Reverse transcription loop-mediated isothermal amplification based rapid detection of Sugarcane mosaic virus and Sugarcane streak mosaic virus associated with mosaic disease of sugarcane

A rapid visual detection method for Sugarcane streak mosaic virus based on one-tube RPA-CRISPR/Cas12a

Sugarcane is the most important crop for sugar production. Sugarcane streak mosaic virus (SCSMV) triggered sugarcane mosaic disease can lead to substantial reductions in both yield and sucrose content. In the process of disease prevention and control, target pathogen detection technology is indispensable. However, traditional detection methods are time-consuming and require expensive equipment, making them less efficient for timely disease control and unfavorable to disease resistance breeding. Here, we introduce a novel detection technology that combines recombinase polymerase amplification (RPA) with CRISPR-Cas12a. The method utilizes crude extracts from sugarcane leaves as the reaction template, significantly simplifying and expediting the preparation process. By combining RPA and CRISPR-Cas12a in a single reaction tube, the risk of aerosol contamination has decreased markedly. The entire process, from sample preparation to result interpretation, only takes 50 min, and the reaction equipment only a water bath pot, and results can be blue light spectrometer or UV flashlight assessed visually. Importantly, the method demonstrates high sensitivity, detecting a minimum of 50 copies of the plasmid, which surpasses the sensitivity of reverse transcription polymerase chain reaction (RT-PCR) and is comparable to quantitative RT-PCR (RT-qPCR). The method exhibits excellent specificity, showing no cross-reactivity with other common sugarcane viruses, including Sugarcane mosaic virus, Sugarcane yellow leaf virus, and Sorghum mosaic virus. The practicality of this technique was validated through the detection of leaf crude extracts from 40 field samples. The detection results were consistent with those obtained from RT-PCR and RT-qPCR using leaf RNA as the template, indicating its suitability for laboratory detection and field applications.

Development of rapid and simple detection of bean common mosaic virus (BCMV) in mung beans (Vigna radiata) using reverse transcription-loop mediated isothermal amplification (RT-LAMP)

Bean common mosaic virus (BCMV) is one of the most serious and devastating Potyvirus of leguminous crops. In mung bean (Vigna radiata), BCMV is an emerging virus causing enormous losses to the crop, thereby reducing the production and profitability of the crop. Being seed borne and aphid transmitted virus, it important to reduce the spread and prevent its transfer to new geographical locations using rapid, specific and sensitive detection techniques. In this study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was devised to rapidly and specifically detect BCMV. Three pairs of specific primers were designed targeting the BCMV genome. To determine the ideal temperature, reactions were carried out across a temperature range of 45 °C to 70 °C, with intervals of 5 °C. The optimal temperature for the assay was determined to be 60 °C with a 30-min incubation period. Comparison between the RT-LAMP and conventional reverse transcription polymerase chain reaction (RT-PCR) revealed that former can detect the BCMV upto 10- 9 and was one hundred times more sensitive than later. It was also determined that RT-LAMP was specific only in detecting BCMV, with no cross-reactivity with other closely related non-target viruses [potato virus Y (PVY), bean common mosaic necrosis virus (BCMNV), clover yellow vein virus (ClYVV) and soybean mosaic virus (SMV)]. After incubating the reactions at constant temperature of (60 °C/30 min), a characteristic ladder like banding pattern was observed on agarose gel for positive samples. Colorimetric tests (SYBR Green I) were also performed to reduce the requirement of laboratory equipment for visualizing RT-LAMP results. The results developed by SYBR Green I were comparable to that of agarose gel and can be visualized with naked eye. The developed RT-LAMP assay enables rapid detection of BCMV at 60 °C within a time period of 30-min.

Historical Review of Sugarcane Streak Mosaic Virus that Has Recently Emerged in Africa

Sugarcane streak mosaic virus (SCSMV), now assigned to the genus Poacevirus of the family Potyviridae, was reported for the first time in 1932 in Louisiana and was believed to be strain F of sugarcane mosaic virus (SCMV) for more than six decades. SCMV-F was renamed SCSMV in 1998 after partial sequencing of its genome and phylogenetic investigations. Following the development of specific molecular diagnostic methods in the 2000s, SCSMV was recurrently found in sugarcane exhibiting streak mosaic symptoms in numerous Asian countries but not in the Western hemisphere or in Africa. In this review, we give an overview of the current knowledge on this disease and the progression in research on SCSMV. This includes symptoms, geographical distribution and incidence, diagnosis and genetic diversity of the virus, epidemiology, and control. Finally, we highlight future challenges, as sugarcane streak mosaic has recently been found in Africa, where this disease represents a new threat to sugarcane production.

Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viruses infecting patchouli (Pogostemon cablin)

Patchouli (Pogostemon cablin), a highly valued medicinal plant, suffers significant economic losses following infection with Broad bean wilt virus 2 (BBWV-2) and Peanut stripe virus (PStV). In this study, a field-based isothermal technique called reverse transcription loop-mediated isothermal amplification (RT-LAMP) was established for an early and specific detection of BBWV-2 and PStV. The oligo primers were designed to target the coat protein genes of PStV and BBWV-2. The reaction conditions, such as temperature and time duration, were optimized to 65 °C for 60 min. The LAMP amplicons positive for PStV and BBWV-2 revealed characteristic ladder-type bands following agarose gel electrophoresis. Further, a colorimetric assay using a metal ion-based indicator (Hydroxy-naphthol blue, HNB) was conducted to visualize the amplified products with the naked eye, thus facilitating accessibility to field practices. The assay developed in this study was found to be virus specific, and was 100 times more sensitive than RT-PCR. Thus, the RT-LAMP assay established in this study is quick, reliable, and cost-effective for the accurate identification of BBWV-2 and PStV. It will facilitate the screening of patchouli planting materials.  Further, it may reduce the risk of virus spread and could be helpful in phytosanitary programs.

Ultrasensitive nano-gold labelled, duplex lateral flow immunochromatographic assay for early detection of sugarcane mosaic viruses

Sugarcane is one of the important food and bioenergy crops, cultivated all over the world except European continent. Like many other crops, sugarcane production and quality are hampered by various plant pathogens, among them viruses that infect systemically and cause severe impact to cane growth. The viruses are efficiently managed by their elimination through tissue culture combined with molecular diagnostics, which could detect virus titre often low at 10-12 g mL-1. To harmonize the virus diagnostics by molecular methods, we established a nanocatalysis-based high sensitive lateral flow immunochromatographic assay (LFIA) simultaneously to detect two major sugarcane viruses associated with mosaic disease in sugarcane. LFIA is known for poor sensitivity and stability with its signalling conjugates. However, we synthesized positively charged Cysteamine-gold nanoparticles and used them to prepare highly stable to sensitive immunoconjugates and as a colourimetric detection label. Further nanogold signal enhancement was performed on LFIA to obtain a high detection sensitivity, which is higher than the conventional immunoassays. The linear detection range of the nano-LIFA was 10-6 to 10-9 g mL-1, and with the signal enhancement, the LOD reached up to 10-12 g ml-1. This research paper provides relative merits and advancement on nano-LFIA for specific detection of sugarcane viruses in sugarcane for the first time.

Comprehensive account of present techniques for in-field plant disease diagnosis

The early detection of plant pathogens is an appropriate preventive strategy for the management of crop yield and quality. For this reason, effective diagnostic techniques and tools, which are simple, specific, rapid and economic, are needed to be developed. Although several such technologies have been developed still most of them suffer one or the other limitation. Major limitations of the widely used diagnostic methods are requirement of trained staff and laboratory setup. Development of point-of-care diagnostic devices (handy portable devices) that require no specialized staff and can directly be used in fields is need of the hour. The aim of this review is to compile the information on current promising techniques that are in use for plant-pathogen diagnosis. Additionally, it focuses on the latest in-field pathogen diagnostic techniques with associated advantages and limitations.

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.