scholarly journals Virus Pathogens in Australian Vineyards with an Emphasis on Shiraz Disease

Viruses ◽  
2020 ◽  
Vol 12 (8) ◽  
pp. 818 ◽  
Author(s):  
Qi Wu ◽  
Nuredin Habili ◽  
Fiona Constable ◽  
Maher Al Rwahnih ◽  
Darius E. Goszczynski ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Management Strategies ◽  
Virus Transmission ◽  
Virus Detection ◽  
Scale Insects ◽  
Wine Quality ◽  
Novel Technologies ◽  
Grapevine Virus A ◽  
Significant Yield ◽  
Leafroll Virus

Grapevine viruses are found throughout the viticultural world and have detrimental effects on vine productivity and grape and wine quality. This report provides a comprehensive and up-to-date review on grapevine viruses in Australia with a focus on “Shiraz Disease” (SD) and its two major associated viruses, grapevine virus A (GVA) and grapevine leafroll-associated virus 3 (GLRaV-3). Sensitive grapevine cultivars like Shiraz infected with GVA alone or with a co-infection of a leafroll virus, primarily GLRaV-3, show symptoms of SD leading to significant yield and quality reductions in Australia and in South Africa. Symptom descriptors for SD will be outlined and a phylogenetic tree will be presented indicating the SD-associated isolates of GVA in both countries belong to the same clade. Virus transmission, which occurs through infected propagation material, grafting, and naturally vectored by mealybugs and scale insects, will be discussed. Laboratory and field-based indexing will also be discussed along with management strategies including rogueing and replanting certified stock that decrease the incidence and spread of SD. Finally, we present several cases of SD incidence in South Australian vineyards and their effects on vine productivity. We conclude by offering strategies for virus detection and management that can be adopted by viticulturists. Novel technologies such as high throughput sequencing and remote sensing for virus detection will be outlined.

Green peach aphid and potato leafroll virus: transmission and control

2020 ◽  
Author(s):  
R.A. Bagrov ◽  
◽  
V.I. Leunov
Keyword(s):  
Myzus Persicae ◽  
Green Peach Aphid ◽  
Virus Transmission ◽  
Potato Leafroll Virus ◽  
Factors Affecting ◽  
Potato Viruses ◽  
Tuber Necrosis ◽  
Aphid Vectors ◽  
Leafroll Virus ◽  
And Control

The mechanisms of transmission of potato viruses from plants to aphid vectors and from aphids to uninfected plants are described, including the example of the green peach aphid (Myzus persicae, GPA). Factors affecting the spreading of tuber necrosis and its manifestation on plants infected with potato leafroll virus (PLRV) are discussed. Recommendations for PLRV and GPA control in the field are given.

scholarly journals Application of Oxford Nanopore Technology to Plant Virus Detection

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1424
Author(s):  
Lia W. Liefting ◽  
David W. Waite ◽  
Jeremy R. Thompson
Keyword(s):  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Diagnostic Methods ◽  
Plant Virus Detection ◽  
Sequencing Technologies ◽  
Oxford Nanopore ◽  
Virus Diagnostics ◽  
Post Entry ◽  
Read Accuracy

The adoption of Oxford Nanopore Technologies (ONT) sequencing as a tool in plant virology has been relatively slow despite its promise in more recent years to yield large quantities of long nucleotide sequences in real time without the need for prior amplification. The portability of the MinION and Flongle platforms combined with lowering costs and continued improvements in read accuracy make ONT an attractive method for both low- and high-scale virus diagnostics. Here, we provide a detailed step-by-step protocol using the ONT Flongle platform that we have developed for the routine application on a range of symptomatic post-entry quarantine and domestic surveillance plant samples. The aim of this methods paper is to highlight ONT’s feasibility as a valuable component to the diagnostician’s toolkit and to hopefully stimulate other laboratories towards the eventual goal of integrating high-throughput sequencing technologies as validated plant virus diagnostic methods in their own right.

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.

Virus Vector Relationship of Yellow Mosaic Virus and Whitefly, Bemisia tabaci (Gennadius) in Soybean

2021 ◽  
Author(s):  
M. Swathi ◽  
Neeta Gaur ◽  
Kamendra Singh
Keyword(s):  
Mosaic Virus ◽  
Virus Disease ◽  
Management Strategies ◽  
Virus Transmission ◽  
Virus Vector ◽  
Yellow Mosaic Virus ◽  
Starvation Period ◽  
Mungbean Yellow Mosaic Virus ◽  
Biological Relationship ◽  
Relationship Of

Background: Whitefly is one of the most destructive sucking pest in the tropical and subtropical regions of the world and causing significant crop losses directly by sucking sap from the plants and indirectly through the transmission of viral diseases specifically caused by the genus Begomovirus. The Begomovirus species viz., Mungbean yellow mosaic India virus (MYMIV) and Mungbean yellow mosaic virus (MYMV) are causing yellow mosaic virus disease in soybean, which is transmitted by whiteflies. The disease accounts to 30-70 per cent yield loss and increases up to 80 - 100 per cent during severe incidence. Hence, there is a need for development of integrated pest management strategies against disease and whiteflies, for this the knowledge on virus-vector relationship is required. But, the studies on biological relationship of yellow mosaic virus disease and whitefly in soybean are scarce. At this juncture, considering the importance of disease in soybean, the present investigation was carried out to know the virus -vector relationship of the YMV and whitefly in soybean.Methods: The experiment on virus-vector relationship of yellow mosaic virus and whitefly in soybean was conducted at Department of Entomology, College of Agriculture, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand during 2016-17. The data on number of whiteflies per plant, acquisition and inoculation access feeding period and pre and post starvation period required for effective transmission of virus was recorded.Result: A single viruliferous whitefly was able to transmit virus and ten viruliferous whiteflies per plant were required for cent per cent transmission of virus. The minimum acquisition access and inoculation access feeding periods required for virus transmission was 0.25h (15 min) each; while the 100 per cent virus transmission was recorded with acquisition and inoculation period of 12h, each. The per cent transmission was increased with the increase of acquisition and inoculation periods. The rate of transmission was positively correlated with pre-acquisition starvation period and negatively correlated with post- acquisition starvation period.

scholarly journals Current Perspectives on High-Throughput Sequencing (HTS) for Adventitious Virus Detection: Upstream Sample Processing and Library Preparation

Viruses ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 566 ◽  
Author(s):  
Siemon Ng ◽  
Cassandra Braxton ◽  
Marc Eloit ◽  
Szi Feng ◽  
Romain Fragnoud ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Nucleic Acids ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Extraction Methods ◽  
Control Measures ◽  
Acid Extraction ◽  
Library Preparation ◽  
Sample Processing

A key step for broad viral detection using high-throughput sequencing (HTS) is optimizing the sample preparation strategy for extracting viral-specific nucleic acids since viral genomes are diverse: They can be single-stranded or double-stranded RNA or DNA, and can vary from a few thousand bases to over millions of bases, which might introduce biases during nucleic acid extraction. In addition, viral particles can be enveloped or non-enveloped with variable resistance to pre-treatment, which may influence their susceptibility to extraction procedures. Since the identity of the potential adventitious agents is unknown prior to their detection, efficient sample preparation should be unbiased toward all different viral types in order to maximize the probability of detecting any potential adventitious viruses using HTS. Furthermore, the quality assessment of each step for sample processing is also a critical but challenging aspect. This paper presents our current perspectives for optimizing upstream sample processing and library preparation as part of the discussion in the Advanced Virus Detection Technologies Interest group (AVDTIG). The topics include: Use of nuclease treatment to enrich for encapsidated nucleic acids, techniques for amplifying low amounts of virus nucleic acids, selection of different extraction methods, relevant controls, the use of spike recovery experiments, and quality control measures during library preparation.

Identifying and Characterizing Summer Diseases on ‘Babygold’ Peach in South Carolina

2006 ◽  
Vol 7 (1) ◽  
pp. 30 ◽  
Author(s):  
Guido Schnabel ◽  
Wenxuan Chai ◽  
Kerik D. Cox
Keyword(s):  
South Carolina ◽  
Dna Analysis ◽  
Management Strategies ◽  
Disease Outbreaks ◽  
Geotrichum Candidum ◽  
Fruit Rot ◽  
Colletotrichum Acutatum ◽  
Significant Yield ◽  
Rot Disease

Summer diseases can cause significant yield losses in processing peach varieties, such as the ‘Babygold’ lines. In this study we identified and characterized the pathogens responsible for disease outbreaks in two orchards (PH and JC) located in the northern ‘Piedmont’ area of South Carolina. Three pathogens, Geotrichum candidum, Colletotrichum acutatum, and Botryosphaeria dothidea, the causal agents of sour rot, anthracnose, and Botryosphaeria fruit rot disease respectively, were identified on fruit from orchard PH using symptomology, culture and spore morphology, and ribosomal DNA analysis. G. candidum and C. acutatum were also isolated from symptomatic fruit from orchard JC. The QoI fungicide azoxystrobin and a mixture of pyraclostrobin and boscalid were evaluated for their in vitro efficacy against five isolates of each of the three pathogens to investigate their possible usefulness in designing management strategies. Azoxystrobin inhibited mycelial growth of C. acutatum isolates (EC50 values of 0.01 to 0.55 mg/liter) but was ineffective against mycelium of G. candidum and B. dothidea isolates (EC50 values >300 mg/liter). The pyraclostrobin-boscalid mixture was highly effective against mycelium of C. acutatum (EC50 values of 0.01 to 0.05 mg/liter) and B. dothidea isolates (EC50 values of 0.02 to 0.03 mg/liter), but only marginally effective against mycelium of G. candidum (EC50 values 15.79 to 39.03 mg/liter). This study provides a diagnostic guide of pathogens that can cause summer diseases on ‘Babygold’ peaches and reports their in vitro sensitivity to registered respiration inhibitor fungicides. Accepted for publication 23 December 2005. Published 1 March 2006.

scholarly journals High Throughput Sequencing For Plant Virus Detection and Discovery

2019 ◽  
Vol 109 (5) ◽  
pp. 716-725 ◽  
Author(s):  
D. E. V. Villamor ◽  
T. Ho ◽  
M. Al Rwahnih ◽  
R. R. Martin ◽  
I. E. Tzanetakis
Keyword(s):  
High Throughput ◽  
Plant Virus ◽  
High Throughput Sequencing ◽  
Virus Detection ◽  
Agricultural Crops ◽  
Virus Discovery ◽  
Plant Virus Detection ◽  
Virus Biology ◽  
Disease Causality

Over the last decade, virologists have discovered an unprecedented number of viruses using high throughput sequencing (HTS), which led to the advancement of our knowledge on the diversity of viruses in nature, particularly unraveling the virome of many agricultural crops. However, these new virus discoveries have often widened the gaps in our understanding of virus biology; the forefront of which is the actual role of a new virus in disease, if any. Yet, when used critically in etiological studies, HTS is a powerful tool to establish disease causality between the virus and its host. Conversely, with globalization, movement of plant material is increasingly more common and often a point of dispute between countries. HTS could potentially resolve these issues given its capacity to detect and discover. Although many pipelines are available for plant virus discovery, all share a common backbone. A description of the process of plant virus detection and discovery from HTS data are presented, providing a summary of the different pipelines available for scientists’ utility in their research.

scholarly journals 73 Managing health during the receiving period

2019 ◽  
Vol 97 (Supplement_1) ◽  
pp. 25-25
Author(s):  
John T Richeson
Keyword(s):  
Great Plains ◽  
Health Management ◽  
Management Strategies ◽  
Clinical Signs ◽  
Virus Transmission ◽  
Management Program ◽  
Water Tank ◽  
Early Disease Detection ◽  
Increased Risk ◽  
Cattle Health

Abstract Cattle originating from the southeastern United States and received in stocker and feedlot facilities in the southern Great Plains are at increased risk for bovine respiratory disease (BRD) and other health disorders because the marketing and relocation process may result in stress-induced immunosuppression, increased respiratory virus transmission, and poor nutritional status. Cattle health directly affects growth performance because stress and the inflammatory response to infection results in tissue catabolism and anorexia. Preconditioning practices at the ranch origin, such as vaccination, castration, weaning, and feed bunk and water tank exposure, can significantly improve health outcome during the receiving period; however, this practice is underutilized, resulting in high-risk, commingled calves entering subsequent production sectors. Antimicrobial metaphylaxis is one of the most effective management strategies to control an anticipated outbreak of BRD in newly received calves, yet antimicrobial use in food animals is under intense scrutiny. Antimicrobial alternatives such as direct-fed microbial products may provide health benefits but uncertainty regarding the route and timing of application, effective dose, and product selection will require further research to improve application. Nutritional stress resulting from reduced feed and water intake before, during, and after relocation and potential trace mineral deficiency upon arrival must be considered in a comprehensive health management program. Finally, detection of BRD or other diseases in large groups of cattle is challenging because of the prey instinct to disguise clinical signs of illness. Technology that continuously monitor individual cattle behavior may provide early disease detection with greater sensitivity and specificity than traditional methods but several barriers to adoption exist. This symposium presentation will outline the multitude of factors to consider in managing cattle health during the receiving period and provide research-based evidence that challenge paradigm regarding health management of newly received cattle.

New Frontiers in Mucositis

2012 ◽  
pp. 545-551 ◽  
Author(s):  
Douglas E. Peterson ◽  
Dorothy M. Keefe ◽  
Stephen T. Sonis
Keyword(s):  
Kinase Inhibitors ◽  
Management Strategies ◽  
Mammalian Target Of Rapamycin ◽  
Cancer Therapeutics ◽  
Mtor Inhibitors ◽  
Mucosal Injury ◽  
Mucosal Damage ◽  
Nucleotide Polymorphisms ◽  
Oncology Patient ◽  
Novel Technologies

Overview: Mucositis is among the most debilitating side effects of radiotherapy, chemotherapy, and targeted anticancer therapy. Research continues to escalate regarding key issues such as etiopathology, incidence and severity across different mucosae, relationships between mucosal and nonmucosal toxicities, and risk factors. This approach is being translated into enhanced management strategies. Recent technology advances provide an important foundation for this continuum. For example, evolution of applied genomics is fostering development of new algorithms to rapidly screen genomewide single-nucleotide polymorphisms (SNPs) for patient-associated risk prediction. This modeling will permit individual tailoring of the most effective, least toxic treatment in the future. The evolution of novel cancer therapeutics is changing the mucositis toxicity profile. These agents can be associated with unique mechanisms of mucosal damage. Additional research is needed to optimally manage toxicity caused by agents such as mammalian target of rapamycin (mTOR) inhibitors and tyrosine kinase inhibitors, without reducing antitumor effect. There has similarly been heightened attention across the health professions regarding clinical practice guidelines for mucositis management in the years following the first published guidelines in 2004. New opportunities exist to more effectively interface this collective guideline portfolio by capitalizing upon novel technologies such as an Internet-based Wiki platform. Substantive progress thus continues across many domains associated with mucosal injury in oncology patients. In addition to enhancing oncology patient care, these advances are being integrated into high-impact educational and scientific venues including the National Cancer Institute Physician Data Query (PDQ) portfolio as well as a new Gordon Research Conference on mucosal health and disease scheduled for June 2013.

scholarly journals Wine Yeast Terroir: Separating the Wheat from the Chaff—for an Open Debate

2020 ◽  
Vol 8 (5) ◽  
pp. 787 ◽  
Author(s):  
Hervé Alexandre
Keyword(s):  
Microbial Communities ◽  
High Throughput Sequencing ◽  
Abiotic Factors ◽  
Soil Microbial Communities ◽  
Consumer Preference ◽  
Wine Yeast ◽  
Wine Quality ◽  
Critical Feature ◽  
Wine Production ◽  
Sequencing Technologies

Wine terroir is characterized by a specific taste and style influenced by the cultivar of the fermented grapes, geographical factors such as the vineyard, mesoclimate, topoclimate, and microclimate, soil geology and pedology, and the agronomic approach used. These characteristics together define the concept of “terroir”. Thus, regional distinctive flavors in wine have been the subject of many studies aimed at better understanding the link between the wine and the vineyard. Indeed, the identification of key environmental elements involved in the regional variation of grape and wine quality characteristics is a critical feature for improving wine production in terms of consumer preference and economic appreciation. Many studies have demonstrated the role of abiotic factors in grape composition and consequently in wine style. Biotic factors are also involved such as grape microbial communities. However, the occurrence and effects of region-specific microbiota in defining wine characteristics are more controversial issues. Indeed, several studies using high throughput sequencing technologies have made it possible to describe microbial communities and revealed a link between grape must and soil microbial communities, and the geography of the territory. Based on these observations, the concept of “microbial terroir” emerged. However, this concept has been subject to contradictory studies. The aim of this opinion article is to take a step back and examine in perspective the concept of microbial terroir, by comparing numerous data from different studies and providing arguments in favor of or against this concept to stimulate discussion and point out that experimental research is still needed to study the contribution of this assembly of microorganisms to the final product and to support or refute the concept.

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