Development and evaluation of a rapid recombinase polymerase amplification assay for detection of coxsackievirus A6

Recent Developments in Isothermal Amplification Methods for the Detection of Foodborne Viruses

Foodborne and enteric viruses continue to impose a significant public health and economic burden globally. As many of these viruses are highly transmissible, the ability to detect them portably, sensitively, and rapidly is critical to reduce their spread. Although still considered a gold standard for detection of these viruses, real time polymerase chain reaction (PCR)-based technologies have limitations such as limited portability, need for extensive sample processing/extraction, and long time to result. In particular, the limitations related to the susceptibility of real time PCR methods to potential inhibitory substances present in food and environmental samples is a continuing challenge, as the need for extensive nucleic acid purification prior to their use compromises the portability and rapidity of such methods. Isothermal amplification methods have been the subject of much investigation for these viruses, as these techniques have been found to be comparable to or better than established PCR-based methods in portability, sensitivity, specificity, rapidity, and simplicity of sample processing. The purpose of this review is to survey and compare reports of these isothermal amplification methods developed for foodborne and enteric viruses, with a special focus on the performance of these methods in the presence of complex matrices.

Development and evaluation of a rapid detection assay for severe fever with thrombocytopenia syndrome virus based on reverse-transcription recombinase polymerase amplification

Rapid detection of severe fever with thrombocytopenia syndrome virus (SFTSV) is crucial for its control and surveillance. In this study, a rapid isothermal real-time reverse-transcription recombinase polymerase amplification (RT-RPA) assay was developed for the detection of SFTSV. The detection limit at 95% probability was 241 copies per reaction. A test of 120 serum samples of suspected severe fever with thrombocytopenia syndrome (SFTS) patients revealed that the sensitivity and specificity of the RT-RPA assay was approximately 96.00% (95%CI: 80.46%–99.79%) and 98.95% (95% CI: 94.28%–99.95%), respectively; the kappa value was 0.9495 (P＜0.001). The Bland-Altman analysis showed that 87.50% of the different data points were located within the 95% limits of agreement, indicating a good correlation between the results from RT-RPA assays and those of RT-qPCR assays. In conclusion, the rapid and efficient RT-RPA assay can be a promising candidate for point-of-care detection method of SFTSV.

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A RT-RPA assay was developed to detect SFTSV RNA isothermally.

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The assay can rapidly produce a result in 15 min at 39 °C.

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The detection limit of the assay is 241 RNA sequences.

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The results of RT-RPA compare well with RT-qPCR.

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The RT-RPA assay may be used for field detection of SFTSV in resource-limited settings.

Development and evaluation of a time-saving RT-qRPA method for the detection of genotype 4 HEV presence in raw pork liver

Hepatitis E virus (HEV) is a zoonotic pathogen spreading worldwide. Pig was known as its first and main animal reservoir. In China, pork consumption is very large and the risk of potential HEV contamination should not be underestimated. The present study aims to develop a quantitative real-time reverse transcription combining recombinase polymerase amplification assay (RT-qRPA) for the rapid detection of HEV RNA presence in raw pork liver on the Jinzhou markets in China. Methods: the specific primers and probes for RT-qRPA assay were designed targeting the ORF2/3 conserved region in genotype 4 swine HEV isolate (accession no. DQ279091.2) according to the TwistDx manual instructions. The specificity, sensitivity and reproducibility evaluations of the RT-qRPA method were subsequently conducted in assessing agreement with the standard RT-qPCR method. Results: the qRPA method step exhibited the obvious time-saving advantage which worked under the isothermal condition at 39 °C within about 30 min to complete the run while the compared standard qPCR method in the same cycle took almost 60 min to do. Both methods could exclusively detect the HEV genome equivalents from the quantified HEV-VLPs spiked samples. And both methods shared the same limit of detection (LOD) that was estimated at 1.25 × 10³ genome equivalents copies/g spiked sample by the probit analysis. The recovery rate of HEV-VLPs reached a range of 9.56-14.65% by the RT-qRPA method which was higher than that of 1.34-2.34% by the standard RT-qPCR method. The detected HEV RNA positive rate in the field was 1.8% (1 out of 55) by both methods under Cohen's kappa statistic accessing with perfect agreement (κ = 1.00, p < 0.0005). The viral load in positive sample detected by the RT-qRPA method was estimated at 2.2125 × 10⁵ genome copies/g pork liver sample. Conclusions, the present reported RT-qRPA method mainly targeting genotype 4 HEV is a rapid and reliable method. Its time-saving quality offers a promising for the development of a portable tool used in the routine monitoring of HEV contamination in the field.

Rapid detection of the pathogenic fungi causing blackleg of Brassica napus using a portable real-time fluorescence detector

The fungus Leptosphaeria maculans leading to Phoma stem canker (blackleg) of Brassica napus (oilseed rape, canola) produces the phytotoxin sirodesmin PL, which is responsible for major yield losses of oilseed rape worldwide. Polymerase chain reaction (PCR) remains the gold standard diagnostic tool for L. maculans, but the required expensive equipment and long time make it inappropriate for fast field test. Herein, a portable system for rapid assaying L. maculans and L. biglobosa is designed around recombinase polymerase amplification (RPA) with fluorescent probe as the signal indicator, which allowed the real-time assay of amplification performed on a portable device between 37 and 42 °C. The time needed to observe the positive reaction results is controlled within 30 min. The proposed assay system is a good choice for on-site disease screening of oilseed rape plant where rapid detection is valuable, including port quarantine, agriculture quality testing, and pathogen spreading control.

Development and evaluation of a rapid recombinase polymerase amplification assay for the detection of human enterovirus 71

Enterovirus 71 (EV71) is one of the most common pathogens of hand, foot, and mouth disease (HFMD). A rapid reverse transcription recombinase polymerase amplification (RT-RPA) assay was established to detect EV71 subgenotype C4 (EV71-C4). The 95% detection limit of the RT-RPA was 3.767 log10 genomic copies (LGC)/reaction. The specificity was 100%. In a clinical sample evaluation, this approach demonstrated sufficient clinical performance when compared with a commercial RT-qPCR diagnostic kit. Thus, the RT-RPA assay may be a promising alternative for the detection of EV71-C4.

Recombinase polymerase amplification: Basics, applications and recent advances

Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.

Rapid identification of quarantine invasiveSolanum elaeagnifoliumby real-time, isothermal recombinase polymerase amplification assay

An easy-to-implement strategy to identifySolanum elaeagnifoliumby utilizing recombinase polymerase amplification (RPA) technology was developed.