Recent advances of virus diagnostics in horticultural crops

Kapoor, Reetika; Kumar, Swagat; Srivastava, Nishant

doi:10.1016/b978-0-12-818654-1.00002-5

Cited by 4 publications

(5 citation statements)

References 90 publications

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“…The development of a robust and sensitive diagnostic method is of utmost importance to control plant viruses. Several methods have been developed, including, but not limited to, enzyme-linked immunosorbent assay (ELISA), molecular hybridization, polymerase chain reaction (PCR), reverse transcription followed by PCR (RT-PCR), loop (or RT-loop) mediated isothermal amplifications (LAMP and RT-LAMP), and microarrays (Baranwal et al, 2020;Hadidi et al, 2020;Rubio et al, 2020). ELISA depends on binding viralspecific antibodies to the virus coat protein (Clark and Adams, 1977).…”

Section: Introductionmentioning

confidence: 99%

Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay

et al. 2020

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Most viruses that infect plants use RNA to carry their genomic information; timely and robust detection methods are crucial for efficient control of these diverse pathogens. The RNA viruses, potexvirus (Potexvirus, family Alphaflexiviridae), potyvirus (Potyvirus, family Potyviridae), and tobamovirus (Tobamovirus, family Virgaviridae) are among the most economically damaging pathogenic plant viruses, as they are highly infectious and distributed worldwide. Their infection of crop plants, alone or together with other viruses, causes severe yield losses. Isothermal nucleic acid amplification methods, such as loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), and others have been harnessed for the detection of DNA- and RNA-based viruses. However, they have a high rate of non-specific amplification and other drawbacks. The collateral activities of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease Cas systems such as Cas12 and Cas14 (which act on ssDNA) and Cas13 (which acts on ssRNA) have recently been exploited to develop highly sensitive, specific, and rapid detection platforms. Here, we report the development of a simple, rapid, and efficient RT- RPA method, coupled with a CRISPR/Cas12a-based one-step detection assay, to detect plant RNA viruses. This diagnostic method can be performed at a single temperature in less than 30 min and integrated with an inexpensive commercially available fluorescence visualizer to facilitate rapid, in-field diagnosis of plant RNA viruses. Our developed assay provides an efficient and robust detection platform to accelerate plant pathogen detection and fast-track containment strategies.

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Section: Introductionmentioning

confidence: 99%

Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay

et al. 2020

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“…Once infected, plants harbor the virus throughout their life, and visible symptoms of viral diseases appear. So far, it is very difficult to prevent the spread of viruses and their vectors into new territories through international trade, mainly given by the exchange of plant materials across borders [239]. Therefore, early diagnosis of viral diseases is a key factor that determines the timely use of protective measures to confine the viruses, thereby preventing yield losses and a decrease in the quality of fruit products.…”

Section: Diagnosis Of Plant Virus Diseasesmentioning

confidence: 99%

“…The first way to detect viral infections was according to the symptoms they produced. Such an approach was based on biological indexing tests, which were time-consuming and unreliable, especially in cases in which the virus infection was latent or plants exhibited virus-like symptoms unrelated to virus etiology [239,240]. Then, virus detection at the microscopic level began in the late 1930s with electron microscopy; however, this technique cannot be applied for large-scale detection due to the dimensions and costs of the equipment, as well as the operating conditions.…”

Section: Diagnosis Of Plant Virus Diseasesmentioning

confidence: 99%

“…Subsequently, the application of serological assay like enzyme-linked immunosorbent assay (ELISA) [241] and nucleic acid-based assay for in vitro DNA amplification called polymerase chain reaction (PCR) [242] represented important advances in plant viral diagnosis. With the progress in molecular biology, nucleic acid-based techniques evolved significantly from conventional PCR to reverse transcription PCR (RT-PCR), nested PCR, multiplex PCR, real-time PCR, immunocapture-PCR (IC-PCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), rolling circle amplification (RCA), and microarray and next-generation sequencing (NGS) to improve specificity, sensitivity, and multi-sample processing [239].…”

Section: Diagnosis Of Plant Virus Diseasesmentioning

confidence: 99%

“…Some crops, such as bananas, contain very high levels of polyphenols and other secondary metabolites that interfere with PCR amplification. Therefore, an efficient method adapted for nucleic acid isolation is important [239].…”

Section: Computer-assisted Epitope Identification To Improve Antibody...mentioning

confidence: 99%

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Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective

Rodríguez‐Verástegui

Ramírez-Zavaleta²,

Capilla-Hernández³

et al. 2022

Plants

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Trees and herbs that produce fruits represent the most valuable agricultural food commodities in the world. However, the yield of these crops is not fully achieved due to biotic factors such as bacteria, fungi, and viruses. Viruses are capable of causing alterations in plant growth and development, thereby impacting the yield of their hosts significantly. In this work, we first compiled the world′s most comprehensive list of known edible fruits that fits our definition. Then, plant viruses infecting those trees and herbs that produce fruits with commercial importance in the global market were identified. The identified plant viruses belong to 30 families, most of them containing single-stranded RNA genomes. Importantly, we show the overall picture of the host range for some virus families following an evolutionary approach. Further, the current knowledge about plant-virus interactions, focusing on the main disorders they cause, as well as yield losses, is summarized. Additionally, since accurate diagnosis methods are of pivotal importance for viral diseases control, the current and emerging technologies for the detection of these plant pathogens are described. Finally, the most promising strategies employed to control viral diseases in the field are presented, focusing on solutions that are long-lasting.

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Diagnostics of viral infections using high-throughput genome sequencing data

Ning,

Boyes,

Numanagić

et al. 2024

Briefings in Bioinformatics

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Plant viral infections cause significant economic losses, totalling $350 billion USD in 2021. With no treatment for virus-infected plants, accurate and efficient diagnosis is crucial to preventing and controlling these diseases. High-throughput sequencing (HTS) enables cost-efficient identification of known and unknown viruses. However, existing diagnostic pipelines face challenges. First, many methods depend on subjectively chosen parameter values, undermining their robustness across various data sources. Second, artifacts (e.g. false peaks) in the mapped sequence data can lead to incorrect diagnostic results. While some methods require manual or subjective verification to address these artifacts, others overlook them entirely, affecting the overall method performance and leading to imprecise or labour-intensive outcomes. To address these challenges, we introduce IIMI, a new automated analysis pipeline using machine learning to diagnose infections from 1583 plant viruses with HTS data. It adopts a data-driven approach for parameter selection, reducing subjectivity, and automatically filters out regions affected by artifacts, thus improving accuracy. Testing with in-house and published data shows IIMI’s superiority over existing methods. Besides a prediction model, IIMI also provides resources on plant virus genomes, including annotations of regions prone to artifacts. The method is available as an R package (iimi) on CRAN and will integrate with the web application www.virtool.ca, enhancing accessibility and user convenience.

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Recent advances of virus diagnostics in horticultural crops

Cited by 4 publications

References 90 publications

Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay

Efficient, Rapid, and Sensitive Detection of Plant RNA Viruses With One-Pot RT-RPA–CRISPR/Cas12a Assay

Viruses Infecting Trees and Herbs That Produce Edible Fleshy Fruits with a Prominent Value in the Global Market: An Evolutionary Perspective

Diagnostics of viral infections using high-throughput genome sequencing data

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