Name: reverse transcription-loop-mediated isothermal amplification (rt-lamp) assay for zika virus and housekeeping genes in urine, serum, and mosquito samples
Uploaded: 2018-09-14T15:00:00
Description: Watch this Scientific Journal Video about Reverse Transcription-Loop-mediated Isothermal Amplification RT-LAMP Assay for Zika Virus and Housekeeping Genes in Urine, Serum, and Mosquito Samples Video a

This work was supported by the Maureen and Ronald Hirsch family philanthropic contribution and Field Neurosciences Institute, St. Mary&#39;s of Michigan. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We also thank Dr. Bernadette Zwaans and Elijah Ward for their critical review of the manuscript.

All methods described here have been approved by the Institutional Review Board (IRB) of Beaumont Health. All experiments were performed in accordance with relevant guidelines and regulations.
CAUTION: All potentially infectious materials should be handled according to Biosafety Level 2 standards including the use of personal protective equipment. Any procedures which may produce aerosol should be performed in a biosafety cabinet. Additionally, work with live mosquitoes should be performed in ...

<ol>
	<li>Petersen, L. R., Jamieson, D. J., Powers, A. M., Honein, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Zika+Virus.">Zika Virus.</a> New England Journal of Medicine. 374 (16), 1552-1563 (2016).</li><li>Francois, P., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Robustness+of+a+loop-mediated+isothermal+amplification+reaction+for+diagnostic+applications.">Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications.</a> Federation of European Microbiological Societies Immunology and Medical Microbiology. 62 (1), 41-48 (2011).</li><li>Tomita, N., Mori, Y., Kanda, H., Notomi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Loop-mediated+isothermal+amplification+(LAMP)+of+gene+sequences+and+simple+visual+detection+of+products.">Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products.</a> Nature Protocols. 3 (5), 877-882 (2008).</li><li>Gandasegui, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Rapid-Heat+LAMPellet+Method:+A+Potential+Diagnostic+Method+for+Human+Urogenital+Schistosomiasis.">The Rapid-Heat LAMPellet Method: A Potential Diagnostic Method for Human Urogenital Schistosomiasis.</a> Public Library of Science Neglected Tropical Diseases. 9 (7), 0003963 (2015).</li><li>Barkway, C. P., Pocock, R. L., Vrba, V., Blake, D. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Loop-mediated+isothermal+amplification+(LAMP)+assays+for+the+species-specific+detection+of+Eimeria+that+infect+chickens.">Loop-mediated isothermal amplification (LAMP) assays for the species-specific detection of Eimeria that infect chickens.</a> The Journal of Visualized Experiments. (96), (2015).</li><li>Lamb, L. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+Detection+of+Zika+Virus+in+Urine+Samples+and+Infected+Mosquitos+by+Reverse+Transcription-Loop-Mediated+Isothermal+Amplification.">Rapid Detection of Zika Virus in Urine Samples and Infected Mosquitos by Reverse Transcription-Loop-Mediated Isothermal Amplification.</a> Scientific Reports. 8 (1), 3803 (2018).</li><li>Faye, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=One-step+RT-PCR+for+detection+of+Zika+virus.">One-step RT-PCR for detection of Zika virus.</a> Journal of Clinical Virology. 43 (1), 96-101 (2008).</li><li>Schrader, C., Schielke, A., Ellerbroek, L., Johne, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=PCR+inhibitors+-+occurrence,+properties+and+removal.">PCR inhibitors - occurrence, properties and removal.</a> Journal of Applied Microbiology. 113 (5), 1014-1026 (2012).</li><li>Poole, C. B., Tanner, N. A., Zhang, Y., Evans, T. C., Carlow, C. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Diagnosis+of+brugian+filariasis+by+loop-mediated+isothermal+amplification.">Diagnosis of brugian filariasis by loop-mediated isothermal amplification.</a> Public Library of Science Neglected Tropical Diseases. 6 (12), 1948 (2012).</li><li>Tanner, N. A., Zhang, Y., Evans, T. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simultaneous+multiple+target+detection+in+real-time+loop-mediated+isothermal+amplification.">Simultaneous multiple target detection in real-time loop-mediated isothermal amplification.</a> Biotechniques. 53 (2), 81-89 (2012).</li><li>Chan, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid,+Affordable+and+Portable+Medium-Throughput+Molecular+Device+for+Zika+Virus.">Rapid, Affordable and Portable Medium-Throughput Molecular Device for Zika Virus.</a> Scientific Reports. 6, 38223 (2016).</li><li>Lee, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Simple+and+Highly+Sensitive+Molecular+Diagnosis+of+Zika+Virus+by+Lateral+Flow+Assays.">Simple and Highly Sensitive Molecular Diagnosis of Zika Virus by Lateral Flow Assays.</a> Analytical Chemistry. 88 (24), 12272-12278 (2016).</li><li>Pardee, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Low-Cost+Detection+of+Zika+Virus+Using+Programmable+Biomolecular+Components.">Low-Cost Detection of Zika Virus Using Programmable Biomolecular Components.</a> Cell. 165 (5), 1255-1266 (2016).</li><li>Song, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Instrument-Free+Point-of-Care+Molecular+Detection+of+Zika+Virus.">Instrument-Free Point-of-Care Molecular Detection of Zika Virus.</a> Analytical Chemistry. 88 (14), 7289-7294 (2016).</li><li>Yaren, O., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Point+of+sampling+detection+of+Zika+virus+within+a+multiplexed+kit+capable+of+detecting+dengue+and+chikungunya.">Point of sampling detection of Zika virus within a multiplexed kit capable of detecting dengue and chikungunya.</a> BioMed Central Infectious Diseases. 17 (1), 293 (2017).</li><li>Wang, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rapid+and+sensitive+detection+of+Zika+virus+by+reverse+transcription+loop-mediated+isothermal+amplification.">Rapid and sensitive detection of Zika virus by reverse transcription loop-mediated isothermal amplification.</a> Journal of Virological Methods. 238, 86-93 (2016).</li><li>Priye, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+smartphone-based+diagnostic+platform+for+rapid+detection+of+Zika,+chikungunya,+and+dengue+viruses.">A smartphone-based diagnostic platform for rapid detection of Zika, chikungunya, and dengue viruses.</a> Scientific Reports. 7, 44778 (2017).</li></ol>

The ZIKV RT-LAMP assay described in this paper works using both human and mosquito samples6. The limit of detection was approximately 1 genome equivalent6, which should be sufficient since the typical viral load of a symptomatic ZIKV infected patient is 103 to&#160;106 PFU/mL7. Additionally, this method can detect ZIKV in samples without first isolating RNA and without virus amplification in cell culture. This signifi...

In 2015, Zika virus (ZIKV) gained prominent global attention as an infectious disease of concern because infection during pregnancy was linked to miscarriage, stillbirth, severe neurological birth defects including microcephaly, as well as other congenital birth defects1. In rare cases, ZIKV has been associated with Guillain-Barr&#233; syndrome. ZIKV is primarily transmitted by Aedes mosquitoes; however, it can also be spread through sexual contact1. Given that the infection with ZIKV is asymptomatic in most people or presents with mild flu-like symptoms that overlap with the symptoms of infection of other arborviruses1, there was a need for improved methods for rapid and cost-effective detection of ZIKV to screen both people as well as local mosquito populations.
Quantitative reverse transcription PCR (qRT-PCR) is a reliable assay for ZIKV detection; however, this technique requires expensive specialized equipment, trained personnel, and RNA isolation from the sample of interest. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a one-step nucleic acid amplification method based on PCR technology that only requires one incubation temperature due to the use of a thermophilic DNA polymerase with strand displacement properties. This circumvents the need for a thermocycler and decreases the length of time needed to complete the assay. Additional advantages of RT-LAMP include its high specificity and sensitivity, robustness at a range of pH levels and temperatures, and resistance to many PCR inhibitors2. It has a relatively low cost and reagents are stable at room temperature. Given these characteristics, RT-LAMP can be deployed in a laboratory or in the field. As such, LAMP reactions have been developed to detect a range of pathogens and other types of infection3,4,5. The goal of the RT-LAMP protocol described in this paper is to detect ZIKV without RNA isolation in human serum and urine samples as well as in a single infected mosquito within 30 min through RT-LAMP. This method can be used to replace qRT-PCR as it is a sensitive, rapid diagnostic tool that works quickly and in settings outside of the laboratory.

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	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Bst 2.0 WarmStart DNA polymerase</td>
			<td style="width:223px;">New England Biolabs</td>
			<td style="width:223px;">M0537S</td>
			<td style="width:207px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Isothermal Amplification Buffer&#160;</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">B0537S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">WarmStart RTx Reverse Transcriptase</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">M0380S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Antarctic Thermolabile UDG</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">M0372S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">MgSO4</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">B1003S</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100mM dATP Solution</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">N0440S</td>
			<td>Deoxynucleotide Set N0446S</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100mM dCTP Solution</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">N0441S</td>
			<td>Deoxynucleotide Set N0446S</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100mM dTTP Solution</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">N0443S</td>
			<td>Deoxynucleotide Set N0446S</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100mM dGTP Solution</td>
			<td>New England Biolabs</td>
			<td style="width:223px;">N0442S</td>
			<td>Deoxynucleotide Set N0446S</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">100mM dUTP Solution</td>
			<td style="width:223px;">Thermo Fisher Scientific</td>
			<td style="width:223px;">R0133</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">SYBR Green I Nucleic Acid Gel Stain</td>
			<td style="width:223px;">Invitrogen</td>
			<td style="width:223px;">S7563</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Nancy-520</td>
			<td style="width:223px;">Sigma Aldrich</td>
			<td style="width:223px;">01494</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Low DNA Mass Ladder</td>
			<td style="width:223px;">Invitrogen</td>
			<td style="width:223px;">10-068-013</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Zika Postive Control</td>
			<td style="width:223px;">Robert Koch Institute, Germany</td>
			<td style="width:223px;">N/A</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Agarose</td>
			<td style="width:223px;">Thermo Fisher Scientific</td>
			<td style="width:223px;">BP1600</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">BlueJuice Gel Loading Buffer</td>
			<td style="width:223px;">Invitrogen</td>
			<td style="width:223px;">10816015</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Primers</td>
			<td style="width:223px;">Integrated DNA Technologies</td>
			<td style="width:223px;">Custom Oligo</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Nuclease-Free Water</td>
			<td style="width:223px;">Ambion</td>
			<td style="width:223px;">AM9938</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">Urine Preservative</td>
			<td style="width:223px;">Norgen Biotek</td>
			<td style="width:223px;">18126</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:249px;">ZIKV PCR Standard</td>
			<td>Robert Koch Institute</td>
			<td style="width:223px;">N/A</td>
			<td>Vero E6 cell supernatants</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;">DENV2 New Guinea C Control</td>
			<td style="width:223px;">Connecticut Agricultural Experiment Station</td>
			<td style="width:223px;">N/A</td>
			<td></td>
		</tr>
	</tbody>
</table>

reverse transcription-loop-mediated isothermal amplification (rt-lamp) assay for zika virus and housekeeping genes in urine, serum, and mosquito samples

Infection with Zika virus (ZIKV) can be asymptomatic in adults, however, infection during pregnancy can lead to miscarriage and severe neurological birth defects. The goal of this protocol is to quickly detect ZIKV in both human and mosquito samples. The current gold standard for ZIKV detection is quantitative reverse transcription PCR (qRT-PCR); reverse transcription loop-mediated isothermal amplification (RT-LAMP) may allow for a more efficient and low-cost testing without the need for expensive equipment. In this study, RT-LAMP is used for ZIKV detection in various biological samples within 30 min, without first isolating the RNA from the sample. This technique is demonstrated using ZIKV infected patient urine and serum, and infected mosquito samples. 18S ribosomal ribonucleic acid and actin are used as controls in human and mosquito samples, respectively.

RT-LAMP reactions can be analyzed using three different methods. First, with the addition of a fluorescent nucleic acid dye, positive reactions will be yellow/green in color where negative reactions will appear orange in color to the naked eye. Second, the addition of the fluorescent nucleic acid dye to RT-LAMP reaction results in a fluorescent signal when the samples are excited by UV light. Negative reactions will not have a detectable fluorescent signal over any background fluorescence...

Watch this Scientific Journal Video about Reverse Transcription-Loop-mediated Isothermal Amplification RT-LAMP Assay for Zika Virus and Housekeeping Genes in Urine, Serum, and Mosquito Samples Video a

Reverse Transcription-Loop-mediated Isothermal Amplification RT-LAMP Assay for Zika Virus and Housekeeping Genes in Urine, Serum, and Mosquito Samples Video (Video) | JoVE

This protocol provides an efficient and low-cost method to detect Zika virus or control targets in human urine and serum samples or in mosquitoes by reverse transcription loop-mediated isothermal amplification (RT-LAMP). This method does not require RNA isolation and can be done within 30 min.

Reverse Transcription-Loop-mediated Isothermal Amplification (RT-LAMP) Assay for Zika Virus and Housekeeping Genes in Urine, Serum, and Mosquito Samples

Infection with Zika virus (ZIKV) can be asymptomatic in adults, however, infection during pregnancy can lead to miscarriage and severe neurological birth ...

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