Name: vaccinia reporter viruses for quantifying viral function at all stages of gene expression
Uploaded: 2014-05-15T13:45:00
Description: Watch this Scientific Journal Video about Vaccinia Reporter Viruses for Quantifying Viral Function at All Stages of Gene Expression at JoVE.com

We thank SIGA Technologies (Corvallis, OR) for providing ST-246. D.K.R. was supported by an NIH training grant in immunology to Boston University (5T32AI 7309). This work was supported in part by P41 086180, NIH RO1AI1096159-01, and RO3 &#160;(to J.H.C.).

1. Plate Cells
<ol>
	<li>Dissociate HeLa cells from plate and dilute in growth media (DMEM, 2 mM L-glut, 10% FBS) to approximately 2.0 x 105 cells/ml. Dispense 100 &#956;l/well in a black-walled, clear flat-bottom 96-well plate (20,000 cells/well).</li>
	<li>Incubate cells for 24 hr until confluent in a 37 &#176;C incubator + 5% CO2.</li>
</ol>
2. Infect Cells
<ol>
	<li>Dilute virus and infect cells.
	<ol>
		<li>Thaw TrpV (Triple virus; Early Venus, Intermediate mCherry, ...

<ol>
	<li>Yen, J., Golan, R., Rubins, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vaccinia+virus+infection+&amp;+temporal+analysis+of+virus+gene+expression:+part+1.">Vaccinia virus infection &amp; temporal analysis of virus gene expression: part 1.</a> J Vis Exp. 26 (26), (2009).</li><li>Hansen, S. G., Cope, T. A., Hruby, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=BiZyme:+a+novel+fusion+protein-mediating+selection+of+vaccinia+virus+recombinants+by+fluorescence+and+antibiotic+resistance.">BiZyme: a novel fusion protein-mediating selection of vaccinia virus recombinants by fluorescence and antibiotic resistance.</a> BioTechniques. 32 (5), 1182-1187 (2002).</li><li>Popov, S., Mirshahidi, S., Essono, S., Song, R., Wang, X., Ruprecht, R. 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M., Moss, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualization+of+intracellular+movement+of+vaccinia+virus+virions+containing+a+green+fluorescent+protein-B5R+membrane+protein+chimera.">Visualization of intracellular movement of vaccinia virus virions containing a green fluorescent protein-B5R membrane protein chimera.</a> Journal of Virology. 75 (10), 4802-4813 (2001).</li><li>Johnson, M. C., Damon, I. K., Karem, K. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid,+high-throughput+vaccinia+virus+neutralization+assay+for+testing+smallpox+vaccine+efficacy+based+on+detection+of+green+fluorescent+protein.">A rapid, high-throughput vaccinia virus neutralization assay for testing smallpox vaccine efficacy based on detection of green fluorescent protein.</a> Journal of Virological Methods. 150 (1-2), 14-20 (2008).</li><li>Dower, K., Rubins, K. H., Hensley, L. E., Connor, J. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+Vaccinia+reporter+viruses+for+rapid,+high+content+analysis+of+viral+function+at+all+stages+of+gene+expression.">Development of Vaccinia reporter viruses for rapid, high content analysis of viral function at all stages of gene expression.</a> Antiviral Research. 91 (1), 72-80 (2011).</li><li>Dower, 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=Identification+of+a+pyridopyrimidinone+inhibitor+of+orthopoxviruses+from+a+diversity-oriented+synthesis+library.">Identification of a pyridopyrimidinone inhibitor of orthopoxviruses from a diversity-oriented synthesis library.</a> Journal of Virology. 86 (5), 2632-2640 (2012).</li><li>De Clercq, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+Potential+of+the+Acyclic+Nucleoside+Phosphonates+Cidofovir,+Adefovir,+and+Tenofovir+in+Treatment+of+DNA+Virus+and+Retrovirus+Infections.">Clinical Potential of the Acyclic Nucleoside Phosphonates Cidofovir, Adefovir, and Tenofovir in Treatment of DNA Virus and Retrovirus Infections.</a> Clinical Microbiology Reviews. 16 (4), 569-596 (2003).</li><li>Prichard, M. N., Kern, E. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Orthopoxvirus+Targets+for+the+Development+of+New+Antiviral+Agents.">Orthopoxvirus Targets for the Development of New Antiviral Agents.</a> Antiviral Research. 10, (2012).</li><li>Fenner, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+successful+eradication+campaign.+Global+eradication+of+smallpox.">A successful eradication campaign. Global eradication of smallpox.</a> Reviews of Infectious Diseases. 4 (5), 916-930 (1982).</li><li>Breman, J. G., Henderson, D. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Poxvirus+dilemmas--monkeypox,+smallpox,+and+biologic+terrorism.+The+New+England.">Poxvirus dilemmas--monkeypox, smallpox, and biologic terrorism. The New England.</a> Journal of Medicine. 339 (8), 556-559 (1998).</li><li>Baker, R. O., Bray, M., Huggins, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Potential+antiviral+therapeutics+for+smallpox,+monkeypox+and+other+orthopoxvirus+infections.">Potential antiviral therapeutics for smallpox, monkeypox and other orthopoxvirus infections.</a> Antiviral Research. 57, 1-2 (2003).</li><li>Rimoin, A. W., 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=Major+increase+in+human+monkeypox+incidence+30+years+after+smallpox+vaccination+campaigns+cease+in+the+Democratic+Republic+of+Congo.">Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo.</a> Proceedings of the National Academy of Sciences of the U S A. 107 (37), 16262-167 (2010).</li><li>Sodeik, B., Griffiths, G., Ericsson, M., Moss, B., Doms, R. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Assembly+of+vaccinia+virus:+effects+of+rifampin+on+the+intracellular+distribution+of+viral+protein+p65.">Assembly of vaccinia virus: effects of rifampin on the intracellular distribution of viral protein p65.</a> Journal of Virology. 68 (2), 1103-1114 (1994).</li><li>Grosenbach, D. W., Jordan, R., Hruby, D. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+of+the+small-molecule+antiviral+ST-246+as+a+smallpox+therapeutic.">Development of the small-molecule antiviral ST-246 as a smallpox therapeutic.</a> Future Virology. 6 (5), 653-671 (2011).</li><li>Broyles, S. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Vaccinia+virus+transcription.">Vaccinia virus transcription.</a> Journal of General Virology. 84 (9), 2293-2303 (2003).</li><li>Condit, R. C., Niles, E. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Regulation+of+viral+transcription+elongation+and+termination+during+vaccinia+virus+infection.">Regulation of viral transcription elongation and termination during vaccinia virus infection.</a> Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. 1577 (2), 325-336 (2002).</li><li>D&#237;az-Guerra, M., Rivas, C., Esteban, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Inducible+expression+of+the+2-5A+synthetase/RNase+L+system+results+in+inhibition+of+vaccinia+virus+replication.">Inducible expression of the 2-5A synthetase/RNase L system results in inhibition of vaccinia virus replication.</a> Virology. 227 (1), 220-228 (1997).</li><li>Cohrs, R. J., Condit, R. C., Pacha, R. F., Thompson, C. L., Sharma, O. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+ppp(A2&#8217;p)nA-dependent+RNase+by+a+temperature-sensitive+mutant+of+vaccinia+virus.">Modulation of ppp(A2&#8217;p)nA-dependent RNase by a temperature-sensitive mutant of vaccinia virus.</a> Journal of Virology. 63 (2), 948-951 (1989).</li><li>S&#225;nchez-Puig, J. M., S&#225;nchez, L., Roy, G., Blasco, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Susceptibility+of+different+leukocyte+cell+types+to+Vaccinia+virus+infection.">Susceptibility of different leukocyte cell types to Vaccinia virus infection.</a> Virology Journal. 1 (1), (2004).</li><li>Bengali, Z., Satheshkumar, P. S., Yang, Z., Weisberg, A. 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&#160;Here, we have described the practical usage of a multi-stage vaccinia reporter virus (TrpV), which provides reproducible, real-time feedback measures of virus replication. By using well-defined poxvirus inhibitors, we were able to show that TrpV responds in a manner consistent with the understood mechanism of action for each inhibitor. While the TrpV virus provides the most comprehensive information about virus stage progression, two-stage (IREV, LREV) and single-stage (EV, IV, LV) viruses can also be used similarl...

Traditionally, virus expression is studied using molecular biology techniques (e.g. northern blotting, western blotting, microarray hybridization, etc.) 1. While these methods are capable of providing detailed information with respect to categorizing expression changes of individual mRNAs or proteins, they are typically not amenable to real-time and high-throughput processes. Alternative approaches using fluorescence-based reporters have been applied previously when working with poxviruses; however, their development and usage has been motivated by varied aims. Several such methods were designed for selection of recombinant viruses 2,3. These techniques express EGFP upon proper incorporation and expression of exogenous DNA from recombinant vaccinia clones. Similarly, several vaccinia strains stably expressing soluble EGFP or GFP-tagged proteins expressed under a native vaccinia promoter have been widely used. These are typically used to quantify virus entry and replication during antibody-based neutralization assays, chemical inhibition, or comparison of antiviral effectiveness 4&#8211;6. While these viruses have proven useful, they are limited in their ability to provide detailed information about the point of inhibition due to their usage of a single ambiguous early/late viral promoter. Previous methods have also made use of EGFP protein with suboptimal signal-to-noise characteristics.

Due to the complexity of poxvirus replication and the lack of existing tools available to assay real-time changes in viral gene expression, we have developed a suite of single and multi stage reporter viruses 7,8. As described in previous publications, these viruses express one, two, or three spectrally distinct fluorescent proteins from native vaccinia promoters during early, intermediate, or late stages in infection. These viruses can be used as indicators of virus replication progress using a fluorescence microscope and they are equally well suited for high-throughput plate-and-reader based assays. These viruses are easy to use in place of wild type virus, growing with similar kinetics to reach equivalent titers 7. During the planning and creation of these viruses, much care was taken in selecting fluorophores that have high signal-to-background characteristics with superior folding efficiency to facilitate reliable quantification with rapid feedback to changes in expression (Venus, mCherry and TagBFP). Additionally, combinations of viral promoters were chosen which produce high fidelity, unambiguous stage-specific expression, providing information about the full range of early (C11R promoter), intermediate (G8R promoter) and late (F17R promoter) gene expression, in contrast to ambiguous early/late promoters.

These viruses can be used as a tool for investigating the life cycle of the prototypical poxvirus, vaccinia virus. Much is still not known about the host-virus interaction despite its long history of study. Vaccinia is complex, producing over 200 unique proteins, many of which are immunomodulatory and host antagonistic. Upon infection, vaccinia virus immediately begins early mRNA transcription. This is facilitated by an RNA polymerase and transcription factors that were loaded on the viral genome during virion packaging and held in a paused state until subsequent infection. This early expression mainly produces proteins required for suppression of the host immune system (mRNA decapping, dsRNA sequestration, and decoy receptor proteins as well as inhibitors of apoptosis, stress response, and Toll, IL, and NF-&#954;B signaling) and genome replication. Early expression also produces transcription factors necessary for intermediate expression. Intermediate expression includes the expression of late stage transcription factors. This expression cascade leads to production of structural and enzymatic virus proteins during late stages of infection, which are necessary for complete assembly of the mature vaccinia virion.&#160;&#160;&#160;&#160;&#160;

Our set of fluorescent reporter viruses allows for rapid progress to be made in the understanding of poxvirus biology. One of the most common and time-consuming methods in the field of virology is the growth assay. This typically involves infecting cells, enacting a series of treatments, harvesting virus by lysing infected cells, and quantifying the resulting viral titer by plaque assay. Using the reporter viruses described here allows real-time measurement of virus growth that can be easily assayed and compared between numerous treatments performed in parallel. We foresee this set of reagents will be used in various protocols for identifying alterations in viral gene expression in response to drug treatment, RNAi knockdown, or host range restriction.

This method also enables high-content analysis on a larger scale than previously available, allowing for high-throughput anti-viral drug screens for specifically-defined target stages of interest. While numerous potential treatments to combat poxvirus infection have been identified, the only FDA approved therapies effective for treating poxvirus infection are the acyclic phosphonate nucleoside, Cidofovir, and treatment with vaccinia immune globulin 9,10. Despite the eradication of smallpox in 1977 11, poxviruses remain a significant threat to human health 12. Cessation of widespread vaccination against Variola virus has led to increased susceptibility to other poxviruses 13. For example, regions of Central Africa previously protected by vaccination are experiencing a surge in Monkeypox virus infections 14. Significant concern has also been raised regarding the latent susceptibility to intentional release of Variola virus. Due to the limited therapies currently available, there is an urgent need for development of novel treatments. These reporter viruses allow rapid and high-throughput small molecule inhibitor screening for inhibition of a specific stage of viral replication. Identification of inhibitors that target viral expression stages currently not the target of inhibition will facilitate development of combination therapies with increased potency.


Much can be gleaned about vaccinia cell biology by observing changes in each stage&#8217;s gene expression. Attenuation by chemical or genetic manipulation of an infected host cell is typically expressed in terms of reduced viral titers. However, by comparing changes in each stage of the viral expression cascade, one can obtain a more complete understanding of how virus fitness is impacted by a particular treatment. These data have been shown to correlate well with the traditional virus titer output, but provide more detailed mechanistic information as well as high throughput capabilities 7.

<table border="0" cellpadding="0" cellspacing="0" width="1249">
	<tbody>
		<tr height="24">
			<td height="24" style="height:24px;width:747px;">Dulbecco&#39;s Modified Eagle Medium (DMEM)</td>
			<td style="width:231px;">Gibco</td>
			<td style="width:104px;">11995-065</td>
			<td style="width:167px;"></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Fetal Bovine Serum - Optima, Heat Inactivated (FBS)</td>
			<td>Atlanta Biologicals</td>
			<td>S12450H</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">200 mM L-Glutamine, (L-glut)</td>
			<td>Gibco</td>
			<td>25030-081</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">96 Well Flat Clear Bottom Black Polystyrene TC-Treated Microplates</td>
			<td>Corning</td>
			<td>3603</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">384 Well Flat Clear Bottom Black Polystyrene TC-Treated Microplates</td>
			<td>Corning</td>
			<td>3712</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Trypsin, 2X, Sterile, Irradiated</td>
			<td>Worthington Biochemical Corp.</td>
			<td>TRLVMF</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Phosphate-Buffered Saline (PBS)</td>
			<td>Gibco</td>
			<td>10010-023</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Dimethyl Sulfoxide, Cell Culture (DMSO)</td>
			<td>American Bioanalytical</td>
			<td>AB03091</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">1-&#946;-D-Arabinofuranosylcytosine&#160; (AraC), MW= 280 g/mol</td>
			<td>SigmaAldrich Co</td>
			<td>C6645</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">isatin &#946; -thiosemicarbazone (IBT), MW= 234 g/mol</td>
			<td>Fisher Scientific</td>
			<td>NC9075202</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">Rifampicin, MW= 823 g/mol</td>
			<td>SigmaAldrich Co</td>
			<td>R3501</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">ST-246, MW= 376 g/mol</td>
			<td>SIGA Labs, Corvallis, OR</td>
			<td></td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">8% Paraformaldehyde (formaldehyde) aqueous solution</td>
			<td>Electron Microscopy Sciences</td>
			<td>157-8</td>
			<td></td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;">TempPlate RT optically clear film</td>
			<td>USA Scientific</td>
			<td>2978-2700</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Opti-MEM Reduced Serum Medium</td>
			<td>Gibco</td>
			<td>31985-070</td>
			<td></td>
		</tr>
	</tbody>
</table>

vaccinia reporter viruses for quantifying viral function at all stages of gene expression

Poxviruses are a family of double stranded DNA viruses that include active human pathogens such as monkeypox, molluscum contagiousum, and Contagalo virus. The family also includes the smallpox virus, Variola. Due to the complexity of poxvirus replication, many questions still remain regarding their gene expression strategy. In this article we describe the conceptualization and usage of recombinant vaccinia viruses that enable real-time measurement of single and multiple stages of viral gene expression in a high-throughput format. This is enabled through the use of spectrally distinct fluorescent proteins as reporters for each of three stages of viral replication. These viruses provide a high signal-to-noise ratio while retaining stage specific expression patterns, enabling plate-based assays and microscopic observations of virus propagation and replication. These tools have uses for antiviral discovery, studies of the virus-host interaction, and evolutionary biology.

As an example of the typical usage of these viruses, the triple fluorescence-reporter virus was used to compare the point of inhibition of several well-defined poxvirus inhibitors.
HeLa cells were plated in tissue culture treated black-walled clear flat-bottom 96-well plates and incubated overnight. Confluent monolayers were infected at a multiplicity of infection (MOI) of 10 using either triple reporter virus (TrpV; Table 1) or promoter-less Venus (PLV) as detailed on the pla...

Watch this Scientific Journal Video about Vaccinia Reporter Viruses for Quantifying Viral Function at All Stages of Gene Expression at JoVE.com

Vaccinia Reporter Viruses for Quantifying Viral Function at All Stages of Gene Expression

We describe the usage of a fluorescent reporter vaccinia virus that enables real-time measurement of viral infectivity and gene expression through the stage-specific expression of spectrally distinct reporter fluorophores. We detail a plate-based method for accurately identifying the stage at which virus replication is affected in response to small molecule inhibition.

Poxviruses are a family of double stranded DNA viruses that include active human pathogens such as monkeypox, molluscum contagiousum, and Contagalo virus. ...

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