A rapid, sensitive and inexpensive method for detection of grapevine red blotch virus without tissue extraction using loop-mediated isothermal amplification

Romero-Romero, Jesús L.; Carver, Gavriela D.; Johnson, Patricio Arce; Perry, Keith L.; Thompson, Jeremy R.

doi:10.1007/s00705-019-04207-y

Cited by 33 publications

(24 citation statements)

References 12 publications

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“…We recently developed a method for visual detection of LAMP amplification (9) using pH-sensitive dyes to exploit the change of pH that resulting from proton accumulation due to dNTP incorporation. This method has been used in a large scale field survey of Wolbachia-containing mosquitos (10), Grapevine red blotch virus without DNA extraction (11), testing urine samples for Zika virus (12) and even amplification detection on the International Space Station (13). The breadth of application highlights the applicability of visual detection methods to provide an advantage in simplicity and portability for enabling new, rapid diagnostics.…”

Section: Introductionmentioning

confidence: 99%

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

Zhang

Odiwuor

Xiong

et al. 2020

Preprint

359

477

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The ability to detect an infectious agent in a widespread epidemic is crucial to the success of quarantine efforts in addition to sensitive and accurate screening of potential cases of infection from patients in a clinical setting. Enabling testing outside of sophisticated laboratories broadens the scope of control and surveillance efforts, but also requires robust and simple methods that can be used without expensive instrumentation. Here we report a method to identify SARS-CoV-2 (COVID-19) virus RNA from purified RNA or cell lysis using loop-mediated isothermal amplification (LAMP) using a visual, colorimetric detection. This test was additionally verified using RNA samples purified from respiratory swabs collected from COVID-19 patients in Wuhan, China with equivalent performance to a commercial RT-qPCR test while requiring only heating and visual inspection. This simple and sensitive method provides an opportunity to facilitate virus detection in the field without a requirement for complex diagnostic infrastructure.. CC-BY 4.0 International license It is made available under a author/funder, who has granted medRxiv a license to display the preprint in perpetuity.is the (which was not peer-reviewed) The copyright holder for this preprint .

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Section: Introductionmentioning

confidence: 99%

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

Zhang

Odiwuor

Xiong

et al. 2020

Preprint

359

477

View full text Add to dashboard Cite

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“…Since its discovery in 2008 in California (Calvi, 2011), Grapevine Red Blotch Disease (GRBD)-and its recently confirmed causal agent Grapevine Red Blotch Virus (GRBV) (Yepes et al, 2018)has significantly impacted several major grape-growing areas in the United States (Sudarshana and Zalom, 2017). To date, many research groups have been actively investigating various aspects of GRBD, but most have been focused either on identification and detection (Krenz et al, 2012;Al Rwahnih et al, 2013;Buchs et al, 2018;Romero et al, 2019), genetics and virology (Al Rwahnih et al, 2015;Sudarshana et al, 2015), vector biology and transmission (Bahder et al, 2016;Preto et al, 2018a;Preto et al, 2018b), or disease epidemiology and spread (Cieniewicz et al, 2017;Cieniewicz et al, 2018;Dalton et al, 2019). However, no agronomic studies have been conducted testing interactions between cultural practices and their effects on physiology of GRBV-infected grapevines.…”

Section: Introductionmentioning

confidence: 99%

Water Deficits Do Not Improve Fruit Quality in Grapevine Red Blotch Virus-Infected Grapevines (Vitis vinifera L.)

Levin

2020

Front. Plant Sci.

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Although deficit irrigation is used to improve fruit quality in healthy grapevines, it can potentially amplify negative effects of viral disease and reduce fruit quality in Grapevine Red Blotch Virus (GRBV) infected grapevines. Therefore, a 2-year field experiment was conducted to understand the interaction between GRBV infection and water deficits on disease development and vine physiology. Well-watered (WW) vines were irrigated at 100% of estimated crop evapotranspiration (ET c), while water deficit (WD) vines received water at 66 and 50% ET c in 2017 and 2018, respectively. Healthy (GRBV-) and infected (GRBV+) vines were confirmed by PCR assays. There were no significant effects of water deficits on foliar symptom onset in either year, but more severe water deficits in 2018 resulted in a more rapid symptom progression. GRBV+ vines had a higher Y stem compared to GRBV-vines, but the effects of virus only appeared post-veraison and corresponded to decreased leaf gas exchange. In general, vine vegetative and reproductive growth were not reduced in GRBV+ vines. Yields were highest in WW/ GRBV+ vines due to larger clusters containing larger berries. Consistent treatment effects on berry primary chemistry were limited to sugars, with no interactions between factors. Water deficits were able to somewhat increase berry anthocyanin concentration in GRBV + fruit, but the effects were dependent on year. By comparison, virus status and water deficits interacted on skin tannins concentration such that they were decreased in WD/ GRBV+ vines, but increased in WD/GRBV-vines. Water deficits had no effect on seed phenolics, with only virus status having a significant diminution. Although keeping GRBV+ vines well-watered may mitigate some of the negative effects of GRBD, these results suggest that water deficits will not improve overall fruit quality in GRBV+ vines. Ultimately, the control of fruit ripening imparted by GRBV infection seems to be stronger than abiotic control imparted by water deficits.

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“…Previously, a colorimetric test has been optimized for tomato yellow leaf curl virus detection using different dyes including ethidium bromide, SYBR green, hydroxy naphthol blue and magnesium pyrophosphate as the LAMP-reaction indicator [ 32 ]. Other studies have also reported color-based testing for mosaic and streak viruses [ 25 , 39 , 40 ]. In this study, a colorimetric test has been reported for the detection of an economically important plant virus disease complex by using a reaction mixture which contains phenol red dye as an amplification indicator utilizing its color change capability in different pH environments.…”

Section: Discussionmentioning

confidence: 99%

Development of a LAMP assay using a portable device for the real-time detection of cotton leaf curl disease in field conditions

Rafiq

Ali

Asif

et al. 2021

Biology Methods and Protocols

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Cotton production is seriously affected by the prevalent cotton leaf curl disease (CLCuD) that originated from Nigeria (Africa) to various parts of Asia including Pakistan, India, China and Philippines. Due to CLCuD, Pakistan suffers heavy losses approximately 2 billion USD per annum. Numerous reports showed that CLCuD is associated with multiple species of begomoviruses, alphasatellites and a single species of betasatellite, i.e., Cotton leaf curl Multan betasatellite (CLCuMuB). The most prevalent form of CLCuD is the combination of Cotton leaf curl Kokhran virus-Burewala strain (CLCuKoV-Bur) and CLCuMuB. Thus, the availability of an in-field assay for the timely detection of CLCuD is important for the control and management of the disease. In this study, a robust method using the loop-mediated isothermal amplification (LAMP) assay was developed for the detection of CLCuD. Multiple sets of six primers were designed based on the conserved regions of CLCuKoV-Bur and CLCuMuB-βC1 genes. The results showed that the primer set targeting the CLCuMuB-βC1 gene performed best when the LAMP assay was performed at 58 °C using 100 ng of total plant tissue DNA as a template in a 25 µL reaction volume. The limit of detection (LOD) for the assay was as low as 22 copies of total purified DNA template per reaction. This assay was further adapted to perform as a colorimetric and real-time LAMP assay which proved to be advantageously applied for the rapid and early point-of-care detection of CLCuD in the field. Application of the assay could help to prevent the huge economic losses caused by the disease and contribute to the socio-economic development of underdeveloped countries.

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A rapid, sensitive and inexpensive method for detection of grapevine red blotch virus without tissue extraction using loop-mediated isothermal amplification

Cited by 33 publications

References 12 publications

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

Rapid Molecular Detection of SARS-CoV-2 (COVID-19) Virus RNA Using Colorimetric LAMP

Water Deficits Do Not Improve Fruit Quality in Grapevine Red Blotch Virus-Infected Grapevines (Vitis vinifera L.)

Development of a LAMP assay using a portable device for the real-time detection of cotton leaf curl disease in field conditions

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