Name: VirWaTest, A Point-of-Use Method for the Detection of Viruses in Water Samples (Video) | JoVE Journal
Uploaded: 2019-05-11T14:00:00.000+00:00
Duration: 13 min 32 s
Description: Learn VirWaTest, a portable point-of-use method for detecting enteric viruses in water samples. This cost-effective technique improves water safety monitoring in humanitarian contexts.

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5 minutes

VirWaTest was a research project funded by the HIF (Humanitarian Innovation Funds) program of ELHRA (Enhancing Learning &#38; Research for Humanitarian Assistance). The authors acknowledge the WASH teams who kindly collaborated in this study. The analysis of samples in Ecuador was funded by Oxfam Ecuador and Direcci&#243;n de Investigaciones de la Universidad de las Americas (AMB.BRT.17.01). S. Bofill-Mas is a Serra-Hunter fellow at the University of Barcelona.

1. Preparation and packaging
NOTE: The materials/equipment to be packed is listed in Table 1. Use gloves to handle the reagents required for the process control, the concentration reagents, the nucleic acid extraction reagents&#160;and the&#160;detection reagents. Wear protective glasses to handle the reagents required for nucleic acid extraction.
<ol>
	<li>Process control
	<ol>
		<li>Prepare MS2 bacteriophage stock culture (American Type Culture Collection [ATCC] 15597-B1) containing 1 x 1010 PFU/mL in the laboratory by following the ISO procedure 10705-1:199514.</li>
		<li>Then, aliquot 10 &#181;L of the suspension per tube containing 1 x 108 PFU into 10 mL tubes and let the water evaporate at 37 &#176;C. Use one tube per water sample.</li>
		<li>Additionally, prepare one tube containing 10 mL of sterile distilled water per collected sample.</li>
	</ol>
	</li>
	<li>Concentration reagents
	<ol>
		<li>For the preflocculated skimmed milk solution (PSM), use the following amounts to concentrate five 10 L water samples.
		<ol>
			<li>Prepare a plastic tube containing 5 g of skimmed milk.</li>
			<li>Prepare a zipper plastic bag containing 16.66 g of sea salts.</li>
			<li>Prepare a plastic bottle containing 500 mL of distilled water.</li>
		</ol>
		</li>
		<li>Prepare the reagents required for pH adjustment. Use the following amounts to adjust the pH of the PSM and of five 10 L water samples.
		<ol>
			<li>Add 5 g of citric acid 1-hydrate to a 10 mL plastic tube. 
			CAUTION: Citric acid causes serious irritation when it comes in contact with eyes. If this occurs, rinse the eye cautiously with water for several minutes. If irritation persists, seek medical advice.</li>
			<li>Put 2 g of sodium hydroxide into a 10 mL plastic tube. 
			CAUTION: Sodium hydroxide can cause severe skin burns and eye damage. If swallowed, rinse the mouth. Do not induce vomiting. If it comes in contact with the eyes, rinse cautiously with water for several minutes. Then, seek medical advice.</li>
			<li>Put 25 mL of sterile distilled water into a plastic container.</li>
			<li>Put 50 mL of sterile distilled water into a plastic container.</li>
		</ol>
		</li>
		<li>Prepare the sample conditioning sachet used for the flocculation, the preservative solution used to preserve the nucleic acids, and the neutralizing sachet to neutralize the discarded water and materials. Use the following amounts for each 10 L water sample to be tested.
		<ol>
			<li>Put 15 g of sea salts and 8 g of citric acid 1-hydrate into a zipper plastic bag for the conditioning sachet.</li>
			<li>Add 2 mL of lysis buffer (Table of Materials) and 0.3 mL of nucleic acid preserving agent (Table of Materials) to a 5 mL tube. 
			CAUTION: Lysis buffer contains guanidine thiocyanate and Triton X-100. Contact with acid liberates toxic gas, and it is harmful if swallowed, inhaled, or comes in contact with the skin. If swallowed, rinse the mouth. Do not induce vomiting. If it comes in contact with the skin, wash with plenty of water. Then, seek medical advice. Nucleic acid preserving agent causes skin and eye irritation and is harmful if swallowed. If it comes in contact with the skin or the eyes, rinse with abundant water for several minutes. In any case, especially if swallowed and feeling unwell, seek medical advice.</li>
			<li>Put 40 g of detergent powder into four zipper plastic bags. 
			CAUTION: Powder detergent causes eye irritation. If it comes in contact with the eyes, rinse with abundant water for several minutes. If irritation persists or if swallowed, seek medical advice.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Nucleic acid extraction reagents
	<ol>
		<li>Put 50 &#181;L of magnetic particles (Table of Materials) and 1 mL of ethanol 96% into a 5 mL tube which constitute the Binding Buffer. 
		CAUTION: The magnetic particles buffer contains sodium azide, which forms a toxic gas when it comes in contact with acids or heavy metal ions and is toxic if ingested or when it comes in contact with skin. If ingested or in contact with skin, rinse the mouth or the skin with abundant water and seek medical advice. Ethanol is a highly flammable liquid and vapor and causes serious eye irritation. Keep away from heat, hot surfaces, sparks, and any other ignition source. If it comes in contact with the skin or the eyes, rinse with abundant water. In case of ingestion of large amounts of water and/or if inhaled, go outside into the fresh air. In any case, seek medical advice.</li>
		<li>Add 500 &#181;L, 600 &#181;L, and 200 &#181;L of washing buffers 1, 2, and 3, respectively (Table of Materials), to three 2 mL tubes. 
		CAUTION: Washing buffers contain guanidinium thiocyanate and guanidinium chloride, which are harmful if inhaled or swallowed and irritate the skin and eyes. Contact with acids releases very toxic gas. If they come in contact with the skin or eyes, rinse with abundant water. If swallowed, rinse the mouth with abundant water. Do not induce vomiting. Always seek medical advice.</li>
		<li>Add 120 &#181;L of elution buffer (Table of Materials) to a 0.5 mL tube.</li>
	</ol>
	</li>
	<li>HAdV and MS2 detection reagents 
	NOTE: Two different nucleic acid extraction reactions may be analyzed simultaneously in each PCR assay if an 8-well thermocycler is used. For all PCR assays, prepare molecular biology water aliquoted into 1.5 mL tubes.
	<ol>
		<li>HAdV detection
		<ol>
			<li>Prepare a mix containing 10 &#181;L of 22.5 &#181;M AdF forward primer, 10 &#181;L of 22.5 &#181;M AdR reverse primer, and 5 &#181;L of 11.25 &#181;M AdP probe (Table 2).</li>
			<li>Add 2.5 &#181;L of the mix to tubes 1 to 8 of a tube strip. Let it dry at room temperature, close the tubes, and keep them protected from the light.</li>
			<li>Cut the strip dividing it into two strips: tubes 1-5 and tubes 6-8.</li>
			<li>Prepare a serial dilution of DNA suspensions containing the nucleotide sequence of the amplified HAdV region. Air-dry 1 &#181;L of suspensions containing 1 x 105, 1 x 107, and 1 x 109 GC/mL into tubes 6-8. 
			NOTE: Keep the tubes containing the primers, probe, and the air-dried suspensions protected from light.</li>
		</ol>
		</li>
		<li>MS2 detection
		<ol>
			<li>Prepare a mix containing 10 &#181;L of 25 &#181;M pecson-2F forward primer, 10 &#181;L of 25 &#181;M pecson-2R reverse primer, and 2.5 &#181;L of 25 &#181;M PecP-2 probe (Table 2).</li>
			<li>Add 2.25 &#181;L of the mix to tubes 1 to 8 of a tube strip. Let it dry at room temperature, close the tubes, and keep them protected from the light.</li>
			<li>Cut the strip dividing it into two strips: tubes 1-5 and tubes 6-8.</li>
			<li>Proceed as in step 1.4.1.4 but use a standard suspension designed for MS2 instead.</li>
		</ol>
		</li>
	</ol>
	</li>
</ol>
2. Viral concentration
NOTE: Use gloves at all times during the sample collection, reagent preparation, flocculation, flocs collection, and waste disposal procedures. Wear protective glasses during the reagent preparation procedure.
<ol>
	<li>Sample collection
	<ol>
		<li>Collect a 10 L water sample in a flat bottom bucket with a lid. Collect a minimum of two replicates for each sample. 
		NOTE: It is important to use clear buckets to visualize the pellet. If the water sample contains suspended material (e.g., sand, algae), let it sediment and, then, collect the water supernatant in a new bucket.</li>
		<li>Register the collected volume, as well as the location and collection date, for each water sample.</li>
		<li>Put a magnetic stirrer connected to a battery under a bucket support and place the bucket containing the water sample on its support. 
		NOTE: Look for a flat surface in a fresh place and keep the buckets containing the water samples from direct sunlight.</li>
	</ol>
	</li>
	<li>Reagents preparation
	<ol>
		<li>pH adjustment reagents
		<ol>
			<li>Pour the citric acid powder and the sodium hydroxide pellets into the pots containing 25 and 50 mL of distilled water, respectively.</li>
			<li>Gently shake by hand until the citric acid and the sodium hydroxide are completely dissolved. 
			CAUTION: Do not pour the water over the sodium hydroxide pellets. Instead, pour the sodium hydroxide pellets over the water.</li>
		</ol>
		</li>
		<li>Preflocculated skimmed milk
		<ol>
			<li>Place a stand-up bag on a magnetic stirrer and pour 500 mL of distilled water in it. Drop a stirring magnet inside the bag and turn on the magnetic stirrer.</li>
			<li>Pour the contents of a sea salt sachet and of a skimmed milk tube into the stand-up bag and stir for 5 min at medium speed to dissolve them.</li>
			<li>Add 3 mL of citric acid to the PSM solution using a Pasteur pipette to make sure the pH lies between 3.4 and 3.6. Measure the pH of the PSM solution using pH indicator strips. Add smaller amounts of citric acid and sodium hydroxide as the pH gets closer to 3.5.</li>
			<li>Turn off the magnetic stirrer and make sure the flocs are visible. Use a flashlight to help to visualize the flocs.</li>
		</ol>
		</li>
	</ol>
	</li>
	<li>Flocculation
	<ol>
		<li>Drop a stirring magnet into the water, set the magnetic stirrer at maximum speed, and turn it on. Make sure the stirring magnet starts spinning.</li>
		<li>Add 10 mL of distilled water to a process control tube. Invert the tube a few times to rehydrate the viral stock and pour the solution into the water.</li>
		<li>Pour the contents of one sample conditioning sachet into the water and stir for 5 min.</li>
		<li>Measure the pH of the water sample using pH indicator strips. Add a few drops of citric acid or sodium hydroxide to the water sample to make sure the pH lies between 3.4 and 3.6. Add smaller amounts of citric acid and sodium hydroxide as the pH gets closer to 3.5.</li>
		<li>Add 100 mL of the PSM solution using a 100 mL container.</li>
		<li>Seal the bucket with the lid, set the magnetic stirrer at minimum speed, and leave the water stirring for 8 h.</li>
		<li>Turn off the magnetic stirrer and let the water still for at least 5 h to allow the flocs to settle.</li>
	</ol>
	</li>
	<li>Floc&#160;collection
	<ol>
		<li>Build a siphoning system composed of a pipette controller, two pipettes, and a plastic tube, to aspirate the water supernatant for discharging the water on the flocs.
		<ol>
			<li>Attach a 10 mL tape-end pipette to the pipette controller. Then, attach the tip of the pipette to the plastic tube.</li>
			<li>Remove the filter of a 10 mL open-tip pipette using tweezers and attach the pipette to the plastic tube.</li>
		</ol>
		</li>
		<li>Place an empty bucket on the floor.</li>
		<li>Immerse the tip of the open-tip pipette in the water. Make sure to keep it close to the water surface to avoid disturbing the flocs. Aspirate the water supernatant until it reaches the tape-end pipette.</li>
		<li>Pinch the plastic tube by the end attached to the tape-end pipette and detach it from the pipette.</li>
		<li>Place the tube in an empty bucket. Release the pressure on the tube to let the water flow into the empty bucket.</li>
		<li>Pinch the plastic tube to stop the water flow when the water level is about to reach the stirring magnet and move the pipette away from the bucket.</li>
		<li>Shake the bucket to resuspend the flocs and pour them into a 500 mL stand-up plastic bag. Allow the flocs to settle for 1 h more.</li>
		<li>Carefully aspirate the water supernatant using a 50 mL pipette and a manual pipette controller, avoiding disturbing the flocs.</li>
		<li>Aspirate the flocs using a 100 mL pipette and transfer them to a 50 mL graduated centrifuge tube. Note down the final volume of sample concentrate and transfer 1 mL of it to a 5 mL tube containing the preservative solution, using a Pasteur pipette. 
		NOTE: It is important that the centrifuge tube is graduated so the final volume of the concentrated sample can be measured as accurately as possible and registered.</li>
		<li>Perform the nucleic acid extraction in the field. Alternatively, store the preservative solution containing the viruses at 20-30 &#176;C for up to 15 days or ship them to a reference laboratory for further analysis.</li>
	</ol>
	</li>
	<li>Waste disposal and material reuse
	<ol>
		<li>Add the contents of a neutralizing agent sachet to the bucket containing the discarded water. Mix the water, and then, leave it still for 30 min.</li>
		<li>Dispose of the treated water as general waste.</li>
		<li>Place the pipettes and the plastic tube inside the bucket. Fill the bucket with water and pour in the contents of one neutralizing agent sachet.</li>
		<li>Wash them for at least 30 min to sterilize them and rinse them with abundant clean water to remove any remaining neutralizing agent.</li>
	</ol>
	</li>
</ol>
3. Nucleic acid extraction
NOTE: Use gloves and always wear protective glasses during the nucleic acid extraction procedure.
<ol>
	<li>Magnetic pipette operation
	<ol>
		<li>Get familiarized with the operation of the magnetic pipette before performing the extraction.</li>
	</ol>
	</li>
	<li>Nucleic acid extraction
	<ol>
		<li>Arrange the tubes containing the reagents required for the extraction in a rack, from left to right: binding buffer, washing buffers, and elution buffer. Set the appropriate number of tubes according to the number of samples or replicates being analyzed.</li>
		<li>Transfer 1 mL of sample concentrate to the tube containing the binding buffer, using a disposable Pasteur pipette. Invert the tube 8x to 10x to homogenize the solution.</li>
		<li>Incubate the solution at room temperature for 10 min while continuously mixing, either using a solar-powered orbital or manually.</li>
		<li>Collect the magnetic particles using the magnetic pipette and a clean tip, which can be reused for the three washing buffers.</li>
		<li>Release the magnetic particles into the tube containing 500 &#181;L of washing buffer 1. Wash them by gently shaking the solution with the tip for 30 s and collect them.</li>
		<li>Transfer the magnetic particles to the tube containing 600 &#181;L of washing buffer 2. Wash them by gently shaking the solution with the tip for 30 s and collect them.</li>
		<li>Transfer the magnetic particles to the tube containing 200 &#181;L of washing buffer 3. Wash them by gently shaking the solution with the tip for 30 s and collect them.</li>
		<li>Release the magnetic particles into the tube containing the elution buffer and discard the tip.</li>
		<li>Incubate the solution at room temperature for 5 min while continuously mixing, using the solar-powered orbital. 
		NOTE: Mixing the magnetic particles in the elution buffer is a crucial step. In case of lacking an orbital, continuously mix by hand during the incubation time.</li>
		<li>Replace the tip on the magnetic pipette by a new one and collect the magnetic particles from the elution buffer. Make sure to completely remove the magnetic particles from the elution buffer since they can interfere with molecular detection methods.</li>
		<li>Discard the tip with the particles attached to it. Proceed with the PCR analysis, ship the elution buffer to a reference laboratory, or store the elution buffer in at 4 &#730;C for further analysis.</li>
	</ol>
	</li>
</ol>
4. Viral detection with a battery-operated eight-tube real-time thermocycler
NOTE: Use gloves and always wear protective glasses during the nucleic acid detection procedure. Replace the gloves for new ones when performing a new PCR experiment to avoid cross-contamination.
<ol>
	<li>HAdV quantitative PCR
	<ol>
		<li>Add 14 &#181;L of nuclease-free water to tubes 2, 4, and 5.</li>
		<li>Add 4 &#181;L of PCR mix to tubes 1-5.</li>
		<li>Add 14 &#181;L of nucleic acid extraction from sample A to tube 1 and 14 &#181;L from sample B to tube 3.</li>
		<li>Add 2 &#181;L of extracted nucleic acids from sample A to tube 2 and 2 &#181;L from sample B to tube 4. Close the five-tube strip.</li>
		<li>Add 14 &#181;L of nuclease-free water to tubes 6, 7, and 8.</li>
		<li>Add 4 &#181;L of this mix to tubes 6, 7, and 8, and close them.</li>
		<li>Put both strips in the thermocycler and select the appropriate run (Table 3).</li>
		<li>Discard the water tube and keep the extracted nucleic acid in the freezer, if possible, or, if not, in a fresh place protected from light in case a second test needs to be performed.</li>
		<li>Clean the micropipettes, the rack, the working material, and all material properly with a nucleic acid cleaner, and discard the plastic bag containing the used tip, gloves, and tubes. 
		CAUTION: Nucleic acid remover is a very flammable liquid and steam. Do not breathe in the spray mist and avoid any contact of the liquid with the eyes or the skin. Otherwise, immediately rinse with abundant water and seek medical advice.</li>
		<li>Collect the results and analyze the obtained data.</li>
	</ol>
	</li>
	<li>MS2 quantitative PCR
	<ol>
		<li>Add 14 &#181;L of nuclease-free water to tubes 2, 4, and 5.</li>
		<li>Add 4 &#181;L of PCR mix and 0.5 &#181;L of reverse transcriptase enzyme to tubes 1-5.</li>
		<li>Add 14 &#181;L of nucleic acid extraction from sample A to tube 1 and 14 &#181;L from sample B to tube 3.</li>
		<li>Add 1 &#181;L of extracted nucleic acids from sample A to tube 2 and 1 &#181;L from sample B to tube 4. Close the five-tube strip.</li>
		<li>Add 15.5 &#181;L of nuclease-free water to tubes 5, 6, 7, and 8, and close them.</li>
		<li>Add 4 &#181;L of PCR mix and 0.5 &#181;L of reverse transcriptase enzyme to tubes 6, 7, and 8.</li>
		<li>Put both strips in the thermocycler and select the appropriate run (Table 3).</li>
		<li>Proceed as described in steps 4.1.8 to 4.1.10.</li>
	</ol>
	</li>
</ol>

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<li>Calgua, B., Barardi, C. R. M., Bofill-Mas, S., Rodriguez-Manzano, J., Girones, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Detection+and+quantitation+of+infectious+human+adenoviruses+and+JC+polyomaviruses+in+water+by+immunofluorescence+assay%5BTitle%5D)+AND+%22Journal+of+Virological+Methods%22%5BJournal%5D)">Detection and quantitation of infectious human adenoviruses and JC polyomaviruses in water by immunofluorescence assay.</a> Journal of Virological Methods. 171 (1), 1-7 (2011).</li>
<li>Bofill-Mas, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Cost-effective+method+for+microbial+source+tracking+using+specific+human+and+animal+viruses%5BTitle%5D)+AND+%22Journal+of+Visualized+Experiments%22%5BJournal%5D)">Cost-effective method for microbial source tracking using specific human and animal viruses.</a> Journal of Visualized Experiments. (58), e2820(2011).</li>
<li>Gonzales-Gustavson, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Characterization+of+the+efficiency+and+uncertainty+of+skimmed+milk+flocculation+for+the+simultaneous+concentration+and+quantification+of+water-borne+viruses%2C+bacteria+and+protozoa%5BTitle%5D)+AND+%22Journal+of+Microbiological+Methods%22%5BJournal%5D)">Characterization of the efficiency and uncertainty of skimmed milk flocculation for the simultaneous concentration and quantification of water-borne viruses, bacteria and protozoa.</a> Journal of Microbiological Methods. 134, 46-53 (2017).</li>
</ol>

The authors have nothing to disclose.

The VirWaTest method enables the concentration of viruses and nucleic acid extraction from water samples at the point of use by non-experienced users. It is an affordable, rapid, and simple protocol. The concentration is based on the principle of organic flocculation using skimmed milk, by which the low pH and high conductivity conditions make skimmed milk proteins aggregate into flocs the viruses adsorb to. When the flocs sediment, it is easy to collect them, making it possible to concentrate 10 L of water, whereas trad...

During the first phases of any humanitarian emergency, access to clean water supplies, sanitation, and hygiene are critical for the survival of those affected. Therefore, monitoring water quality is a priority to prevent waterborne outbreaks. It is well-known that contaminated water is frequently the origin of diseases, but it is often difficult to determine the sources of viral outbreaks such as Hepatitis E virus (HEV), even with the availability of conventional laboratory methods. The control of water quality is based on the quantification of FIB1,2,3,4. However, it has been extensively documented that there is no correlation between the absence of FIB and the presence of viral waterborne pathogens such as rotavirus (RoV), norovirus (NoV), or HEV5,6. Thus, using the water quality criteria based on FIB might result in an underestimation of risks associated with the presence of waterborne viral pathogens. The surveillance of indicator viruses, such as human adenoviruses (HAdV), or specific pathogens would be helpful in defining the exposure to viral pathogens and identifying the potential source of human infection7,8,9,10 and in validating the efficacy of sanitation measures11.
Until now, the detection of viruses in these scenarios relied on skilled staff and complex logistics. VirWaTest (virwatest.org) is aimed at the development of a simple, affordable, and portable method for the concentration and subsequent detection of viruses from water samples at the point of use.
The virus concentration is based on the principle of organic flocculation of 10 L water samples, by which viruses are recovered in smaller volumes12,13. The flocs are collected and added to a buffer that lyses the viruses and prevents the nucleic acids from degradation when they stored at room temperature for not more than 2 weeks.
The nucleic acid extraction method is based on the use of magnetic particles to which the nucleic acids get adsorbed. They can be transferred from one washing buffer to another and finally into the elution buffer by using a magnetic pipette to which the particles attach. Viral nucleic acid suspensions obtained can be shipped to a reference laboratory where the detection can be performed using molecular methods based on PCR. For each nucleic acid extraction, two different quantities are tested to rule out enzymatic inhibition originated by the sample. Alternatively, with minimum equipment availability, PCR tests can be run at the point of use. The entire process is designed to be performed independently of a power supply (Figure 1).
A quantitative PCR assay to detect HAdV, excreted by humans and found in wastewater samples in high concentrations, has been adapted to be run at the point of use. HAdV are used as human fecal viral indicators. A PCR for the quantification of MS2 bacteriophage has been also adapted since MS2 is used in VirWaTest as process control. The method can be customized for the detection of any virus of interest.
After development, the VirWaTest method has been applied by the users in two different settings in the Republic of Central Africa (RCA) and Ecuador, providing feedback on the application of the protocol in real situations.
To our knowledge, this is the first procedure that allows the concentration and detection of viruses at the point of use, independent of any power supply, large equipment, and freezing/cooling conditions. It is recommended to collect two replicates of each water sample in order to obtain robust results.

<table><tbody><tr><td>5x HOT FIREPol Probe qPCR Mix Plus (ROX)</td><td>Solis BioDyne</td><td>08-14-00001</td><td>Includes Solis Biodyne&#039;s 5x HOT FIREPol Probe qPCR Mix Plus (qPCR Mix), 50 Reactions</td></tr><tr><td>8-Microtube Strips with Caps</td><td>dD Biolab</td><td>840637</td><td>Low Profile, Thin Walls, Adapted for Quantitative and Qualitative PCR</td></tr><tr><td>Batteries and Power Adapters for Magnetic Stirrer</td><td>GenIUL</td><td>900011674</td><td>Includes 12V car power adapter</td></tr><tr><td>Bucket Support</td><td>GenIUL</td><td>900011648</td><td>Aluminium support</td></tr><tr><td>Bucket, 10 L</td><td>Cater4You</td><td>10LTR</td><td>Polypropilene, Tamperproof, Clear color</td></tr><tr><td>Centrifuge Tube, 50 mL</td><td>LabBox</td><td>CTSP-E50-050</td><td>Polypropylene, Sterile, Graduated, With Skirt</td></tr><tr><td>Citric Acid 1-Hydrate, 500 g</td><td>PanReac AppliChem</td><td>1410181211</td><td>Pure, Pharma Grade, 1 Kilogram</td></tr><tr><td>Clear PET Bottle</td><td>LabBox</td><td>FPET-500-088</td><td>Clear Color, PET, Cap Not Included</td></tr><tr><td>Difco Skim Milk, 500 g</td><td>Becton Dickinson</td><td>232100</td><td>Dehydrated</td></tr><tr><td>DNA/RNA Shield, 250 mL</td><td>Zymo Research</td><td>R1100-250</td><td>DNA/RNA Preservation Medium, 250 mL</td></tr><tr><td>Easy9 Pipette Controller</td><td>LabBox</td><td>EAS9-001-001</td><td>0.3 &amp;mu;m filter, Pipettes from 0.1 to 100 mL, Autoclavable silicone pipette holder</td></tr><tr><td>Eppendorf Tube, 0.5 mL</td><td>Eppendorf</td><td>0030121023</td><td>Polypropilene, Safe-Lock</td></tr><tr><td>Eppendorf Tube, 2 mL</td><td>Eppendorf</td><td>0030120094</td><td>Polypropilene, Safe-Lock</td></tr><tr><td>Eppendorf Tube, 5 mL</td><td>dD Biolab</td><td>999542</td><td>Polypropylene, Sterile, Graduated</td></tr><tr><td>Ethanol 96% V/V, 1 L</td><td>Panreac AppliChem</td><td>361085-1611</td><td>For UV, IR&amp;nbsp; and HPLC</td></tr><tr><td>Laboratory Tweezers</td><td>LabBox</td><td>FORS-007-002</td><td>Thin, Curved End, L= 120 mm</td></tr><tr><td>Magnetic Stirrer</td><td>GenIUL</td><td>900017000</td><td>Battery-powered</td></tr><tr><td>Marker</td><td>dD Biolab</td><td>929203</td><td>Black, Extra fine Tip, Water Resistant, Fast Drying, For Plastic and Glassware</td></tr><tr><td>Micro Rota-Rack for Microtubes</td><td>dD Biolab</td><td>37782</td><td>4 Modules, L x W x H= 208 x 100 x 100 mm</td></tr><tr><td>Mini8 Real-Time PCR Cycler</td><td>Coyote Biosciences, China</td><td>Mini-8</td><td>Portable, Works with 12V Power Supplies or External Batteries, Two channels, Capacity for 8 Tubes</td></tr><tr><td>NucliSens Lysis Buffer</td><td>Biomerieux</td><td>200292</td><td>Reagents for up to 48 Isolations, Store at Ambient Temperature</td></tr><tr><td>Open Tip Serological Pipette, 10 mL</td><td>Deltalab</td><td>900136N</td><td>Sterile, Individually Wrapped (Paper/Plastic)</td></tr><tr><td>PE Screw Cap PP28</td><td>LabBox</td><td>TP28-004-020</td><td>For PET Bottles</td></tr><tr><td>pH Indicator Strip</td><td>LabBox</td><td>WSPH-001-001</td><td>Range pH 2.8 to pH 4.4, 50 Strips per Pack</td></tr><tr><td>Plastic Test Tube</td><td>Quimikals</td><td>300913</td><td>Includes Cap</td></tr><tr><td>Polyethylene Pasteur Pipette</td><td>LabBox</td><td>PIPP-003-500</td><td>Graduated, 7 mL Overall Volume, Non-Sterile</td></tr><tr><td>Polypropylene Screw Flask With Screw Cap, 150 mL</td><td>Deltalab</td><td>409726</td><td>Screw cap, Sterile, graduated up to 100 mL</td></tr><tr><td>Polypropylene Screw Flask With Screw Cap, 60 mL</td><td>Deltalab</td><td>409526G</td><td>Screw cap, Sterile, Graduated up to 50 mL</td></tr><tr><td>Powder Powder Detergent</td><td>-</td><td>-</td><td>Regular Powder Soap for washing clothes</td></tr><tr><td>Power Cables for Magnetic Stirrer</td><td>GenIUL</td><td>900011692</td><td>Connection between batteries and magnetic stirrers</td></tr><tr><td>QuickPick Magnetic Tool</td><td>BioNobile</td><td>24001</td><td>Hand-held tool for magnetic particles</td></tr><tr><td>QuickPick Tips in Box</td><td>BioNobile</td><td>24296</td><td>RNase-Free, Autoclaved, 96 Units</td></tr><tr><td>QuickPick XL gDNA Magnetic Particles</td><td>BioNobile</td><td>SN51100</td><td>3.2 mL</td></tr><tr><td>Sea Salts</td><td>Sigma-Aldrich</td><td>S9883-500G</td><td>An artificial salt mixture closely resembling the composition of the dissolved salts of ocean water</td></tr><tr><td>Silicone Tubing</td><td>LabBox</td><td>SILT-006-005</td><td>Roll of 5 Meters, Inner&amp;nbsp; &amp;oslash; x Outer&amp;nbsp; &amp;oslash;= 6 x 10 mm</td></tr><tr><td>Sodium Hydroxide Pellets, 98.5 - 100.5%</td><td>VWR Chemicals</td><td>28244295</td><td>Pellets, 1 Kg</td></tr><tr><td>Solar Rotary Platform</td><td>SOL-EXPERT Group</td><td>70020</td><td>Acrylic Plate, 10 RPM, Supports up to 300 Grams</td></tr><tr><td>SOLIScript 1-step Probe Kit</td><td>Solis BioDyne</td><td>08-57-00250</td><td>Includes Solis Biodyne&#039;s 5x One-Step Probe Mix (qPCR Mix) and 40x One-Step SOLIScript Mix (Reverse Transcriptase Enzyme), 250 Reactions</td></tr><tr><td>SPEEDTOOLS RNA Virus Extraction Kit</td><td>BioTools</td><td>21.141-4197</td><td>Includes BioTools&#039;s BAW Buffer (Washing Buffer 1), BAV3 Buffer (Washing Buffer 2 and 3) and BRE Buffer (Elution Buffer).</td></tr><tr><td>SpinBar Octhaedral Stirring Magnet</td><td>dD Biolab</td><td>045926</td><td>Pivot Ring, L x&amp;nbsp; &amp;oslash; = 38 x 8 mm, Blue</td></tr><tr><td>Tape-End Serological Pipette, 10 mL</td><td>Deltalab</td><td>PN10E1</td><td>Sterile, Individually Wrapped (Paper/Plastic)</td></tr><tr><td>Tape-End Serological Pipette, 50 mL</td><td>Deltalab</td><td>900043</td><td>Sterile, Individually Wrapped (Paper/Plastic)</td></tr><tr><td>Termi-DNA-Tor - Nucleic Acid Remover</td><td>BioTools</td><td>22001-4291</td><td>Remover of nucleic acids, bacteria, fungi and mycoplasma from material and surfaces, 450 mL</td></tr><tr><td>Water Molecular Biology Reagent, 1L</td><td>Sigma-Aldrich</td><td>W4502-1L</td><td>Nuclease and Protease Free, 0.1 &amp;mu;m Filtered</td></tr><tr><td>Whirl-Pak Bag, 540 mL</td><td>Deltalab</td><td>200361</td><td>Stable bottom</td></tr><tr><td>Zip Lock Plain Bag</td><td>LabBox</td><td>BZIP-080-100</td><td>Polyethylene, L x W= 120 x 80 mm</td></tr></tbody></table>

virwatest, a point-of-use method for the detection of viruses in water samples

VirWaTest, A Point-of-Use Method for the Detection of Viruses in Water Samples

Viruses excreted by humans and animals may contaminate water sources and pose a risk to human health when this water is used for drinking, food irrigation, washing, etc. The classical fecal bacteria indicator does not always check for the presence of viral pathogens so the detection of viral pathogens and viral indicators is relevant in order to adopt measures of risk mitigation, especially in humanitarian scenarios and in areas where water-borne viral outbreaks are frequent.
At present, several commercial tests allowing the quantification of fecal indicator bacteria (FIB) are available for testing at the point of use. However, such commercial tests are not available for the detection of viruses. The detection of viruses in environmental water samples requires concentrating several liters into smaller volumes. Moreover, once concentrated, the detection of viruses relies on methods such as nucleic acid extraction and molecular detection (e.g., polymerase chain reaction [PCR]-based assays) of the viral genomes.
The method described here allows the concentration of viruses from 10 L water samples, as well as the extraction of viral nucleic acids at the point of use, with simple and portable equipment. This allows the testing of water samples at the point of use for several viruses and is useful in humanitarian scenarios, as well as at any context where an equipped laboratory is not available. Alternatively, the method allows concentrating viruses present in water samples and the shipping of the concentrate to a laboratory at room temperature for further analysis.

Method development 
This procedure has been developed in the Laboratory of Viruses Contaminants of Water and Food with the collaboration of GenIUL and Oxfam Intermón. It comprises of three different steps. The first one, the viral particle concentration, is an adaptation of a skimmed milk flocculation method previously described12,17,<sup clas...

Here we present VirWaTest, which is a simple, affordable and portable method for the concentration and detection of viruses from water samples at the point of use.

Viruses excreted by humans and animals may contaminate water sources and pose a risk to human health when this water is used for drinking, food ...

virwatest-point-use-method-for-detection-viruses-water

Research

JoVE Journal

Immunology and Infection

The turnover rate of viruses in marine and freshwater systems can be estimated by a reduction and reoccurrence technique. The data allow researchers to infer rates of virus-mediated microbial mortality in aquatic systems.

Estimating Virus Production Rates in Aquatic Systems

The study describes a cost-effective method for the identification of the source of fecal/urine contamination or contamination by nitrates in water using qPCR for the specific quantification of human/porcine/bovine DNA viruses, adenoviruses and polyomaviruses, proposed as MST tools.

Cost-effective Method for Microbial Source Tracking Using Specific Human and Animal Viruses

This protocol describes the use of a tangential flow hollow-fiber ultrafiltration sample concentration system and a heat dissociation as alternative steps for the detection of waterborne Cryptosporidium and Giardia species using EPA Method 1623.

A Modified EPA Method 1623 that Uses Tangential Flow Hollow-fiber Ultrafiltration and Heat Dissociation Steps to Detect Waterborne Cryptosporidium and Giardia spp.

Source: Fout, G. S., Cashdollar, J. L. EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay. J. Vis. Exp. (2016)This video demonstrates the use of a total culturable virus assay to quantify infectious viruses in water samples. It outlines host cell inoculation, observation of cytopathic effect, and statistical quantification of infectious virus concentration.

Quantifying Infectious Viruses in Water Samples Using an In Vitro Total Culturable Virus Assay

An approach was developed for identifying optimal viral concentration conditions for small volume water samples using spikes of human adenovirus. The techniques described here are used to identify concentration parameters for other viral targets, and applied to large-scale viral concentration experimentation.

A Small Volume Procedure for Viral Concentration from Water

EPA Method 1615 uses an electropositive filter to concentrate enteroviruses and noroviruses in environmental and drinking waters. This manuscript describes the procedure for collecting samples for Method 1615 analyses.

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. I. Collection of Virus Samples

Here we present a procedure to measure total culturable viruses using the Buffalo Green Monkey kidney cell line. The procedure provides a standardized tool for measuring the occurrence of infectious viruses in environmental and drinking waters.

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. II. Total Culturable Virus Assay

Here we present a procedure to quantify enterovirus and norovirus in environmental and drinking waters using reverse transcription-quantitative PCR. Mean virus recovery from groundwater with this standardized procedure from EPA Method 1615 was 20% for poliovirus and 30% for murine norovirus.

EPA Method 1615. Measurement of Enterovirus and Norovirus Occurrence in Water by Culture and RT-qPCR. Part III. Virus Detection by RT-qPCR

An anion exchange resin-based method, adapted to liquid impingement-based bioaerosol sampling of viruses is demonstrated. When coupled with downstream molecular detection, the method allows for facile and sensitive detection of viruses from bioaerosols.

Detection of Viruses from Bioaerosols Using Anion Exchange Resin

Virus concentration from environmental water and wastewater samples is a challenging task, carried out primarily for the identification and quantification of viruses. While several virus concentration methods have been developed and tested, we demonstrate here the effectiveness of ultrafiltration and skimmed milk flocculation for RNA viruses with different sample types.

Concentration of Virus Particles from Environmental Water and Wastewater Samples Using Skimmed Milk Flocculation and Ultrafiltration

Learn VirWaTest, a portable point-of-use method for detecting enteric viruses in water samples. This cost-effective technique improves water safety monitoring in humanitarian contexts.

VirWaTest, A Point-of-Use Method for the Detection of Viruses in Water Samples

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