Name: dna virus detection system based on rpa-crispr/cas12a-spm and deep learning
Uploaded: 2024-05-10T12:30:00
Description: Watch this Scientific Journal Video about DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning at JoVE.com

This work is supported by the National Natural Science Foundation of China 31970752, Science, Technology, Innovation Commission of Shenzhen Municipality JCYJ20190809180003689, JSGG20200225150707332, JSGG20191129110812708, WDZC20200820173710001; Shenzhen Bay Laboratory Open Funding, SZBL2020090501004; China Postdoctoral Science Foundation 2020M680023; and General Administration of Customs of the People&#39;s Republic of China 2021HK007.

1. Processing of samples
<ol>
	<li>Take Frog Virus 3 (FV3, genera Ranavirus, family Iridoviridae), a double-stranded DNA virus. Select the major capsid (mcp) gene as the target for the detection of FV3 since it is highly conserved and usually regarded as the target for ranavirus detection. The target sequence selected is shown in Table 1. 
	NOTE: Frog Virus 3 is taken as an example in this protocol.</li>
	<li>For target DNA fragments preparation, use DNA...

<ol>
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In this method, we develop a fast, easy-to-implement, highly sensitive, sequence-specific, and POC DNA virus detection system with AI assistance. After obtaining samples, RPA is applied to amplify the target sequence, and then CRISPR/Cas12a can recognize the target DNA and release fluorescence, which enlarges the detection signal. Portable smartphone microscopy is built to take fluorescence images, and deep learning models with transfer learning are used for binary classification of the positive and negative samples' ima...

In recent years, epidemics of infectious diseases caused by different viruses have occurred frequently, including the Ebola virus disease (EVD) epidemic in 20141 and 20182, the Middle East Respiratory Syndrome (MERS) in 20153, the Zika virus disease epidemic in 20154, the Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)5 and the continuing Monkeypox caused by Monkeypox virus (MKPV) in 20226. These sudden outbreaks of epidemic infectious diseases cause a large number of deaths and bring huge economic losses and social unrest. A rapid and accurate detection system is urgently required to quickly diagnose the infection and prevent the virus&#39;s further spread.
Recently, clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins have gained worldwide attention and have shown promising results in nucleic acid detection7,8,9,10,11,12,13,14,15. The CRISPR/Cas12a protein, guided by CRISPR RNA (crRNA), binds to and cleaves the target DNA. This activity leads to the release of nonspecific single-stranded DNA (ssDNA), known as trans-cleavage, and can be utilized to enhance the detection signal for nucleic acid detection. Some traditional detection methods like polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and enzyme-linked immunosorbent assay (ELISA) are complicated, time-consuming, and costly for point-of-care (POC) detection. Our previous work successfully developed an automated, integrated, and cost-effective detection system for the African swine fever virus (ASFV) based on CRISPR/Cas12a technology. In this system, we achieved a detection limit of 1 pM within a 2-h time frame without the need for amplification. The CRISPR/Cas12a system and recombinase polymerase amplification (RPA) are combined to improve the sensitivity and specificity for trace DNA detection. Compared with other isothermal amplification techniques, RPA is simple in design and convenient in operation since it has a shorter reaction time without sophisticated temperature control equipment.
For POC detection of pathogens, instruments such as smartphone microscopy (SPM), handheld fluorimeter, or lateral flow strips are developed for the results readouts16,17,18. SPM captures images through a camera and uploads them to some mobile applications for fast data analysis. Such microscopy makes a portable, cheap, and miniatured signal acquisition system with high sensitivity and has shown advantages in detecting pathogens such as H5N1, the Zika virus, and SARS-CoV-219,20.&#160;Therefore, we build a portable SPM to catch the fluorescence signals triggered by RPA-CRISPR/Cas12a detection of the target DNA virus. The ssDNA reporter probe linking a fluorophore and a quencher will be cleaved when CRISPR/Cas12a recognizes the target DNA virus, and the fluorescence emitted by the fluorophore can be captured by SPM.
Compared to the professional software usually used to obtain the results information from the fluorescence images from SPM21,&#160;some experts use machine learning and deep learning to quantify the concentrations of virus DNA after attaining fluorescence images22, which is more time-consuming. When it comes to classifying medical images, conventional neural networks (CNNs) are often used to learn features from the raw pixelated images in an end-to-end manner23,24,25,26. Popular CNN-based deep learning models like AlexNet, DenseNet-121, and EfficientNet-B7 have been successfully applied in this field27,28. However, obtaining large data sets in specific domains can be challenging, necessitating transfer learning29,30. This approach pre-trains a deep learning model with a large dataset, and the pre-trained model is used as the starting point for a new task with a small dataset. This technique can reduce the need for large data sets, combat overfitting, and reduce training time31. Herein, we use deep learning models with transfer learning for the binary classification of the positive and negative samples&#39; fluorescence images.
In this method, we combine RPA and the CRISPR/Cas12a system for the trace detection of DNA viruses. Target DNA is amplified and recognized by RPA and CRISPR/Cas12a separately, which triggers the collateral cleavage activity of Cas12a that cleaves a fluorophore-quencher labeled DNA reporter and generalizes fluorescence. We build a portable SPM to take the fluorescent images for POC detection and develop deep learning models for binary classification. The schematic of the built POC detection system is shown in Figure 1.&#160;Without skilled operators and bulky instruments, the RPA-CRISPR/Cas12a-SPM with artificial intelligence (AI) assisted classification shows great potential for POC DNA virus detection.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64833/64833fig01.jpg" /> 
Figure 1: The schematic of the RPA-CRISPR/Cas12-SPM detection system along with AI classification for collected images. The nucleic acids of animal-derived samples are released by PINDBK. The Target DNA of the virus is amplified and recognized specifically by the RPA-CRISPR/Cas12a system. CRISPR/Cas12a bonds with crRNA and the Cas12a-crRNA complex bonds with target DNA, which triggers the collateral cleavage of CRISPR/Cas12a on the ssDNA reporter probes. The fluorophore on the reporter is released, and the fluorescence is detected by a commercialized plate reader or the SPM we build. Three different deep learning models, including AlexNet, DenseNet-121, and EfficientNet-B7 with transfer learning, are used to classify the fluorescence images. This figure is reused with permission from Lei et al.35. <a href="https://www.jove.com/files/ftp_upload/64833/64833fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>20x amplification</td>
			<td>OLYMPUS</td>
			<td>OPLN20X</td>
			<td></td>
		</tr>
		<tr>
			<td>532 nm green laser</td>
			<td>Thorlabs</td>
			<td>PL201</td>
			<td>with 0.9 mW output power</td>
		</tr>
		<tr>
			<td>535 nm cutoff wavelength</td>
			<td>chrome</td>
			<td>AT535</td>
			<td></td>
		</tr>
		<tr>
			<td>6x DNA loading buffer</td>
			<td>Thermo scientific</td>
			<td>R0611</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well black microplate</td>
			<td>Corning Incorporated</td>
			<td>3603</td>
			<td>Black with flat clear bottom</td>
		</tr>
		<tr>
			<td>Aspherical lens</td>
			<td>Lubang</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Bandpass filter</td>
			<td>SEMROCK</td>
			<td>FF01-542/27-25</td>
			<td></td>
		</tr>
		<tr>
			<td>Bsu DNA Polymerase</td>
			<td>ATG Biotechnology</td>
			<td>M103</td>
			<td>Large Fragment</td>
		</tr>
		<tr>
			<td>crRNA</td>
			<td>Sangon Biotech</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA fragments</td>
			<td>Sangon Biotech</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichroic holders</td>
			<td>Ruicage</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Dichroic mirror</td>
			<td>SEMROCK</td>
			<td>FF555-Di03-25x36</td>
			<td>with a cutoff wavelength of 535 nm</td>
		</tr>
		<tr>
			<td>E.Z.N.A Gel Extraction Kit</td>
			<td>Omega Biotek</td>
			<td>D2500-02</td>
			<td></td>
		</tr>
		<tr>
			<td>EnGen Lba Cas12a (Cpf1)</td>
			<td>New England Biolabs (Beijing) LTD</td>
			<td>M0653T</td>
			<td></td>
		</tr>
		<tr>
			<td>Filter holders</td>
			<td>Ruicage</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Fluorophore-ssDNA-Quencher reporter probes</td>
			<td>Sangon Biotech</td>
			<td>N/A</td>
			<td>TAMRA (carboxy tetramethylrhodamine) as the fluorophore at the 5 ends; BHQ2 (Black Hole Quencher-2) as the quencher at the 3 ends</td>
		</tr>
		<tr>
			<td>GP32</td>
			<td>ATG Biotechnology</td>
			<td>M104</td>
			<td></td>
		</tr>
		<tr>
			<td>ImageJ</td>
			<td>Open-source</td>
			<td>Version 1.53t 24</td>
			<td>Downloaded from https://imagej.nih.gov/ij/&#160;</td>
		</tr>
		<tr>
			<td>Microplate reader</td>
			<td>SPARK, TECAN</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Multi-Block thermal Cycler PCR instrument</td>
			<td>LongGene</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>NanoDrop 2000/2000c Spectrophotometers</td>
			<td>Thermo Scientific</td>
			<td>ND-2000</td>
			<td></td>
		</tr>
		<tr>
			<td>NEBuffer r2.1</td>
			<td>New England Biolabs (Beijing) LTD</td>
			<td>B6002S</td>
			<td>10x CRISPR/Cas12a Reaction buffer</td>
		</tr>
		<tr>
			<td>Oxygen plasma treatment&#160;</td>
			<td>Electro-Technic&#160; Products</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Pathogen Inactivate, Nucleic acid extraction-free, Direct-to-PCR Buffer with Proteinase K (PINDBK)</td>
			<td>Ebio</td>
			<td>PINDBK -25mL</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR primer pairs</td>
			<td>Sangon Biotech</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>PDMS</td>
			<td>Dow Corning</td>
			<td>Sylgard 184</td>
			<td></td>
		</tr>
		<tr>
			<td>RPA primer pairs</td>
			<td>Sangon Biotech</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Smartphone</td>
			<td>Huawei</td>
			<td>Mate10</td>
			<td></td>
		</tr>
		<tr>
			<td>Translation stages</td>
			<td>Ruicage</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Transmitted neutral density filters</td>
			<td>Thorlabs</td>
			<td>ND40A</td>
			<td></td>
		</tr>
		<tr>
			<td>Triplet achromatic lenses</td>
			<td>Thorlabs</td>
			<td>TRH127-020-A</td>
			<td></td>
		</tr>
		<tr>
			<td>UvsX</td>
			<td>ATG Biotechnology</td>
			<td>M105</td>
			<td></td>
		</tr>
		<tr>
			<td>UvsY</td>
			<td>ATG Biotechnology</td>
			<td>M106</td>
			<td></td>
		</tr>
	</tbody>
</table>

dna virus detection system based on rpa-crispr/cas12a-spm and deep learning

We report a fast, easy-to-implement, highly sensitive, sequence-specific, and point-of-care (POC) DNA virus detection system, which combines recombinase polymerase amplification (RPA) and CRISPR/Cas12a system for trace detection of DNA viruses. Target DNA is amplified and recognized by RPA and CRISPR/Cas12a separately, which triggers the collateral cleavage activity of Cas12a that cleaves a fluorophore-quencher labeled DNA reporter and generalizes fluorescence. For POC detection, portable smartphone microscopy is built to take fluorescent images. Besides, deep learning models for binary classification of positive or negative samples, achieving high accuracy, are deployed within the system. Frog virus 3 (FV3, genera Ranavirus, family Iridoviridae) was tested as an example for this DNA virus POC detection system, and the limits of detection (LoD) can achieve 10 aM within 40 min. Without skilled operators and bulky instruments, the portable and miniature RPA-CRISPR/Cas12a-SPM with artificial intelligence (AI) assisted classification shows great potential for POC DNA virus detection and can help prevent the spread of such viruses.

This method focuses on a fast, easy-to-implement, highly sensitive, and point-of-care (POC) detection system for DNA viruses. Primer pairs design for the RPA reaction and crRNA design for CRISPR/Cas12a reaction are two of the essential parts since they will affect the efficiency of the RPA-CRISPR/Cas12a reaction and influence the subsequent detection and classification.
In this method, FV3 is regarded as an example of DNA virus detection. Some RPA primer pairs for FV3 are...

Watch this Scientific Journal Video about DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning at JoVE.com

DNA Virus Detection System Based on RPA-CRISPR/Cas12a-SPM and Deep Learning

We present a protocol that combines recombinase polymerase amplification with a CRISPR/Cas12a system for trace detection of DNA viruses and builds portable smartphone microscopy with an artificial intelligence-assisted classification for point-of-care DNA virus detection.

We report a fast, easy-to-implement, highly sensitive, sequence-specific, and point-of-care (POC) DNA virus detection system, which combines recombinase ...

Our protocol introduces a rapid and highly sensitive detection system for frog virus 3. Significantly, this method enables point of care detection of DNA viruses, playing a crucial role in preventing the occurrence of pandemic diseases. The primary advantage of this technique lies in its integration of RPA with the CRISPR/Cas12a system, complimented by a portable smartphone-based microscope and AI classification.This integration significantly enhances detection efficiency and accuracy while simultaneously reducing errors attributed to human factors. To begin, add the four key RPA enzymes in the reaction buffer. Then add the pre-designed primers to the mixture.Vortex the mixture thoroughly. Add one microliter of the target DNA obtained from frog virus 3 to each RPA reaction, and vortex to mix well. Next, pipette seven microliters of 100 millimolar magnesium chloride to initiate the reaction.Incubate the mixture at 37 degrees Celsius for 30 minutes to complete the assay. Prepare the Lachnospiraceae bacterium CAS12a protein with CRISPR RNA to form functional complexes. Mix the bacterial protein and 10 X CRISPR/Cas12a reaction buffer.Now add 500 nanomolar single-stranded DNA reporter probe. Add one microliter of RPA reaction product to the CRISPR/Cas12a CRISPR RNA reaction mixture. Incubate the mixture at 37 degrees Celsius for 30 minutes.Measure the fluorescent signals with a microplate reader. For detection with a smartphone microscope, first, pipette the prepared reaction mixture onto a retreated glass slide. Then cover it with a coverslip before incubation.Place the slide on the stage of the smartphone microscope, and adjust the focal length and clarity. Capture an image to measure the fluorescent signals. Use ImageJ to measure the mean gray value of each image and the standard deviation of the mean gray value in a concentration group.Adopt the deep learning model AlexNet 33 for classification. Now use Python to reshape the input images to 224 by 224 by three channels. Finally, use a pre-trained backbone network with ImageNet dataset to extract image features.The sixth pair of primers provided the maximum amplification efficiency, and were selected. CRISPR RNA-3 proved to be the most efficient for collateral cleavage. The use of a developed detection system with selected RPA primers and CRISPR RNA resulted in significant differences between 10 aM FV3 and control.The most important point to remember is the specific CAS 12a detection step. The CRISPR RNA of the reaction can be modified or redesigned to target other DNA viruses based on CAS 12a detection. The proposed method can assist in the preliminary assessment of the target virus's quantity.Based on this, other methods like qPCR can be employed to obtain a more accurate viral load. This technique provides a preliminary attempt towards portable detection of DNA viruses. As for the frog virus 3 used in this protocol, timely detection can prompt effective protective measures, reducing losses in the breeding industry.

Research

JoVE Journal

Biology

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