This work was supported by King Abdullah University of Science and Technology through core funding and the National Term Grand Challenge (NTGC) to S.M.H.

1. Taq polymerase expression and purification
<ol>
	<li>Construct a plasmid with a cleavable hexa-histidine tag at the C-terminus of the enzyme.</li>
	<li>Transform 50 ng of the expression vector into E. coli BL21-(DE3) strain following the standard protocol38.</li>
	<li>Inoculate the transformed cells in four 6 L flasks each containing 2 L of 2YT media broth at 37 &#176;C with shaking at 170 rpm until the OD 600 of 0.8 or cell number 6.4 x 108 is reached.</li>
	<li>Induce Taq polymerase expression with 0.5 mM of isopropyl-&#946;-d-thiogalactopyranoside (IPTG) and further incubate at 16 &#176;C for 18 h with shaking.</li>
	<li>Harvest the cells by spinning them down at 4 &#176;C at 7808 x g for 10 min. Resuspend the pellets in 200 mL of an ice-cold Taq polymerase lysis buffer (Table 1) in 5 mL/g of cell pellet.</li>
	<li>Incubate the cells with lysozyme (2 mg/mL of lysis buffer) and protease inhibitors for 45 min and then pass the lysate through a cell disruptor at 30 kPsi and centrifuge at 22,040 x g for 30 min at 4 &#176;C to separate the cell debris.</li>
	<li>Heat the supernatant for 15 min at 85 &#176;C. Spin down at 95,834 x g for 1 h at 4 &#176;C. Collect the supernatant and filter it on ice using 0.45 &#181;m filter.</li>
	<li>Perform protein purification using Fast Protein Liquid Chromatography (FPLC) by first passing the sample through a Ni-NTA HP 5 mL column at 4 mL/min flow rate using Taq polymerase buffer A (Table 2; Figure 1A).</li>
	<li>Wash with 10 column volumes (CV) of Taq polymerase buffer A and 4% of Taq polymerase buffer B (Table 2). Elute the bound protein with a linear gradient using Taq polymerase Buffer B over 20 CV in a 100 mL bottle.</li>
	<li>Pass the eluent in the 100 mL bottle through a cation exchange 5 mL column at 4 mL/min using Taq polymerase buffer C (Table 2; Figure 1A).</li>
	<li>Wash with 20 CV of 100% Taq polymerase buffer C and 5% Taq polymerase buffer D (Table 2).</li>
	<li>Elute with a linear gradient using Taq polymerase buffer D (Table 2) starting from 5% to 100%.</li>
	<li>Check the eluted fractions by performing SDS-PAGE gel electrophoresis 39 followed by gel staining 40 as previously described. Briefly, take 10 &#181;L of each fraction and add an equal volume of 2x SDS loading dye. Denature the sample at 90oC for 10 min. Load the samples onto 10% SDS-PAGE gel and run the gel for 25 min at 200 V. Stain the gel using Coomassie Brilliant Blue and then de-stain.</li>
	<li>Collect all the fractions that contain purified Taq polymerase and dialyze against taq polymerase storage buffer (Table 3) at 4 &#176;C. Briefly, prepare 2 L of the storage buffer and immerse the dialysis cassette in the buffer for 2 min to hydrate. Inject the collected fractions using a needle into the dialysis cassette and leave it overnight in the dialysis buffer at 200 rpm on the stirrer.</li>
	<li>After dialysis, measure the protein concentration using a spectrophotometer, make 10 &#181;L aliquots, snap freeze in liquid nitrogen and store at -80 &#176;C. 
	&#8203;NOTE: Filter all buffers for purification using a 0.45 &#181;m filter before loading them into the FPLC system.</li>
</ol>
2. MMLV-RT expression in insect cell expression system and purification
<ol>
	<li>Bacmid DNA generation and isolation
	<ol>
		<li>Clone the sequence of MMLV-RT with a C-terminus cleavable TEV-8xHis-Strep tag as previously described41.</li>
		<li>Mix 100 ng of the expression vector into 50 &#956;L of DH10Bac cells and mix gently by tapping the tube.</li>
		<li>Incubate the cells on ice for 15 min. Heat-shock the cells for 1 min at 42 &#176;C.</li>
		<li>Immediately transfer on ice and add 400 &#956;L of S.O.C medium. Incubate at 37 &#176;C with shaking for 4 h.</li>
		<li>Plate 10 &#956;L and 15 &#956;L of the mixture on LB Agar plates containing three antibiotics; 50 &#956;g/mL Kanamycin, 10 &#956;g/mL Tetracycline and 7 &#956;g/mL Gentamicin along with 40 &#956;g/mL IPTG and 100 &#956;g/mL X-Gal for blue-white selection.</li>
		<li>Incubate the plates at 37 &#176;C for 48 h. Pick several white colonies and one blue colony as a control, and re-streak them on fresh LB agar plates containing the above antibiotics. Incubate the plates overnight at 37 &#176;C.</li>
		<li>After confirming the white phenotype, pick a couple of colonies and inoculate them into 10 mL of LB media containing 50 &#956;g/mL Kanamycin, 10 &#956;g/mL Tetracycline, and 7 &#956;g/mL Gentamicin in 50 mL tubes.</li>
		<li>Incubate the culture at 37 &#176;C with shaking at 170 rpm overnight. Pellet down the cells by spinning them down at 22,040 x g for 10 min.</li>
		<li>Decant the supernatant and resuspend the pellet in 250 &#181;L of resuspension solution from miniprep kit (this solution needs to be handled in accordance with the manufacturer&#39;s instructions), then transfer the solution to a 1.5 mL microcentrifuge tube.</li>
		<li>Add 250 &#181;L of lysis solution, gently mix and incubate for 3 min. Add 350 &#181;L of neutralizing solution, invert 2x-3x and centrifuge at 22,040 x g for 10 min.</li>
		<li>Transfer the supernatant to a fresh tube and add an equal volume of ice-cold isopropanol and incubate for 30 min at -20 &#176;C.</li>
		<li>Pellet down the precipitated DNA by spinning at 22,040 x g for 10 min. Discard the supernatant and wash the pellet with 700 &#181;L of 70% ice-cold ethanol, 2x.</li>
		<li>Remove the supernatant with a pipette without touching the pellet. Let the pellet air dry in the laminar flow hood for 5-10 min or until no liquid is seen in the tube. Dissolve the pellet in 100 &#181;L of EB buffer.</li>
	</ol>
	</li>
	<li>Bacmid transfection and virus amplification
	<ol>
		<li>P1 virus preparation
		<ol>
			<li>In a 6-well tissue culture plate, seed ~ 9 x 105 cells/well in 2 mL of insect cell culture medium.</li>
			<li>Incubate the plate for ~30 min at room temperature to allow the cells to attach.</li>
			<li>Prepare Bacmid/Fugene mix as follows: mix 1 &#181;g of Bacmid DNA and 300 &#181;L of insect cells media in one tube. In another tube, mix 8 &#181;L of transfection reagent and 300 &#181;L of insect cells media. Mix both mixtures by gentle pipetting and leave for ~30 min at room temperature for the bacmid/transfection reagent complex to form.</li>
			<li>Add bacmid complex mix (~210 &#181;L) to each well dropwise and seal the plate with a transparent film.</li>
			<li>Incubate the plate at 27 &#176;C for 3-4 days.</li>
			<li>Take the medium which that contains the virus, add FBS (final concentration 2%), filter using 0.45 &#181;m filter and store at 4&#176;C in the dark as P1 virus stock.</li>
		</ol>
		</li>
		<li>P2 virus preparation
		<ol>
			<li>Transfect 50 mL of insect cells at 2 x 106 cells/mL with 3 mL of P1 virus in a culturing flask.</li>
			<li>Incubate at 27 &#176;C with shaking at 100 rpm for 4-6 days until the percentage of dead cells reaches 25%-30%.</li>
			<li>Centrifuge at 300 x g for 10 min and collect the supernatant that contains the virus.</li>
			<li>Add FBS to a final concentration of 2%, filter through 0.45 &#181;m filter and aliquot 1 mL each and store at -80 &#176;C as P2 virus stock.</li>
		</ol>
		</li>
		<li>P3 virus preparation
		<ol>
			<li>Transfect 100 mL of insect cells at 2 x 106 cells/mL with the 2 mL of P2 virus in a culturing flask.</li>
			<li>Incubate at 27 &#176;C with shaking at 100 rpm for 3-4 days until the percentage of dead cells reaches 15%-20%.</li>
			<li>Centrifuge the cells at 300 x g for 10 min and collect the supernatant that contains the virus.</li>
			<li>Add FBS to a final concentration of 2%. Filter through a 0.45 &#181;m filter. It can be stored in the dark at 4 &#176;C for 1 month.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Expression and purification of MMLV-RT in insect cells
	<ol>
		<li>Add 5 mL of P3 virus to fresh insect cells at a density of 2 x 106 cells/mL (700 mL/2L flask) in total 6 flasks.</li>
		<li>Harvest the cells after 55-60 h of post-transfection by spinning at 7808 x g for 10 min.</li>
		<li>Resuspend the cell pellets in 200 mL of MMLV-RT lysis buffer (Table 4). Pass the lysate through a cell disruptor at 15 kPsi and centrifuge at 22,040 x g for 30 min at 4 &#176;C.</li>
		<li>Transfer the supernatant into new tubes and spin down again at 95,834 x g at 4 &#176;C for 1 h. Collect the supernatant and filter it on ice using a 0.45 &#181;m filter.</li>
		<li>Start protein purification using FPLC by first passing the sample through Ni-NTA Excel 5 mL column (Figure 1B) at 4 mL/min flow rate by using MMLV-RT buffer A (Table 5).</li>
		<li>Wash the column with 10 CV of MMLV-RT buffer A and 4% of MMLV-RT buffer B (Table 5) and elute the protein with the linear gradient of MMLV-RT buffer B over 20 CV in a 100 mL bottle.</li>
		<li>Pass the eluted sample through the Strep 5 mL column (Figure 1B) equilibrated with MMLV-RT buffer C (Table 5).</li>
		<li>Wash the column with 10 CV of 100% MMLV-RT buffer C and elute the protein with a linear gradient with 20 CV of buffer D (Table 5).</li>
		<li>Check the eluted fractions by performing SDS-PAGE as done is steps 1.13.-1.14. and collect the fractions that contain purified MMLV-RT to be dialyzed against MMLV-RT storage buffer (Table 6) at 4 &#176;C.</li>
		<li>Measure the protein concentration using Nanodrop, aliquot, snap freeze in liquid nitrogen and store at -80 &#176;C. 
		&#8203;NOTE: Filter all buffers for purification using a 0.45 &#181;m filter before loading them into the FPLC system.</li>
	</ol>
	</li>
</ol>
3. Preparation of in-house multiplex R3T one-step RT-qPCR kit components
<ol>
	<li>Buffer mix preparation
	<ol>
		<li>Prepare the 2x buffer for the RT-qPCR reaction that contains the reagents previously shown in37. Prepare all the reagents in DNase/RNase-Free water and the buffer mix stored in a -20&#160;&#176;C&#160;freezer.</li>
	</ol>
	</li>
	<li>Primer and Probe Sets and primers mixture preparation 
	NOTE: The probes and primers used are listed in Table 7. The Influenza and SARS-CoV-2 multiplexed kit contains 3 probes and 4 forward and reverse primer sets. The probes are labeled at the 5&#8242; ends using reporters 6-carboxyfluorescein (FAM) for InfA, Texas Red-XN for SARS-CoV-2 (N gene) and Yakima Yellow for InfB. The MERS-CoV and SARS-CoV-2 multiplexed kit contains 3 probes and 3 forward and reverse primer sets. The probes are also labeled at the 5&#8242; ends using reporters Texas Red-XN for MERS-CoV (ORF1a gene), VIC for MERS-CoV (UpE gene) and 6-carboxyfluorescein (FAM) SARS-CoV-2 (N gene).
	<ol>
		<li>Prepare a primer mix containing all the primers and probes listed in Table 7 with a final concentration of 6.7 &#181;M for each forward and reverse primer and 1.25 &#181;M for each probe in a 1.5 mL tube. Store the primer mix in the -20&#160;&#176;C&#160;freezer. Use elution buffer to make up the required volume.</li>
	</ol>
	</li>
	<li>Enzyme mix preparation
	<ol>
		<li>Prepare Taq polymerase (30 U/&#181;L) and MMLV-RT (60 ng/&#181;L) enzyme mix in the Taq polymerase storage buffer as shown in Table 3 to make up the required volume. Perform this step on ice and store the enzyme mix at -20 &#176;C.</li>
	</ol>
	</li>
	<li>RNA template
	<ol>
		<li>Resuspend synthetic RNAs of SARS-CoV-2, Influenza A H1N1, Influenza A H3N2, Influenza B and MERS-CoV separately in 100 &#181;L of 1x Tris-EDTA buffer (10 mM Tri-Cl and 1 mM EDTA (pH 8.0) to make a stock of 1 x 106 RNA copies/&#181;L.</li>
		<li>Mix synthetic RNAs for RT-qPCR in the following configurations: 1) SARS-CoV-2, Influenza A and Influenza B by adding 5 &#181;L of each virus stock to 50 &#181;L volume to make 1 x 105 RNA copies/&#181;L; 2) SARS-CoV-2, MERS-CoV by adding 5 &#181;L of each virus stock to 50 &#181;L volume to make 1 x 105 RNA copies/&#181;L. Make 10-fold serial dilutions of each synthetic RNA mixture ranging from 1 x 105 RNA copies/&#181;L to 10 RNA copies/&#181;L. 
		&#8203;NOTE: Make sure to use ice-cold DNase/RNase-Free water to prepare the serial dilution of the templates.</li>
	</ol>
	</li>
</ol>
4. In-house multiplexed SARS-CoV-2, Influenza A, Influenza B and SARS-CoV-2, MERS-CoV one-step RT-qPCR test
NOTE: Disinfect workstation surfaces and use a 96-well plate template to plan the PCR plate layout.
<ol>
	<li>Preparation of 96-well plate
	<ol>
		<li>Thaw 2x buffer and primer mix. Keep enzyme mix on ice.</li>
		<li>To each well, add 10 &#181;L of 2x buffer mix, 1.5 &#181;L of the primer mix, 1 &#181;L of enzyme mix, 6.5 &#181;L of DNase/RNase-Free Water, and 1 &#181;L of corresponding RNA mixture that needs to be tested. The final volume in each well is 20 &#181;L. Please refer to the prepared layout for help with this step. 
		NOTE: It is recommended to make a master mix based on the number of reactions that contain all the reagents except the RNA sample to avoid pipetting bias. In addition, perform the reactions in duplicate or triplicate to avoid technical errors.</li>
		<li>Seal the plate with an adhesive PCR plate seal and centrifuge briefly for 1 min to collect all liquid at the bottom of the plate. Ensure that each well has the same volume of liquid and is free of bubbles before transferring the samples to the qPCR machine. 
		NOTE: All the PCR reactions need to be set up on ice.</li>
	</ol>
	</li>
	<li>PCR program
	<ol>
		<li>Open the real-time qPCR machine program and choose the following experimental properties: 
		The block type: Fast 96-well (0.1 mL) 
		Experiment setup: Standard curve 
		Reagents: TaqMan reagents 
		&#8203;Run properties: Standard.</li>
		<li>Define all the gene targets and their reporter dye as presented in Table 7. In addition, define sample names for each reaction to be tested for easier analysis of the amplification curves.</li>
		<li>Assign targets and samples to the program&#39;s plate layout based on the 96-well plate.</li>
		<li>Set the following cycle program in the PCR instrument as follows: 
		55&#160;&#176;C for 10 min 
		40&#160;cycles: 94&#160;&#176;C for 1 min 
		94 &#176;C for 10 s 
		68 &#176;C for 10 s 
		&#8203;68&#160;&#176;C for 20 s; here acquire fluorescence.</li>
		<li>Transfer the plate to the real-time qPCR machine and place it in the holder ensuring the correct orientation of the plate and start the run.</li>
		<li>Choose the file location to save the experimental data.</li>
	</ol>
	</li>
	<li>Data analysis
	<ol>
		<li>It is essential to first examine the amplification plots produced by the qPCR program. Analyze the limit of detection to assess the minimum RNA concentration that can be detected.</li>
		<li>Plot the log of RNA copy number on the x-axis and the corresponding average Ct value on the y-axis to assess the sensitivity of the assay. The slope and the R2 indicate the reliability and efficiency of the reaction.</li>
	</ol>
	</li>
</ol>

Multiplex RT-qPCR Assay for Respiratory Virus Detection

The authors declare that they have no competing financial interests.

There is a heavy economic burden on the healthcare system worldwide resulting from the high infection and mortality rates due to the spread of common respiratory viruses such as SARS-CoV-2, Influenza A/B and MERS-CoV variants12,19,20. Motivated by the sense of responsibility towards alleviating this burden, we realized the need for a quick, precise and accessible diagnostic assay such as RT-qPCR to distinguish between these comm...

The pandemic of the ongoing coronavirus disease 2019 (COVID-19) is caused by the novel coronavirus known as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)1. Due to SAR-CoV-2&#39;s strong contagiousness and capacity for rapid transmission, the COVID-19 pandemic emerged in Wuhan City, China, and spread quickly throughout the world. This eventually led to the start of respiratory distress signs and even death2,3,4. COVID-19 has been declared a pandemic in more than 213 countries, expecting a steep increase in the number of confirmed cases, as evidenced by the papers published by different research studies3,5. COVID-19 is transmitted primarily by small respiratory droplets that infected individuals release into the environment and then get exposed to vulnerable individuals through inhalation or close contact with contaminated surfaces. When these droplets come into contact with the mucosa of the eyes, mouth, or nose, a person may become infected6. Statistics released by the World Health Organization (WHO) show that there have been more than 76 million confirmed cases of the pandemic worldwide, with a staggering 7 million deaths7. Thus, the United Nations classified the pandemic caused by COVID-19 disease as a disaster because of its direct impact on the lives of billions of people around the globe and had far-reaching economic, environmental, and social effects.
Public health initiatives including thorough testing, early detection, contact tracing, and case isolation have all been shown to be crucial in keeping this pandemic under control8,9,10,11. The winter months will increase the circulation of other respiratory viruses like Influenza A and B with COVID-19-like symptoms making it difficult to identify, track down, and isolate COVID-19 instances early on. Every year, Influenza A and B outbreak starts in the late fall or early January with a predictable seasonality12. Numerous epidemiological traits are shared by SARS-CoV-2 and Influenza viruses. Besides, sharing similarities in the susceptible populations which include children, the elderly, immunocompromised, and individuals with chronic comorbidities such as asthma, chronic obstructive pulmonary disease, cardiac and renal failure, or diabetes12,13. These viruses not only share vulnerable populations but also transmission routes of contact and respiratory droplets14. It is anticipated that patients may likely contract more than one of these respiratory viruses as flu season approaches14. For that, the screening of SARS-CoV-2 and the Influenza viruses needs to be done on symptomatic patients before they are isolated. Running separate tests for the three viruses (SARS-CoV-2, Influenza A, and Influenza B) is not possible due to the global lack of resources for nucleic acid extraction and diagnostics. In order to screen them all in one reaction, a method or test needs to be developed.
Middle East respiratory syndrome (MERS)-CoV is a human coronavirus (CoV) family member. The first MERS-CoV virus isolates came from a hospitalized patient in Saudi Arabia who had died in September 2012 due to acute respiratory issues15. There is evidence that suggests that a prominent reservoir host for MERS-CoV is dromedary camels. It has been proven that viruses from infected dromedary camels are zoonotic and thus can infect humans16,17. Humans infected with this virus can spread it to others through close contact18. As of January 26th,&#160;2018, there had been 2143 laboratory-confirmed cases of MERS-CoV infection including 750 deaths globally19. The most typical MERS-CoV symptoms are coughing, fever, and shortness of breath. MERS-CoV infections have also been reported to exhibit pneumonia, diarrhea and gastrointestinal sickness symptoms20. Currently, no commercial vaccine or specific treatment for MERS-CoV is available. Therefore, prompt and precise diagnosis is essential for preventing the widespread MERS-CoV outbreaks and differentiating MERS-CoV from SARS-CoV-2 disease.
To date, many approaches have been proposed to detect these viruses such as multiplex RT-PCR21,22,23,24,25, CRISPR/Cas1226,27, CRISPR/Cas928, and CRISPR/Cas329, lateral flow immunoassay30, paper-based biomolecular sensors31, SHERLOCK testing in one pot32, DNA aptamer33, loop-mediated isothermal amplification (LAMP)19,34, etc. Each of the aforementioned methods has unique benefits and drawbacks in terms of sensitivity and specificity. Among these methods, the nucleic acid amplification-based test: multiplex qRT-PCR, is the most common and is considered to be the gold standard for the diagnosis of SARS-CoV-2, Influenza A, Influenza B, and MERS-CoV.
In this study, we designed and assessed various primer combinations and probes for the effective, accurate, and simultaneous detection of SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV utilizing standard twist synthetic viral RNAs. The multiplexed assays developed for either MERS-CoV or SARS-CoV-2 target genes are recommended by the World Health Organization (WHO). These genes generally encode proteins and complexes that contribute to the formation of a replication/transcription complex (RTC)35 such as the region within the open reading frame 1a (ORF1a) that is used for MERS-CoV assay. In addition, structural proteins are encoded by the genes utilized in diagnostic assays such as the upstream region of envelope gene (upE) and nucleocapsid gene (N) which are used for MERS-CoV and SARS-Cov-2 assays, respectively35,36. We used in-house R3T one-step RT-qPCR kit to establish the RT-qPCR for the detection of viruses37. Virus detection, sensitivity, specificity, and dynamic range of our R3T one-step RT-qPCR kit and primer sets were tested and evaluated using 10-fold serial dilutions of the standard twist synthetic RNAs. The lowest practical detection limit was approximately 10 transcripts copies per reaction. As a result, the in-house R3T one-step RT-qPCR kit and primer/probe sets can be successfully used and implemented for routine simultaneous diagnosis of SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV.

<table><tbody><tr><td>0.45 &amp;mu;m filter cups</td><td>Thermo Scientific</td><td>291-4545</td><td></td></tr><tr><td>10X Tris-Glycine SDS running buffer</td><td>Novex</td><td>LC2675</td><td></td></tr><tr><td>6-well tissue culturing plates</td><td>Corning</td><td>353046</td><td></td></tr><tr><td>Ammonium sulfate</td><td>Fisher Scientific</td><td>A701-3</td><td></td></tr><tr><td>Ampicillin</td><td>Corning</td><td>61-238-RH</td><td></td></tr><tr><td>Cation exchange (HiTrap SP HP) 5 mL</td><td>Cytiva</td><td>17-1152-01</td><td></td></tr><tr><td>D-(+)-Biotin, 98+%</td><td>Thermo Scientific</td><td>A14207.60</td><td></td></tr><tr><td>DH10Bac competent cells</td><td>Fisher Scientific</td><td>10361012</td><td></td></tr><tr><td>Dialysis bag (Snakeskin 10,000 MWC)</td><td>Thermo Scientific</td><td>68100</td><td></td></tr><tr><td>Dithiothreitol (DTT)</td><td>Thermo Scientific</td><td>R0862</td><td></td></tr><tr><td>Dnase/Rnase Free Distilled Water</td><td>Ambion</td><td>AM9930</td><td></td></tr><tr><td>dNTPs</td><td>Thermo Scientific</td><td>R0192</td><td></td></tr><tr><td>&lt;em&gt;E. coli&lt;/em&gt; BL21(DE3) competent cells</td><td>Invitrogen</td><td>C600003</td><td></td></tr><tr><td>EDTA</td><td>Fisher Scientific</td><td>BP120-1</td><td></td></tr><tr><td>Elution Buffer</td><td>Qiagen</td><td>19086</td><td></td></tr><tr><td>ESF 921 insect cell culture medium (Insect cells media)</td><td>Expression Systems</td><td>96-001-01</td><td></td></tr><tr><td>FBS Solution</td><td>Gibco</td><td>A38400-01</td><td></td></tr><tr><td>Fugene (transfection reagent)</td><td>Promega</td><td>E2311</td><td></td></tr><tr><td>Gentamicin</td><td>Fisher Scientific</td><td>15750060</td><td></td></tr><tr><td>Glycerol</td><td>Sigma Aldrich</td><td>G5516-500</td><td></td></tr><tr><td>IGEPAL CA-630</td><td>Sigma Aldrich</td><td>I8896-100ml</td><td></td></tr><tr><td>Imidazole</td><td>Sigma Aldrich</td><td>56750-1Kg</td><td></td></tr><tr><td>Influenza A (H1N1) synthetic RNA</td><td>Twist Bioscience</td><td>103001</td><td></td></tr><tr><td>Influenza A (H3N2)&amp;nbsp; synthetic RNA</td><td>Twist Bioscience</td><td>103002</td><td></td></tr><tr><td>Influenza B synthetic RNA</td><td>Twist Bioscience</td><td>103003</td><td></td></tr><tr><td>IPTG</td><td>Gold Biotechnology</td><td>I3481C100</td><td></td></tr><tr><td>Kanamycin</td><td>Gibco</td><td>11815-032</td><td></td></tr><tr><td>LB Agar</td><td>Fisher Scientific</td><td>BP1425-500</td><td></td></tr><tr><td>LB Broth media</td><td>Fisher Scientific</td><td>BP1426-500</td><td></td></tr><tr><td>Lysozyme</td><td>Sigma Aldrich</td><td>L6876-10G</td><td></td></tr><tr><td>Magnesium Chloride</td><td>Sigma Aldrich</td><td>13152-1Kg</td><td></td></tr><tr><td>MERS-CoV synthetic RNA</td><td>Twist Bioscience</td><td>103015</td><td></td></tr><tr><td>MicroAmp Fast Optical 96-well Reaction plates with Barcode (0.1 mL)</td><td>Applied Biosystems</td><td>10310855</td><td></td></tr><tr><td>Mini- PROTEAN TGX Precast Gel</td><td>Bio-Rad</td><td>456-1093</td><td></td></tr><tr><td>Miniprep kit</td><td>Qiagen</td><td>27106</td><td></td></tr><tr><td>Ni-NTA Excel (HisTrap Excel) 5 mL</td><td>Cytiva</td><td>17-3712-06</td><td></td></tr><tr><td>Ni-NTA HP (HisTrap HP) 5 mL</td><td>Cytiva</td><td>17-5248-02</td><td></td></tr><tr><td>Optical Adhesice Covers (PCR Compatible,DNA/Rnase/PCR Inhibitors Free</td><td>Applied Biosystems</td><td>4311971</td><td></td></tr><tr><td>Potassium Chloride</td><td>Fisher Bioreagents</td><td>BP366-1</td><td></td></tr><tr><td>Primers and Probes</td><td>Integrated DNA Technologies, Inc.</td><td></td><td></td></tr><tr><td>Protease Inhibitor Mini tablets EDTA-Free</td><td>Thermo Scientific</td><td>A32955</td><td></td></tr><tr><td>Protein marker</td><td>Fermentas</td><td>26616</td><td></td></tr><tr><td>RT-qPCR machine (QuantStudio 7 Flex)</td><td>Applied Biosystems</td><td></td><td></td></tr><tr><td>S.O.C medium</td><td>Fisher Scientific</td><td>15544034</td><td></td></tr><tr><td>SARS-CoV-+A2:C442 synthetic RNA</td><td>Twist Bioscience</td><td>102024</td><td></td></tr><tr><td>Sf9 insect cells</td><td>Gibco</td><td>A35243</td><td></td></tr><tr><td>Sodium Chloride</td><td>Sigma Aldrich</td><td>S3014-1Kg</td><td></td></tr><tr><td>StrepTrap XT 5 mL</td><td>Cytiva</td><td>29401323</td><td></td></tr><tr><td>Tetracycline</td><td>IBI Scientific</td><td>IB02200</td><td></td></tr><tr><td>Tris Base Molecular Biology Grade</td><td>Promega</td><td>H5135</td><td></td></tr><tr><td>Tris-HCl</td><td>Affymetrix</td><td>22676</td><td></td></tr><tr><td>Tween 20</td><td>Sigma Aldrich</td><td>P1379-100ml</td><td></td></tr><tr><td>X-Gal</td><td>Invitrogen</td><td>B1690</td><td></td></tr></tbody></table>

development of multiplex real-time rt-qpcr assays for the detection of sars-cov-2, influenza a/b, and mers-cov

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) is a serious threat to the general public&#39;s health. During influenza seasons, the spread of SARS-CoV-2 and other respiratory viruses may cause a population-wide burden of respiratory disease that is difficult to manage. For that, the respiratory viruses SARS-CoV-2, Influenza A, Influenza B, and Middle East respiratory syndrome (MERS-CoV) will need to be carefully watched over in the upcoming fall and winter seasons, particularly in the case of SARS-CoV-2, Influenza A, and Influenza B, which share similar epidemiological factors like susceptible populations, mode of transmission, and clinical syndromes. Without target-specific assays, it can be challenging to differentiate among cases of these viruses owing to their similarities. Accordingly, a sensitive and targeted multiplex assay that can easily differentiate between these viral targets will be useful for healthcare practitioners. In this study, we developed a real-time reverse transcriptase-PCR-based assay utilizing an in-house developed R3T one-step RT-qPCR kit for simultaneous detection of SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV. With as few as 10 copies of their synthetic RNAs, we can successfully identify SARS-CoV-2, Influenza A, Influenza B, and MERS-CoV targets simultaneously with 100% specificity. This assay is found to be accurate, reliable, simple, sensitive, and specific. The developed method can be used as an optimized SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV diagnostic assay in hospitals, medical centers, and diagnostic laboratories as well as for research purposes.

In recent years, there have been significant advances in the diagnostic approach for detecting common respiratory viruses using PCR approaches21,22,23,24,25. However, despite these advancements, the multiplexed approach, which allows for detecting multiple viruses in a single test, has not been widely implemented, particularly in the RT-qPCR platform. This met...

Watch this Scientific Journal Video about Advancements in Multiplex Detection of Respiratory Viruses at JoVE.com

Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses 

We present two probe-based in-house one-step RT-qPCR kits for common respiratory viruses. The first assay is for SARS-CoV-2 (N), Influenza A (H1N1 and H3N2), and Influenza B. The second is for SARS-Cov-2 (N) and MERS (UpE and ORF1a). These assays can be successfully implemented in any specialized laboratory.

Development of Multiplex Real-Time RT-qPCR Assays for the Detection of SARS-CoV-2, Influenza A/B, and MERS-CoV

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) is a serious threat to the general ...

development-multiplex-real-time-rt-qpcr-assays-for-detection-sars-cov

Research

JoVE Journal

Biology

1.1K Views.  King Abdullah University of Science and Technology (KAUST). We present two probe-based in-house one-step RT-qPCR kits for common respiratory viruses. The first assay is for SARS-CoV-2 (N), Influenza A (H1N1 and H3N2), and Influenza B. The second is for SARS-Cov-2 (N) and MERS (UpE and ORF1a). These assays can be successfully implemented in any specialized laboratory. 

Video: Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses 

Multiplexed Isothermal Amplification Based Diagnostic Platform to Detect Zika, Chikungunya, and Dengue 1

Zika, dengue, and chikungunya viruses are transmitted by mosquitoes, causing diseases with similar patient symptoms. However, they have different downstream patient-to-patient transmission potentials, and require very different patient treatments. Thus, recent Zika outbreaks make it urgent to develop tools that rapidly discriminate these viruses in patients and trapped mosquitoes, to select the correct patient treatment, and to understand and manage their epidemiology in real time.
Unfortunately, current diagnostic tests, including those receiving 2016 emergency use authorizations and fast-track status, detect viral RNA by reverse transcription polymerase chain reaction (RT-PCR), which requires instrumentation, trained users, and considerable sample preparation. Thus, they must be sent to &#34;approved&#34; reference laboratories, requiring time. Indeed, in August 2016, the Center for Disease Control (CDC) was asking pregnant women who had been bitten by a mosquito and developed a Zika-indicating rash to wait an unacceptable 2 to 4 weeks before learning whether they were infected. We very much need tests that can be done on site, with few resources, and by trained but not necessarily licensed personnel.
This video demonstrates an assay that meets these specifications, working with urine or serum (for patients) or crushed mosquito carcasses (for environmental surveillance), all without much sample preparation. Mosquito carcasses are captured on paper carrying quaternary ammonium groups (Q-paper) followed by ammonia treatment to manage biohazards. These are then directly, without RNA isolation, put into assay tubes containing freeze-dried reagents that need no chain of refrigeration. A modified form of reverse transcription loop-mediated isothermal amplification with target-specific fluorescently tagged displaceable probes produces readout, in 30 min, as a three-color fluorescence signal. This is visualized with a handheld, battery-powered device with an orange filter. Forward contamination is prevented with sealed tubes, and the use of thermolabile uracil DNA glycosylase (UDG) in the presence of dUTP in the amplification mixture.

Current multiplexed diagnostics to detect Zika, chikungunya, and dengue viruses require complex sample preparation and expensive instrumentation, and are difficult to use in low resource environments. We show a diagnostic that uses isothermal amplification with target-specific strand displaceable probes to detect and differentiate these viruses with high sensitivity and specificity.

Zika, dengue, and chikungunya viruses are transmitted by mosquitoes, causing diseases with similar patient symptoms. However, they have different ...

Biochemistry

Microfluidic Chip Fabrication and Method to Detect Influenza

Fast and effective diagnostics play an important role in controlling infectious disease by enabling effective patient management and treatment. Here, we present an integrated microfluidic thermoplastic chip with the ability to amplify influenza A virus in patient nasopharyngeal (NP) swabs and aspirates. Upon loading the patient sample, the microfluidic device sequentially carries out on-chip cell lysis, RNA purification and concentration steps within the solid phase extraction (SPE), reverse transcription (RT) and polymerase chain reaction (PCR) in RT-PCR chambers, respectively. End-point detection is performed using an off-chip Bioanalyzer (Agilent Technologies, Santa Clara, CA). For peripherals, we used a single syringe pump to drive reagent and samples, while two thin film heaters were used as the heat sources for the RT and PCR chambers. The chip is designed to be single layer and suitable for high throughput manufacturing to reduce the fabrication time and cost. The microfluidic chip provides a platform to analyze a wide variety of virus and bacteria, limited only by changes in reagent design needed to detect new pathogens of interest.

An integrated microfluidic thermoplastic chip has been developed for use as a molecular diagnostic. The chip performs nucleic acid extraction, reverse transcriptase, and PCR. Methods for fabricating and running the chip are described.

Fast  and effective diagnostics play an important role in controlling infectious  disease by enabling effective patient management and treatment. Here, we ...

Bioengineering

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Wastewater-based epidemiology has emerged as a promising and efficacious surveillance system for SARS-CoV-2 and other infectious diseases in many nations. The process typically involves wastewater concentration, nucleic acid extraction, amplification of selected genomic segments, and detection and quantification of the amplified genomic segment. This methodology can similarly be leveraged to detect and quantify infectious agents, such as SARS-CoV-2, in air samples. Initially, SARS-CoV-2 was presumed to spread primarily through close personal contact with droplets generated by an infected individual while speaking, sneezing, coughing, singing, or breathing. However, a growing number of studies have reported the presence of SARS-CoV-2 RNA in the air of healthcare facilities, establishing airborne transmission as a viable route for the virus. This study presents a composite of established protocols to facilitate environmental detection, quantification, and sequencing of viruses from both wastewater and air samples.

This protocol aims to quantify SARS-CoV-2 RNA in wastewater and air samples to be used for wastewater-based epidemiology studies and to assess the exposure risk to SARS-CoV-2 in indoor and outdoor aerosols. This protocol also describes a tiled amplicon long-template sequencing approach for SARS-CoV-2 whole genome characterization.

Wastewater-based epidemiology has emerged as a promising and efficacious surveillance system for SARS-CoV-2 and other infectious diseases in many nations. ...

Environment

High-throughput Detection of Respiratory Pathogens in Animal Specimens by Nanoscale PCR

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of combining reactions together. We designed and evaluated a panel based on this principle to rapidly identify the presence of common disease agents in dogs and horses with acute respiratory illness. This manuscript describes a nanoscale diagnostic PCR workflow for sample preparation, amplification, and analysis of target pathogen sequences, focusing on procedures that are different from microliter scale reactions. In the respiratory panel presented, 18 assays were each set up in triplicate, accommodating up to 48 samples per plate. A universal extraction and pre-amplification workflow was optimized for high-throughput sample preparation to accommodate multiple matrices and DNA and RNA based pathogens. Representative data are presented for one RNA target (influenza A matrix) and one DNA target (equine herpesvirus 1). The ability to quickly and accurately test for a comprehensive, syndrome-based group of pathogens is a valuable tool for improving efficiency and ergonomics of diagnostic testing and for acute respiratory disease diagnosis and management.

High-throughput testing of DNA and RNA based pathogens by nanoscale PCR is described using a syndromic canine and equine respiratory PCR panel.

Nanoliter scale real-time PCR uses spatial multiplexing to allow multiple assays to be run in parallel on a single plate without the typical drawbacks of ...

Immunology and Infection

High-Performance Graphene-Modified Sensing Chip for SARS-CoV-2 Detection

This sensing prototype model involves the development of a reusable, twofold graphene oxide (GrO)-glazed double inter-digitated capacitive (DIDC) detecting chip for detecting severe acute respiratory syndrome coronavirus 2 virus (SARS-CoV-2) specifically and rapidly. The fabricated DIDC comprises a Ti/Pt-containing glass substrate glazed with graphene oxide (GrO), which is further chemically modified with EDC-NHS to immobilize antibodies (Abs) hostile to SARS-CoV-2 based on the spike (S1) protein of the virus. The results of insightful investigations showed that GrO gave an ideal engineered surface for Ab immobilization and enhanced the capacitance to allow higher sensitivity and low sensing limits. These tunable elements helped accomplish a wide sensing range (1.0 mg/mL to 1.0 fg/mL), a minimum sensing limit of 1 fg/mL, high responsiveness and good linearity of 18.56 nF/g, and a fast reaction time of 3 s. Besides, in terms of developing financially viable point-of-care (POC) testing frameworks, the reusability of the GrO-DIDC biochip in this study is good. Significantly, the biochip is specific against blood-borne antigens and is stable for up to 10 days at 5 &#176;C. Due to its compactness, this scaled-down biosensor has the potential for POC diagnostics of COVID-19 infection. This system can also detect other severe viral diseases, although an approval step utilizing other virus examples is under development.

The present protocol describes the fabrication of low-cost biosensing prototypes based on useful nanosystems for accurately detecting viral proteins (at the Fg level). Such a tiny sensor platform allows for point-of-care applications that can be integrated with the Internet of Medical Things (IoMT) to meet telemedicine objectives.

This sensing prototype model involves the development of a reusable, twofold graphene oxide (GrO)-glazed double inter-digitated capacitive (DIDC) ...

A Rapid, Multiplex Dual Reporter IgG and IgM SARS-CoV-2 Neutralization Assay for a Multiplexed Bead-Based Flow Analysis System

The COVID-19 pandemic has underscored the need for rapid high-throughput methods for sensitive and specific serological detection of infection with novel pathogens, such as SARS-CoV-2. Multiplex serological testing can be particularly useful because it can simultaneously analyze antibodies to multiple antigens that optimizes pathogen coverage, and controls for variability in the organism and the individual host response. Here we describe a SARS-CoV-2 IgG 3-plex fluorescent microsphere-based assay that can detect both IgM and IgG antibodies to three major SARS-CoV-2 antigens-the spike (S) protein, spike angiotensin-converting enzyme-2 (ACE2) receptor-binding domain (RBD), and nucleocapsid (Nc). The assay was shown to have comparable performance to a SARS-CoV-2 reference assay for IgG in serum obtained at &#8805;21 days from symptom onset but had higher sensitivity with samples collected at &#8804;5 days from symptom onset. Further, using soluble ACE2 in a neutralization assay format, inhibition of antibody binding was demonstrated for S and RBD.

A flow analysis system for bead-based multiplexed assays which provides a two-reporter readout was used for the development of multiplex serological and antibody neutralization assays that can simultaneously measure neutralizing IgG and IgM antibodies for SARS-CoV-2.

The COVID-19 pandemic has underscored the need for rapid high-throughput methods for sensitive and specific serological detection of infection with novel ...

Efficient SARS-CoV-2 Quantitative Reverse Transcriptase PCR Saliva Diagnostic Strategy utilizing Open-Source Pipetting Robots

The emergence of the recent SARS-CoV-2 global health crisis introduced key challenges for epidemiological research and clinical testing. Characterized by a high rate of transmission and low mortality, the COVID-19 pandemic necessitated accurate and efficient diagnostic testing, particularly in closed populations such as residential universities. Initial availability of nucleic acid testing, like nasopharyngeal swabs, was limited due to supply chain pressure which also delayed reporting of test results. Saliva-based reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) testing has shown to be comparable in sensitivity and specificity to other testing methods, and saliva collection is less physically invasive to participants. Consequently, we developed a multiplex RT-qPCR diagnostic assay for population surveillance of Clemson University and the surrounding community. The assay utilized open-source liquid handling robots and thermocyclers instead of complex clinical automation systems to optimize workflow and system flexibility. Automation of saliva-based RT-qPCR enables rapid and accurate detection of a wide range of viral RNA concentrations for both large- and small-scale testing demands. The average turnaround for the automated system was &#60; 9 h for 95% of samples and &#60; 24 h for 99% of samples. The cost for a single test was $2.80 when all reagents were purchased in bulk quantities.

The protocol describes a SARS-CoV-2 diagnostic method that utilizes open-source automation to perform RT-qPCR molecular testing of saliva samples. This scalable approach can be applied to clinical public health surveillance as well as to increase the capacity of smaller university laboratories.

The emergence of the recent SARS-CoV-2 global health crisis introduced key challenges for epidemiological research and clinical testing. Characterized by ...

Analysis of SARS-CoV-2 Using Dual-Reporter and Multiplex Technology

Profiling of Surface Protein Epitopes on Viral Particles by Multiplex Dual-Reporter Strategy

Membrane proteins on enveloped viruses play an important role in many biological functions involving virus attachment to target cell receptors, fusion of viral particles to host cells, host-virus interactions, and disease pathogenesis. Furthermore, viral membrane proteins on virus particles and presented on host cell surfaces have proven to be excellent targets for antivirals and vaccines. Here, we describe a protocol to investigate surface proteins on intact severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles using the dual-reporter flow cytometric system. The assay exploits multiplex technology to obtain a triple detection of viral particles by three independent affinity reactions. Magnetic beads conjugated to recombinant human angiotensin-converting enzyme-2 (ACE2) were used to capture viral particles from the supernatant of cells infected with SARS-CoV-2. Then, two detection reagents labeled with R-phycoerythrin (PE) or Brilliant Violet 421 (BV421) were applied simultaneously. As a proof-of-concept, antibody fragments targeting different epitopes of the SARS-CoV-2 surface protein Spike (S1) were used. The detection of viral particles by three independent affinity reactions provides strong specificity and confirms the capture of intact virus particles. Dose-dependency curves of SARS-CoV-2 infected cell supernatant were generated with replicate coefficient variances (mean/SD) &#706;14%. Good assay performance in both channels confirmed that two virus surface target protein epitopes are detectable in parallel. The protocol described here could be applied for (i) high-multiplex, high-throughput profiling of surface proteins expressed on enveloped viruses; ii) detection of active intact viral particles; and (iii) assessment of specificity and affinity of antibodies and antiviral drugs for surface epitopes of viral antigens.The application can be potentially extended to any type of extracellular vesicles and bioparticles, exposing surface antigens in body fluids or other liquid matrices.

Author Spotlight: Advancing Antiviral Strategies Through Novel Immunocapture and Mass Spectrometry Techniques

Here, we describe a newly developed multiplex fluorescent immunoassay that uses a dual-reporter flow cytometric system to concurrently detect two unique spike protein epitopes on intact severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viral particles that had been captured by angiotensin-converting enzyme-2-coupled magnetic microspheres.

Membrane proteins on enveloped viruses play an important role in many biological functions involving virus attachment to target cell receptors, fusion of ...

Dynamic Monitoring of Seroconversion using a Multianalyte Immunobead Assay for Covid-19

Multiplex technologies for interrogating multiple biomarkers in concert have existed for several decades; however, methods to evaluate multiple epitopes on the same analyte remain limited. This report describes the development and optimization of a multiplexed immunobead assay for serological testing of common immunoglobulin isotypes (e.g., IgA, IgM, and IgG) associated with an immune response to SARS-CoV-2 infection or vaccination. Assays were accomplished using a flow-based, multiplex fluorescent reader with dual-channel capability. Optimizations focused on analyte capture time, detection antibody concentration, and detection antibody incubation time. Analytical assay performance characteristics (e.g., assay range (including lower and upper limits of quantitation); and intra- and inter-assay precision) were established for either IgG/IgM or IgA/IgM serotype combination in tandem using the 'dual channel' mode. Analyte capture times of 30 min for IgG, 60 min for IgM, and 120 min for IgA were suitable for most applications, providing a balance of assay performance and throughput. Optimal detection antibody incubations at 4 &#181;g/mL for 30 min was observed and are recommended for general applications, given the overall excellent precision (percent coefficient of variance (%CV) &#8804; 20%) and sensitivity values observed. The dynamic range for the IgG isotype spanned several orders of magnitude for each assay (Spike S1, Nucleocapsid, and Membrane glycoproteins), which supports robust titer evaluations at a 1:500 dilution factor for clinical applications. Finally, the optimized protocol was applied to monitoring Spike S1 seroconversion for subjects (n = 4) that completed a SARS-CoV-2 vaccine regimen. Within this cohort, Spike S1 IgG levels were observed to reach maximum titers at 14 days following second dose administration, at a much higher (~40-fold) signal intensity than either IgM or IgA isotypes. Interestingly, we observed highly variable Spike S1 IgG titer decay rates that were largely subject-dependent were observed, which will be the topic of future studies.

This article describes a convenient method for monitoring dynamic changes in antibody titers for two immunoglobulin isotypes concurrently (either IgA, IgM, or IgG) resulting from an immune response to SARS-CoV-2 infection or vaccination. This 'Multianalyte Covid-19 Immune Response Panel' employs three indirect immunoassays built on coded microspheres that are read using a flow-based multiplex reader with 'dual-channel' capability.

Multiplex technologies for interrogating multiple biomarkers in concert have existed for several decades; however, methods to evaluate multiple epitopes ...

Medicine

Two-Step Reverse Transcription Droplet Digital PCR Protocols for SARS-CoV-2 Detection and Quantification

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) is the gold standard for SARS-CoV-2 diagnosis as no permanent solution is available. However effective this technique may be, research has emerged showing its limitations in detection and diagnosis especially when it comes to low abundant targets. In contrast, droplet digital PCR (ddPCR), a recent emerging technology with superior advantages over qPCR, has been shown to overcome the challenges of RT-qPCR in diagnosis of SARS-CoV-2 from low abundant target samples. Prospectively, in this article, the capabilities of RT-ddPCR are further expanded by showing steps on how to develop simplex, duplex, triplex probe mix, and quadruplex assays using a two-color detection system. Using primers and probes targeting specific sites of the SARS-CoV-2 genome (N, ORF1ab, RPP30, and RBD2), the development of these assays is shown to be possible. Additionally, step by step detailed protocols, notes, and suggestions on how to improve the assays workflow and analyze data are provided. Adapting this workflow in future works will ensure that the maximum number of targets can be sensitively detected in a small sample significantly improving on cost and sample throughput.

This work summarizes steps on developing different assays for SARS-CoV-2 detection using a two color ddPCR system. The steps are elaborate and notes have been included on how to improve the assays and experiment performance. These assays may be used for multiple SARS-CoV-2 RT-ddPCR applications.

Diagnosis of the ongoing SARS-CoV-2 pandemic is a priority for all countries across the globe. Currently, reverse transcription quantitative PCR (RT-qPCR) ...