
Qrt Pcr ◽  
Propagation Material

Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. Due to the multiple possibilities of infection, they have become widespread. The use of healthy propagation material, free of viroids, viruses and bacteria, is an important strategy in disease control in viticulture. The early and accurate detection of plant viruses is an essential component of their control. Due to the widespread of Grapevine fanleaf virus (GFLV) and its devastating potential, various diagnostic methods are being used. GFLV detection methods based on the specificity of the protein cover (ELISA) and nucleic acid-based virus detection methods (RT-PCR, qRT-PCR). Symptoms of viral diseases are often not distinct and can be confused with those of abiotic stresses, so visual inspection is not reliable enough.

scholarly journals Comprehensive Real-Time RT-PCR Assays for the Detection of Fifteen Viruses Infecting Prunus spp.

Plants ◽  
2020 ◽  
Vol 9 (2) ◽  
pp. 273
Author(s):  
Alfredo Diaz-Lara ◽  
Kristian Stevens ◽  
Vicki Klaassen ◽  
Deborah Golino ◽  
Maher Al Rwahnih
Keyword(s):  
Genetic Diversity ◽  
Real Time ◽  
Germplasm Collection ◽  
Fruit Trees ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Economic Losses ◽  
Rt Pcr ◽  
Pcr Assays ◽  
Prunus Spp

Viruses can cause economic losses in fruit trees, including Prunus spp., by reducing yield and marketable fruit. Given the genetic diversity of viruses, reliable diagnostic methods relying on PCR are critical in determining viral infection in fruit trees. This study evaluated the broad-range detection capacity of currently available real-time RT-PCR assays for Prunus-infecting viruses and developed new assays when current tests were inadequate or absent. Available assays for 15 different viruses were exhaustively evaluated in silico to determine their capacity to detect virus isolates deposited in GenBank. During this evaluation, several isolates deposited since the assay was designed exhibited nucleotide mismatches in relation to the existing assay’s primer sequences. In cases where updating an existing assay was impractical, we performed a redesign with the dual goals of assay compactness and comprehensive inclusion of genetic diversity. The efficiency of each developed assay was determined by a standard curve. To validate the assay designs, we tested them against a comprehensive set of 87 positive and negative Prunus samples independently analyzed by high throughput sequencing. As a result, all the real-time RT-PCR assays described herein successfully detected the different viruses and their corresponding isolates. To further validate the new and updated assays a Prunus germplasm collection was surveyed. The sensitive and reliable detection methods described here will be used for the large-scale pathogen testing required to maintain the highest quality nursery stock.

scholarly journals Rapid functionalisation and detection of viruses via a novel Ca2+-mediated virus-DNA interaction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Nicole C. Robb ◽  
Jonathan M. Taylor ◽  
Amy Kent ◽  
Oliver J. Pambos ◽  
Barak Gilboa ◽  
...  
Keyword(s):  
Virus Detection ◽  
Dna Interaction ◽  
Single Particle Tracking ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Intact Virus ◽  
Wide Range ◽  
Particle Size Determination ◽  
Pathogenic Viruses ◽  
Chemical Groups

Abstract Current virus detection methods often take significant time or can be limited in sensitivity and specificity. The increasing frequency and magnitude of viral outbreaks in recent decades has resulted in an urgent need for diagnostic methods that are facile, sensitive, rapid and inexpensive. Here, we describe and characterise a novel, calcium-mediated interaction of the surface of enveloped viruses with DNA, that can be used for the functionalisation of intact virus particles via chemical groups attached to the DNA. Using DNA modified with fluorophores, we have demonstrated the rapid and sensitive labelling and detection of influenza and other viruses using single-particle tracking and particle-size determination. With this method, we have detected clinical isolates of influenza in just one minute, significantly faster than existing rapid diagnostic tests. This powerful technique is easily extendable to a wide range of other enveloped pathogenic viruses and holds significant promise as a future diagnostic tool.

Detection of the influenza virus yesterday and now.

2014 ◽  
Vol 61 (3) ◽  
Author(s):  
Agnieszka Woźniak-Kosek ◽  
Bogumiła Kempińska-Mirosławska ◽  
Grażyna Hoser
Keyword(s):  
Influenza Virus ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Clinical Samples ◽  
Serological Tests ◽  
Human Influenza Virus ◽  
Rapid Spread ◽  
Influenza Virus Detection

Demographic changes and the development of transportation contribute to the rapid spread of influenza. Before an idea of a 'person to person' spread appeared, divergent theories were developed to explain influenza epidemics in the past. Intensified virological and serological tests became possible after isolation of the human influenza virus in 1933. The first influenza virus detection methods were based on its isolation in egg embryos or cell lines and on demonstration of the presence of the viral antigens. Molecular biology techniques associated with amplification of RNA improved the quality of tests as well as sensitivity of influenza virus detection in clinical samples. It became possible to detect mixed infections caused by influenza types A and B and to identify the strain of the virus. Development of reliable diagnostic methods enabled fast diagnosis of influenza which is important for choosing an appropriate medical treatment.

scholarly journals Extraction-free rapid cycle RT-qPCR and extreme RT-PCR for SARS-CoV-2 virus detection

2021 ◽  
Vol 156 (Supplement_1) ◽  
pp. S139-S139
Author(s):  
J C Lownik ◽  
J S Farrar ◽  
G Way ◽  
R K Martin
Keyword(s):  
Supply Chain ◽  
Diagnostic Testing ◽  
Rna Extraction ◽  
Virus Detection ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Sample Collection ◽  
Rt Pcr ◽  
Hydrolysis Probe ◽  
Time Requirements

Abstract Introduction/Objective Since the start of the coronavirus disease 2019 (COVID-19) pandemic, molecular diagnostic testing for detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has faced substantial supply chain shortages and noteworthy delays in result reporting after sample collection. Supply chain shortages have been most evident in reagents for RNA extraction and rapid diagnostic testing. In this study, we explored the kinetic limitations of extraction-free rapid cycle RT-qPCR for SARS-CoV-2 virus detection using the commercially available capillary based LightCycler. Methods/Case Report We optimized reverse transcription and PCR under extraction-free and rapid thermocycling conditions utilizing hydrolysis probe-based detection methods using a Roche LightCycler. Results (if a Case Study enter NA) This protocol improves detection speed while maintaining the sensitivity and specificity of hydrolysis probe-based detection. Percentage agreement between the developed assay and previously tested positive patient samples was 97.6% (n= 40/41) and negative patient samples was 100% (40/40). We further demonstrate that using purified RNA, SARS-CoV-2 testing using extreme RT-PCR and product verification by melting can be completed in less than 3 minutes. Conclusion We developed a protocol for sensitive and specific RT-qPCR of SARS-CoV-2 RNA from nasopharyngeal swabs in less than 20 minutes, with minimal hands-on time requirements. Overall, these studies provide a framework for increasing the speed of SARS-CoV-2 and other infectious disease testing.

scholarly journals Plant Viruses Infecting Solanaceae Family Members in the Cultivated and Wild Environments: A Review

Plants ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 667 ◽  
Author(s):  
Richard Hančinský ◽  
Daniel Mihálik ◽  
Michaela Mrkvová ◽  
Thierry Candresse ◽  
Miroslav Glasa
Keyword(s):  
Plant Virus ◽  
Plant Viruses ◽  
Life Cycles ◽  
Diagnostic Methods ◽  
Wild Plant ◽  
Economic Losses ◽  
Crop Species ◽  
Ecological Interface ◽  
Solanaceae Family

Plant viruses infecting crop species are causing long-lasting economic losses and are endangering food security worldwide. Ongoing events, such as climate change, changes in agricultural practices, globalization of markets or changes in plant virus vector populations, are affecting plant virus life cycles. Because farmer’s fields are part of the larger environment, the role of wild plant species in plant virus life cycles can provide information about underlying processes during virus transmission and spread. This review focuses on the Solanaceae family, which contains thousands of species growing all around the world, including crop species, wild flora and model plants for genetic research. In a first part, we analyze various viruses infecting Solanaceae plants across the agro-ecological interface, emphasizing the important role of virus interactions between the cultivated and wild zones as global changes affect these environments on both local and global scales. To cope with these changes, it is necessary to adjust prophylactic protection measures and diagnostic methods. As illustrated in the second part, a complex virus research at the landscape level is necessary to obtain relevant data, which could be overwhelming. Based on evidence from previous studies we conclude that Solanaceae plant communities can be targeted to address complete life cycles of viruses with different life strategies within the agro-ecological interface. Data obtained from such research could then be used to improve plant protection methods by taking into consideration environmental factors that are impacting the life cycles of plant viruses.

scholarly journals Evaluation of diagnostic methods to distinguish between calves persistently and transiently infected with bovine viral diarrhoea virus in respect to the presence of maternal antibodies

2013 ◽  
Vol 57 (3) ◽  
pp. 311-317
Author(s):  
Magdalena Larska ◽  
Aleksandra Kuta ◽  
Mirosław P. Polak
Keyword(s):  
Virus Detection ◽  
Bovine Viral Diarrhoea Virus ◽  
Diagnostic Methods ◽  
Viral Rna ◽  
Maternal Antibodies ◽  
Bovine Viral Diarrhoea ◽  
Rt Pcr ◽  
Serum Samples ◽  
Virus Genotype ◽  
Diarrhoea Virus

Abstract Two issues concerning virus detection and identification of persistently infected (PI) cattle were analysed in the study: 1) interference by maternal antibodies and 2) discrimination between PI and transiently infected (TI) animals. Antigen ELISA and RT-PCR based methods were compared using serum samples from natural and experimental PI and TI calves. RT-PCR and realtime RT-PCR using primers within 5’UTR region were more sensitive in detecting PI animals than Erns and NS3 antigen capture ELISAs, and they were not influenced by the presence of colostral antibodies in serum or by bovine viral diarrhoea virus genotype. The serum samples with Ct values ≤ 29.10 (corresponding to 104.87 viral RNA copies/μL) identified PI animals with 100% probability, while all samples with Ct values > 32.06 (corresponding to viral RNA load below 104 copies/μL) indicated TI status. The samples with Ct values between 29.10 and 32.06 (17.2% of PI and 11.5% of TI) should be considered as PI suspect and retested.

scholarly journals Nucleic Acid Testing of SARS-CoV-2

2021 ◽  
Vol 22 (11) ◽  
pp. 6150
Author(s):  
Hee-Min Yoo ◽  
Il-Hwan Kim ◽  
Seil Kim
Keyword(s):  
Polymerase Chain Reaction ◽  
Nucleic Acid ◽  
Reverse Transcription ◽  
Diagnostic Methods ◽  
Detection Methods ◽  
Molecular Diagnostic ◽  
Nucleic Acid Testing ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Polymerase Chain

The coronavirus disease 2019 (COVID-19) has caused a large global outbreak. It is accordingly important to develop accurate and rapid diagnostic methods. The polymerase chain reaction (PCR)-based method including reverse transcription-polymerase chain reaction (RT-PCR) is the most widely used assay for the detection of SARS-CoV-2 RNA. Along with the RT-PCR method, digital PCR has emerged as a powerful tool to quantify nucleic acid of the virus with high accuracy and sensitivity. Non-PCR based techniques such as reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) are considered to be rapid and simple nucleic acid detection methods and were reviewed in this paper. Non-conventional molecular diagnostic methods including next-generation sequencing (NGS), CRISPR-based assays and nanotechnology are improving the accuracy and sensitivity of COVID-19 diagnosis. In this review, we also focus on standardization of SARS-CoV-2 nucleic acid testing and the activity of the National Metrology Institutes (NMIs) and highlight resources such as reference materials (RM) that provide the values of specified properties. Finally, we summarize the useful resources for convenient COVID-19 molecular diagnostics.

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 Evaluation of seven different rapid methods for nucleic acid detection of SARS-COV-2 virus

2021 ◽  
Author(s):  
Sally Mahmoud ◽  
Esra Ibrahim ◽  
Subhashini Ganesan ◽  
Bhagyashree Thakre ◽  
Juliet Teddy ◽  
...  
Keyword(s):  
Nucleic Acid ◽  
Gold Standard ◽  
Large Scale ◽  
Virus Detection ◽  
Detection Methods ◽  
Nucleic Acid Detection ◽  
Test Accuracy ◽  
Rt Pcr ◽  
Rapid Methods ◽  
Kappa Value

Background In the current COVID-19 pandemic there is mass screening of SARS-CoV-2 happening round the world due to the extensive spread of the infections. There is a high demand for rapid diagnostic tests to expedite identification of cases and to facilitate early isolation and control spread. Hence this study evaluates seven different rapid nucleic acid detection assays that are commercially available for SARS- CoV- 2 virus detection. Methods Nasopharyngeal samples were collected from 4859 participants and were tested for SARS-CoV-2 virus by the gold standard RT-PCR method along with one of these seven rapid methods of detection. Evaluation of the rapid nucleic acid detection assays was done by comparing the results of these rapid methods with the gold standard RT-qPCR results for SARS-COV-2 detection. Results AQ-TOP had the highest sensitivity (98%) and strong kappa value of 0.943 followed by Genechecker and Abbot ID NOW. The POCKIT (ii RT-PCR) assay had the highest test accuracy of 99.29% followed by Genechecker and Cobas Liat. Atila iAMP showed the highest percentage of invalid reports (35.5%) followed by AQ-TOP with 6% and POCKIT with 3.7% of invalid reports. Conclusion Genechecker system, Abbott ID NOW and Cobas Liat, were found to have best performance and agreement when compared to the standard RT-PCR for COVID-19 detection. With further research, these rapid tests have the potential to be employed in large scale screening of COVID-19.

scholarly journals 235 Seed Treatments for Inactivation of CGMMV in Gourd and Its Detection

HortScience ◽  
1999 ◽  
Vol 34 (3) ◽  
pp. 482E-482
Author(s):  
Du-Hyun Kim ◽  
Jung-Myung Lee ◽  
Jin-Ju Bae
Keyword(s):  
Heat Treatment ◽  
Seed Treatment ◽  
Virus Detection ◽  
Latex Agglutination ◽  
Detection Methods ◽  
Rt Pcr ◽  
Chenopodium Amaranticolor ◽  
Dry Heat ◽  
Complete Inactivation ◽  
Dry Heat Treatment

Cucumber green mottle mosaic virus (CGMMV) is a noxious disease in cucurbits, especially in Asia where grafting is commonly practiced. CGMMV can be easily transmitted by seed, hands, soil, or grafting. Seed companies are rigorously looking for effective and efficient means of CGMMV inactivation in infected seeds. Among the various treatments applied to the seeds, dry heat treatment (35° C 1 day + 50 °C 1 day + 75 °C 3 days) was found to be most suitable for complete inactivation. Various identification methods including high-density latex agglutination test (HDLPAT), ELISA, RT-PCR, and bioassay (Chenopodium amaranticolor) were compared for accurate diagnosis of the presence of virus in seeds. The results from HDLPAT showed the highest correlation with the bioassay results, suggesting that HDLPAT can be safely used for accurate means of virus detection. Details of dry heat treatment, various seed treatment, and other detection methods will be presented.

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