The authors are grateful to Dr. Joshua Beckham at the University of Texas at Austin for technical support with molecular docking. This study was partly supported by funding from the Ministry of Science and Technology of Taiwan (MOST107-2320-B-037-002 to C.-J.L. and L.-T.L.; MOST106-2320-B-038-021 and MOST107-2320-B-038-034-MY3 to L.-T.L.).

NOTE: All cell culture and virus infections must be conducted in certified biosafety hoods that are appropriate for the biosafety level of the samples being handled. The two tannin-class of small molecules chebulagic acid (CHLA) and punicalagin (PUG), that were observed to efficiently block CVA16 infection9, are used as examples of candidate inhibitory agents. For basic principles in virology techniques, virus propagation, determination of virus titer, and concepts of plaque forming units (PFU) or multiplicity of infection (MOI), the reader is referred to reference10.
1. Cell Culture, Virus Preparation, Compound Preparation, and Compound Cytotoxicity
<ol>
	<li>Human rhabdomyosarcoma (RD) cells are host cells permissive to CVA16 infection11. Grow the RD cells in 10 mL of Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 200 U/mL penicillin G, 200 &#181;g/mL streptomycin, and 0.5 &#181;g/mL amphotericin B in T-75 flasks at 37 &#176;C in a 5% CO2 incubator.</li>
	<li>Prepare CVA16 by propagating the virus in RD cells and determine viral titer in PFU/mL. For optimized protocol, please refer to reference11.</li>
	<li>Prepare the test compounds and controls using their respective solvents: for example, dissolve CHLA and PUG in dimethyl sulfoxide (DMSO). For all infection steps, the basal medium consisted of DMEM plus 2% FBS and antibiotics. 
	NOTE: The final concentration of DMSO in the test compound treatments is equal to or below 0.25% in the experiments; 0.25% DMSO is included as a negative control treatment in the assays for comparison.</li>
	<li>Perform cytotoxicity assay of the test compounds on the RD cells using a cell viability determining reagent such as XTT ((2,3-bis[2-methoxy-4-nitro-5-sulfophenyl]-5-phenylamino)-carbonyl]-2H-tetrazolium hydroxide). For detailed protocol, please refer to reference12. Determine the cytotoxicity concentrations of the test compounds using an analytical software such as GraphPad Prism according to manufacturer&#8217;s protocol. Drug concentrations that do not significantly influence the cell viability (&#160;&#8805;95% viable cells) are used for the remainder of the study.</li>
</ol>
2. Time-of-drug-addition Assay
<ol>
	<li>To evaluate the influence of drugs on host cells prior to viral infection (pretreatment)
	<ol>
		<li>Seed RD cells in 12-well plates at a seeding density of 2 x 105 cells/well. Incubate overnight at 37 &#176;C in a 5% CO2 incubator to obtain a monolayer.</li>
		<li>Treat RD cells with test compounds at non-cytotoxic concentrations (determined from step 1.4) in 1 mL of basal media volume for 1 h or 4 h.</li>
		<li>Wash cells with 1-2 mL of PBS before adding 50 PFU/well of virus in basal medium (final volume of the inoculum is 300 &#956;L) for 1 h. Rock the plate every 15 min.</li>
		<li>Following the infection, wash the monolayers again using PBS, then overlay with 1 mL of basal media containing 0.8% methylcellulose for further incubation at 37 &#176;C in a 5% CO2 incubator.</li>
		<li>After 72 h of incubation, remove the overlay media and wash the wells using 2 mL of PBS.</li>
		<li>Fix the wells using 0.5 mL of 37% formaldehyde for 15 min.</li>
		<li>Remove the supernatant and wash again using PBS.</li>
		<li>Stain the wells using 0.5 mL of 0.5% crystal violet solution. Then remove the stain solution within 2 min and wash the wells with a gentle stream of water before air drying.</li>
		<li>Count the viral plaques by placing the plate on a white-light box. Calculate the percent (%) CVA16 infection as follows: (Mean # of plaque virus+drug / Mean # of plaque virus+DMSO control) &#215; 100%.</li>
	</ol>
	</li>
	<li>To evaluate the effect of adding the drugs and the virus concurrently (co-addition)
	<ol>
		<li>Seed RD cells in 12-well plates at a seeding density of 2 x 105 cells/well. Incubate overnight at 37 &#176;C in a 5% CO2 incubator to obtain a monolayer.</li>
		<li>Treat RD cells with the test compounds at the appropriate concentrations and 50 PFU/well of CVA16 (final volume of the inoculum is 300 &#956;L) simultaneously for 1 h. Rock the plate every 15 min.</li>
		<li>Wash cells with 1 mL of PBS and then overlay with 1-2 mL of basal media containing 0.8% methylcellulose for further incubation at 37 &#176;C in a 5% CO2 incubator.</li>
		<li>Stain viral plaques with crystal violet after 72 h post infection and determine the% CVA16 infection as described above.</li>
	</ol>
	</li>
	<li>To evaluate drug treatment effect after viral entry (post-infection)
	<ol>
		<li>Seed RD cells in 12-well plates at a seeding density of 2 x 105 cells/well. Incubate overnight at 37 &#176;C in a 5% CO2 incubator to obtain a monolayer.</li>
		<li>Inoculate the RD cells with 50 PFU/well of CVA16 (final volume of the inoculum is 300 &#956;L) for 1 h. Rock the plate every 15 min.</li>
		<li>Wash the wells with 1-2 mL of PBS and overlay the cells with basal media containing 0.8% methylcellulose and the appropriate concentrations of test compounds.</li>
		<li>Stain viral plaques with crystal violet and count after 72 h post infection and determine the% CVA16 infection incubations described above. 
		NOTE: Perform all PBS washes gently to avoid lifting the cells.</li>
	</ol>
	</li>
</ol>
3. Flow Cytometry-based Binding Assay
<ol>
	<li>Seed RD cells in 12-well plates at a seeding density of 2 x 105 cells/well. Incubate overnight at 37 &#176;C in a 5% CO2 incubator to achieve a monolayer.</li>
	<li>Pre-chill the cell monolayer at 4 &#176;C for 1 h.</li>
	<li>Infect RD cells with CVA16 (MOI = 100) in the presence and absence of the test compounds for 3 h at 4 &#176;C. 
	NOTE: Perform the viral inoculation on ice and the ensuing incubation in a 4 &#176;C refrigerator to maintain the temperature at 4 &#176;C, which permits viral binding but not entry.</li>
	<li>Remove virus inoculum and wash once with 1-2 mL of ice-cold PBS.</li>
	<li>Lift cells by adding 1 mL of ice-cold dissociation buffer to the wells on ice for 3 min, before collecting the cells and resuspending them in ice-cold flow cytometry buffer (1x PBS plus 2% FBS).</li>
	<li>Wash cells twice using the ice-cold flow cytometry buffer and fix the cells with 0.5 mL of 4% paraformaldehyde for 20 min on ice.</li>
	<li>Wash the cells using PBS to remove any unbound or weakly bound viruses, and then stain the cells with 1 mL of anti-VP1 antibody (1:2,000; diluted in PBS containing 3% BSA) on ice for 1 h, followed by incubation with a secondary Alexa 488-conjugated anti-mouse IgG (1:250; diluted in PBS containing 3% BSA) on ice for 1 h. Perform PBS washes (3 times) following each antibody treatment.</li>
	<li>Resuspend the cells in 0.5 mL of the ice-cold flow cytometry buffer and perform flow cytometry analysis on a flow cytometer using standard procedures. Present data in histograms using the associated software and quantitate for bar graph representation.</li>
</ol>
4. Viral Inactivation Assay
<ol>
	<li>Perform the viral inactivation assay as previously described12 using the following conditions: 
	- A starting concentration of 106 PFU/mL of CVA16. 
	- RD cell monolayers in 12-well plates from a seeding density of 2 x 105 cells/well. 
	- 50-fold dilution for titrating out the drug compounds resulting in a final virus concentration of 50 PFU/well. 
	- Wash steps using 1-2 mL of PBS. 
	- Overlay media containing 0.8% methylcellulose.</li>
	<li>Perform final readout of viral infection using the crystal violet staining of viral plaques procedure as detailed above.</li>
</ol>
5. Molecular Docking Analysis
<ol>
	<li>Download 3D molecules of test compounds from PubChem (https://pubchem.ncbi.nlm.nih.gov/). If molecules do not have a 3D structure uploaded, download the 2D structures or use the SMILES string sequence and transform into 3D molecules via a molecular program (e.g. CORINA).</li>
	<li>Download viral biological assembly unit from RCSB Protein Data Bank (https://www.rcsb.org/) and prepare the viral structure model using a biocomputing program (e.g. UCSF Chimera). For example, in the case of CVA16 mature virion crystal structure (PDB: 5C4W)3, delete solvents from the PDB file, replace incomplete side chains using data from the Dunbrach 2010 Rotamer Library, and add hydrogens and charges to the structure as previously reported13. Docking targets can be any relevant viral proteins for the intended analysis with a biological assembly information (Protein Data Bank).</li>
	<li>Dock test compounds onto the prepared virus unit using for example UCSF Chimera, and analyze the output files with a visualization software (e.g., Autodock Vina, PyMol):
	<ol>
		<li>Upload the test compound file into UCSF Chimera as the &#8216;ligand&#8217; and perform blind docking by selecting the whole prepared viral protein as the &#8216;receptor&#8217;. Use the computer mouse or trackpad to resize the search volume to the entire &#8216;receptor&#8217;. In &#8216;Advanced options&#8217;, allow the number of binding modes to be at maximum. Docking frames will be automatically ranked from highest to lowest binding energy.</li>
		<li>(Optional) Further to blind docking, confine the docking site onto the viral protein in regions of interest derived from the blind docking results using the mouse or trackpad again to reduce the search volume (e.g., 100 &#197; x 100 &#197; x 100 &#197;). This step helps confirm the blind docking results and increases specificity.</li>
		<li>Use a molecular graphics system (e.g., PyMol) to analyze the binding modes&#8217; positions by uploading the docking file. Find polar contacts from the compound to the viral protein by selecting the &#8216;ligand&#8217; and identifying polar contacts with the option &#8216;to any atoms&#8217;; examine the results.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>Legay, F., 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=Fatal+coxsackievirus+A-16+pneumonitis+in+adult.">Fatal coxsackievirus A-16 pneumonitis in adult.</a> Emerging Infectious Diseases. 13, 1084-1086 (2007).</li><li>Wang, C. Y., Li Lu, ., Wu, F., H, M., Lee, C. Y., Huang, L. 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The authors declare that they have no conflict of interest.

In this report, we described the protocols that are useful for the identification of antiviral candidates that target viral entry, in particular against the non-enveloped CVA16. The assays are designed in ways to dissect the early events during viral entry, which is helpful to clarify the mechanism(s) of action and potential target(s) of the test agents&#39; antiviral activity. The &#39;time-of-drug-addition assay&#39; permits to broadly determine the potential target of the test compounds, for instance the uninfected ho...

Hand, foot, and mouth disease (HFMD) is a disease most commonly caused by coxsackievirus A16 (CVA16) and enterovirus 71 (EV71) in young children. Recently across the Asia-Pacific region, there has been a significant uptick in CVA16-induced HFMD. While symptoms can be mild, severe complications can occur that affect the brain and the heart, with potential fatality1,2. At present, there are no licensed antiviral therapies or vaccinations available for CVA16, and thus there is a pressing need to develop antiviral strategies to curb future outbreaks and the associated complications.
CVA16 is a non-enveloped virus which has an icosahedral capsid assembled from pentamers that each contain 4 structural proteins namely VP1, VP2, VP3, and VP4. Encircling each five-fold axis in the pentamer is a &#39;canyon&#39; region that shows as a depression and is noted for its role in receptor binding3. At the bottom of this canyon lies a hydrophobic pocket in the VP1 region that contains a natural fatty ligand named sphingosine (SPH). Cellular receptors, such as human P selectin glycoprotein ligand 1 (PSGL-1) and scavenger receptor class B member 2 (SCARB2), have been suggested to play a role in viral binding by displacing this ligand which results in conformational changes to the capsid and the subsequent ejection of viral genome into the host cell4,5,6. Identifying possible inhibitors that block the successive events in the viral entry process could provide potential therapeutic strategies against CVA16 infection.
The steps in the virus life cycle can be dissected through experimental approaches as targets to help identify mode-specific antiviral agents. A time-of-drug-addition analysis examines the drug treatment effect at different times during the viral infection, including pre-entry (added prior to the virus infection), entry (added concurrent to the virus infection), and post-entry (added following the virus infection)7. The impact can be assessed using a standard plaque assay by quantitating the number of viral plaques formed in each of the treatment conditions. The flow cytometry-based viral binding assay determines if the drug prevents viral attachment to host cells. This is achieved by shifting the temperature from 37 &#176;C, at which the majority of human virus infections occur, to 4 &#176;C, where the virions are able to bind to the host cell surface but are unable to enter the cells7. The cell membrane-bound virus particles are then quantified through immunostaining against viral antigens and assessed by flow cytometry. The viral inactivation assay on the other hand helps to assess potential physical interactions of the drug with free virus particles, either shielding or neutralizing the virions, or causing aggregations or conformational changes that render them inactive for subsequent interactions with the host cell surface during the infection8,9. In this experiment, the viral inoculum is allowed to first incubate with the drug before being diluted to titrate out the drug prior to infecting the host cell monolayer and performing a standard plaque assay8. Finally, molecular docking is a powerful tool to predict potential drug interaction sites on the virion surface, including the viral glycoproteins from enveloped viruses and the viral capsid proteins from non-enveloped viruses, by using computational algorithms. This helps to mechanistically pinpoint targets of the drug&#39;s mode of action and provide useful information that can be further validated by downstream assays.
We recently employed the above described methods to identify antiviral compounds that efficiently blocked infection by the non-enveloped CVA169. Herein, the detailed protocols that were used are described and discussed.

<table border="0" cellpadding="0" cellspacing="0" style="width:824px;" width="824">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">4% Paraformaldehyde</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">AL-158127-500G</td>
			<td style="width:232px;"></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:216px;">Alexa 488-conjugated anti-mouse IgG</td>
			<td style="width:205px;">Invitrogen</td>
			<td style="width:171px;">A11029</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Amphotericin B</td>
			<td style="width:205px;">GIBCO</td>
			<td style="width:171px;">15290-018</td>
			<td></td>
		</tr>
		<tr height="61">
			<td height="61" style="height:61px;width:216px;">Anti-VP1 antibody</td>
			<td style="width:205px;">Merck-Millipore</td>
			<td style="width:171px;">MAB979</td>
			<td style="width:232px;">Anti-Enterovirus 71 Antibody, cross-reacts with Coxsackie A16, clone 422-8D-4C-4D</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Beckman Coulter Cytometer</td>
			<td style="width:205px;">Beckman Coulter</td>
			<td style="width:171px;">FC500</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Corina</td>
			<td style="width:205px;">Molecular Networks GmbH</td>
			<td style="width:171px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Crystal violet</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">C3886-100G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMEM</td>
			<td style="width:205px;">GIBCO</td>
			<td style="width:171px;">11995-040</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">DMSO</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">D5879</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">FBS</td>
			<td style="width:205px;">GIBCO</td>
			<td style="width:171px;">26140-079</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Formaldehyde</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">F8775</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Graphpad Prism</td>
			<td style="width:205px;">GraphPad</td>
			<td style="width:171px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Heparin sodium salt</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">H3393</td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:216px;">In vitro toxicology assay kit, XTT-based</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">TOX2</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Methylcellulose</td>
			<td style="width:205px;">Sigma</td>
			<td style="width:171px;">M0512-100G</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PBS pH 7.4</td>
			<td style="width:205px;">GIBCO</td>
			<td style="width:171px;">10010023</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">Penicillin-Streptomycin</td>
			<td style="width:205px;">GIBCO</td>
			<td style="width:171px;">15070-063</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:216px;">PyMol</td>
			<td style="width:205px;">Schr&#246;dinger</td>
			<td style="width:171px;"></td>
			<td></td>
		</tr>
		<tr height="41">
			<td height="41" style="height:41px;width:216px;">UCSF Chimera</td>
			<td style="width:205px;">University of California, San Francisco</td>
			<td style="width:171px;"></td>
			<td></td>
		</tr>
	</tbody>
</table>

use of viral entry assays and molecular docking analysis for the identification of antiviral candidates against coxsackievirus a16

Antiviral assays that mechanistically examine viral entry are pertinent to discern at which step the evaluated agents are most effective, and allow for the identification of candidate viral entry inhibitors. Here, we present the experimental approaches for the identification of small molecules capable of blocking infection by the non-enveloped coxsackievirus A16 (CVA16) through targeting the virus particles or specific steps in early viral entry. Assays include the time-of-drug-addition analysis, flow cytometry-based viral binding assay, and viral inactivation assay. We also present a molecular docking protocol utilizing virus capsid proteins to predict potential residues targeted by the antiviral compounds. These assays should help in the identification of candidate antiviral agents that act on viral entry. Future directions can explore these possible inhibitors for further drug development.

The time-of-drug-addition assay is indicated in Figure 1 and shows the influence from treatment using the small molecules CHLA and PUG on CVA16 infection either pre-viral entry (pretreatment), during viral entry (co-addition), or post-viral entry (post-infection). Both small molecules only produced marginal impact against CVA16 infectivity whether in the pretreatment of the host cells prior to viral infection (Figure 1A) or in th...

Watch this Scientific Journal Video about Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16 at JoVE.com

Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

The goal of the protocol is to illustrate the different assays relating to viral entry that can be used to identify candidate viral entry inhibitors.

Antiviral assays that mechanistically examine viral entry are pertinent to discern at which step the evaluated agents are most effective, and allow for ...

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Immunology and Infection

7.8K Views.  University of Texas at Austin. The goal of the protocol is to illustrate the different assays relating to viral entry that can be used to identify candidate viral entry inhibitors.

Video: Use of Viral Entry Assays and Molecular Docking Analysis for the Identification of Antiviral Candidates against Coxsackievirus A16

The Use of Drip Flow and Rotating Disk Reactors for Staphylococcus aureus Biofilm Analysis

Most microbes in nature are thought to exist as surface-associated communities in biofilms.1 Bacterial biofilms are encased within a matrix and attached to a surface.2 Biofilm formation and development are commonly studied in the laboratory using batch systems such as microtiter plates or flow systems, such as flow-cells. These methodologies are useful for screening mutant and chemical libraries (microtiter plates)3 or growing biofilms for visualization (flow cells)4. Here we present detailed protocols for growing Staphylococcus aureus in two additional types of flow system biofilms: the drip flow biofilm reactor and the rotating disk biofilm reactor.
Drip flow biofilm reactors are designed for the study of biofilms grown under low shear conditions.5 The drip flow reactor consists of four parallel test channels, each capable of holding one standard glass microscope slide sized coupon, or a length of catheter or stint. The drip flow reactor is ideal for microsensor monitoring, general biofilm studies, biofilm cryosectioning samples, high biomass production, medical material evaluations, and indwelling medical device testing.6,7,8,9
The rotating disk reactor consists of a teflon disk containing recesses for removable coupons.10 The removable coupons can by made from any machinable material. The bottom of the rotating disk contains a bar magnet to allow disk rotation to create liquid surface shear across surface-flush coupons. The entire disk containing 18 coupons is placed in a 1000 mL glass side-arm reactor vessel. A liquid growth media is circulated through the vessel while the disk is rotated by a magnetic stirrer. The coupons are removed from the reactor vessel and then scraped to collect the biofilm sample for further study or microscopy imaging. Rotating disc reactors are designed for laboratory evaluations of biocide efficacy, biofilm removal, and performance of anti-fouling materials.9,11,12,13

The Use of Drip Flow and Rotating Disk Reactors for Staphylococcus aureus Biofilm Analysis

Protocols for utilizing open system flow biofilms with drip flow reactors and rotating disk reactors are presented in detail.

Most microbes in nature are thought to exist as surface-associated communities in biofilms.1  Bacterial biofilms are encased within a matrix and attached ...

Quantitative Analyses of all Influenza Type A Viral Hemagglutinins and Neuraminidases using Universal Antibodies in Simple Slot Blot Assays

Hemagglutinin (HA) and neuraminidase (NA) are two surface proteins of influenza viruses which are known to play important roles in the viral life cycle and the induction of protective immune responses1,2. As the main target for neutralizing antibodies, HA is currently used as the influenza vaccine potency marker and is measured by single radial immunodiffusion (SRID)3. However, the dependence of SRID on the availability of the corresponding subtype-specific antisera causes a minimum of 2-3 months delay for the release of every new vaccine. Moreover, despite evidence that NA also induces protective immunity4, the amount of NA in influenza vaccines is not yet standardized due to a lack of appropriate reagents or analytical method5. Thus, simple alternative methods capable of quantifying HA and NA antigens are desirable for rapid release and better quality control of influenza vaccines.
Universally conserved regions in all available influenza A HA and NA sequences were identified by bioinformatics analyses6-7. One sequence (designated as Uni-1) was identified in the only universally conserved epitope of HA, the fusion peptide6, while two conserved sequences were identified in neuraminidases, one close to the enzymatic active site (designated as HCA-2) and the other close to the N-terminus (designated as HCA-3)7. Peptides with these amino acid sequences were synthesized and used to immunize rabbits for the production of antibodies. The antibody against the Uni-1 epitope of HA was able to bind to 13 subtypes of influenza A HA (H1-H13) while the antibodies against the HCA-2 and HCA-3 regions of NA were capable of binding all 9 NA subtypes. All antibodies showed remarkable specificity against the viral sequences as evidenced by the observation that no cross-reactivity to allantoic proteins was detected. These universal antibodies were then used to develop slot blot assays to quantify HA and NA in influenza A vaccines without the need for specific antisera7,8. Vaccine samples were applied onto a PVDF membrane using a slot blot apparatus along with reference standards diluted to various concentrations. For the detection of HA, samples and standard were first diluted in Tris-buffered saline (TBS) containing 4M urea while for the measurement of NA they were diluted in TBS containing 0.01% Zwittergent as these conditions significantly improved the detection sensitivity. Following the detection of the HA and NA antigens by immunoblotting with their respective universal antibodies, signal intensities were quantified by densitometry. Amounts of HA and NA in the vaccines were then calculated using a standard curve established with the signal intensities of the various concentrations of the references used. 
Given that these antibodies bind to universal epitopes in HA or NA, interested investigators could use them as research tools in immunoassays other than the slot blot only.

A simple slot blot method was developed for the quantification of influenza viral hemagglutinin and neuraminidase using universal antibodies targeting their most conserved sequences identified through bioinformatics analyses. This innovative approach may provide a useful alternative to quantitative determination of all viral hemagglutinin and neuraminidase.

Hemagglutinin (HA) and neuraminidase (NA) are two surface proteins of influenza viruses which are known to play important roles in the viral life cycle ...

Amplifying and Quantifying HIV-1 RNA in HIV Infected Individuals with Viral Loads Below the Limit of Detection by Standard Clinical Assays

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below 50-75 copies/ml) is necessary to gain insight to viral dynamics and virus host interactions in patients who naturally control the infection and those who are on combination antiretroviral therapy (cART). 
Here we describe how to amplify viral genomes by single genome sequencing (the SGS protocol) 13, 19 and how to accurately quantify HIV-1 RNA in patients with low viral loads (the single-copy assay (SCA) protocol) 12, 20. 
The single-copy assay is a real-time PCR assay with sensitivity depending on the volume of plasma being assayed. If a single virus genome is detected in 7 ml of plasma, then the RNA copy number is reported to be 0.3 copies/ml. The assay has an internal control testing for the efficiency of RNA extraction, and controls for possible amplification from DNA or contamination. Patient samples are measured in triplicate.
The single-genome sequencing assay (SGS), now widely used and considered to be non-labor intensive 3, 7, 12, 14, 15,is a limiting dilution assay, in which endpoint diluted cDNA product is spread over a 96-well plate. According to a Poisson distribution, when less than 1/3 of the wells give product, there is an 80% chance of the PCR product being resultant of amplification from a single cDNA molecule. SGS has the advantage over cloning of not being subjected to resampling and not being biased by PCR-introduced recombination 19. However, the amplification success of SCA and SGS depend on primer design. Both assays were developed for HIV-1 subtype B, but can be adapted for other subtypes and other regions of the genome by changing primers, probes, and standards.

Quantifying levels of HIV-1 RNA in plasma and sequencing single HIV-1 genomes from individuals with viral loads below the limit of detection (50-75 copies/ml) is difficult. Here we describe how to extract and quantify plasma viral RNA using a real time PCR assay that reliably measures HIV-1 RNA down to 0.3 copies/ml and how to amplify viral genomes by single genome sequencing, from samples with very low viral loads.

Amplifying viral genes and quantifying HIV-1 RNA in HIV-1 infected individuals with viral loads below the limit of detection by standard assays (below ...

Assays for the Identification of Novel Antivirals against Bluetongue Virus

To identify potential antivirals against BTV, we have developed, optimized and validated three assays presented here. The CPE-based assay was the first assay developed to evaluate whether a compound showed any antiviral efficacy and have been used to screen large compound library. Meanwhile, cytotoxicity of antivirals could also be evaluated using the CPE-based assay. The dose-response assay was designed to determine the range of efficacy for the selected antiviral, i.e. 50% inhibitory concentration (IC50) or effective concentration (EC50), as well as its range of cytotoxicity (CC50). The ToA assay was employed for the initial MoA study to determine the underlying mechanism of the novel antivirals during BTV viral lifecycle or the possible effect on host cellular machinery. These assays are vital for the evaluation of antiviral efficacy in cell culture system, and have been used for our recent researches leading to the identification of a number of novel antivirals against BTV.

Three assays, including the cytopathic effect (CPE)-based assay, dose-response assay and Time-of-Addition (ToA) assay have been developed, optimized, validated and utilized to identify novel antivirals against Bluetongue virus (BTV), as well as to determine the possible Mechanism-of-Action (MoA) for newly identified antivirals.

To identify potential antivirals against BTV, we have  developed, optimized and validated three assays presented here. The CPE-based  assay was the first ...

Viral Concentration Determination Through Plaque Assays: Using Traditional and Novel Overlay Systems

Plaque assays remain one of the most accurate methods for the direct quantification of infectious virons and antiviral substances through the counting of discrete plaques (infectious units and cellular dead zones) in cell culture. Here we demonstrate how to perform a basic plaque assay, and how differing overlays and techniques can affect plaque formation and production. Typically solid or semisolid overlay substrates, such as agarose or carboxymethyl cellulose, have been used to restrict viral spread, preventing indiscriminate infection through the liquid growth medium. Immobilized overlays restrict cellular infection to the immediately surrounding monolayer, allowing the formation of discrete countable foci and subsequent plaque formation. To overcome the difficulties inherent in using traditional overlays, a novel liquid overlay utilizing microcrystalline cellulose and carboxymethyl cellulose sodium has been increasingly used as a replacement in the standard plaque assay. Liquid overlay plaque assays can be readily performed in either standard 6 or 12 well plate formats as per traditional techniques and require no special equipment. Due to its liquid state and subsequent ease of application and removal, microculture plate formats may alternatively be utilized as a rapid, accurate and high throughput alternative to larger scale viral titrations. Use of a non heated viscous liquid polymer offers the opportunity to streamline work, conserves reagents, incubator space, and increases operational safety when used in traditional or high containment labs as no reagent heating or glassware are required. Liquid overlays may also prove more sensitive than traditional&#160;overlays for certain heat labile viruses.

Plaque assays are the gold standard for viral quantification, utilizing entrapping overlays on host cellular monolayers to determine viral titers. While various semisolid overlays have traditionally been used, here we demonstrate plaque techniques comparing semisolid overlays to a novel liquid microcrystalline cellulose among several families of viruses.

Plaque assays remain one of the most accurate methods for the direct quantification of infectious virons and antiviral substances through the counting of ...

Immunofluorescence to Monitor the Cellular Uptake of Human Lactoferrin and its Associated Antiviral Activity Against the Hepatitis C Virus

Immunofluorescence is a laboratory technique commonly used to study many aspects of biology. It is typically used to visualize the distribution and/or localization of a target molecule in cells and tissues. Immunofluorescence relies on the specificity of fluorescent-labelled antibodies against their corresponding antigens within a cell. Both direct and indirect immunofluorescence approaches can be used which rely on the use of antibodies linked with a fluorochrome. Direct immunofluorescence is less frequently used because it provides lower signal, involves higher cost and less flexibility. In contrast, indirect immunofluorescence is more commonly used because of its high sensitivity and provides an amplified signal since more than one secondary antibody can attach to each primary antibody. In this manuscript, both epifluorescence microscopy and confocal microscopy were used to monitor the internalization of human lactoferrin, an important component of the immune system, into hepatic cells. Moreover, we monitored the inhibitory potential of hLF on the intracellular replication of the Hepatitis C virus using immunofluorescence. Both the advantages and disadvantages associated with these approaches are discussed.

The human lactoferrin (hLF) is a component of the immune system. In this study, immunofluorescence assays are used to demonstrate both the hepatocellular uptake of hLF and a qualitative reduction in the hepatitis C virus replication upon treatment with hLF.

Immunofluorescence is a laboratory technique commonly used to study many aspects of biology. It is typically used to visualize the distribution and/or ...

Early Viral Entry Assays for the Identification and Evaluation of Antiviral Compounds

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic approach to identify and evaluate antiviral agents that target specific steps of the viral entry. In this report, the methods of examining viral inactivation, viral attachment, and viral entry/fusion as antiviral assays for such purposes are described, using hepatitis C virus as a model. These assays should be useful for discovering novel antagonists/inhibitors to early viral entry and help expand the scope of candidate antiviral agents for further drug development.

Here, we present a protocol that examines specific steps of the viral entry to identify and evaluate novel antiviral agents.

Cell-based systems are useful for discovering antiviral agents. Dissecting the viral life cycle, particularly the early entry stages, allows a mechanistic ...

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. burnetii DNA in cell cultures and clinical samples. PCR requires specialized equipment and extensive end user training, and therefore, it is not suitable for routine work especially in a resource-constrained area. We have developed a loop-mediated isothermal amplification (LAMP) assay to detect the presence of C. burnetii in patient samples. This method is performed at a single temperature around 60 &#176;C in a water bath or heating block. The sensitivity of this LAMP assay is very similar to PCR with a detection limit of about 25 copies per reaction. This report describes the preparation of the reaction using lyophilized reagents and visualization of results using hydroxynaphthol blue (HNB) or a UV lamp with fluorescent intercalating dye in the reaction. The LAMP reagents were lyophilized and stored at room temperature (RT) for one month without loss of detection sensitivity. This LAMP assay is particularly robust because the reaction mixture preparation does not involve complex steps. This method is ideal for use in resource-limited settings where Q fever is endemic.

The Development of Lyophilized Loop-mediated Isothermal Amplification Reagents for the Detection of Coxiella burnetii

We described here a simple loop-mediated isothermal amplification (LAMP) method using lyophilized reagents for the detection of C. burnetii in patient samples.

Coxiella burnetii, the agent causing Q fever, is an obligate intracellular bacterium. PCR based diagnostic assays have been developed for detecting C. ...

Swab Sampling Method for the Detection of Human Norovirus on Surfaces

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the person-to-person route or indirectly through environmental surfaces or food, contaminated fomites and inanimate surfaces are important vehicles for the spread of the virus during norovirus outbreaks.
We developed and evaluated a protocol using macrofoam swabs for the detection and typing of human noroviruses from hard surfaces. Compared with fiber-tipped swabs or antistatic wipes, macrofoam swabs allow virus recovery (range 1.2-33.6%) from toilet seat surfaces of up to 700 cm2. The protocol includes steps for the extraction of the virus from the swabs and further concentration of the viral RNA using spin columns. In total, 127 (58.5%) of 217 swab samples that had been collected from surfaces in cruise ships and long-term care facilities where norovirus gastroenteritis had been reported tested positive for GII norovirus by RT-qPCR. Of these 29 (22.8%) could be successfully genotyped. In conclusion, detection of norovirus on environmental surfaces using the protocol we developed may assist in determining the level of environmental contamination during outbreaks as well as detection of virus when clinical samples are not available; it may also facilitate monitoring of effectiveness of remediation strategies.

A macrofoam based sampling methodology was developed and evaluated for the detection and quantification of norovirus on environmental hard surfaces.

Human noroviruses are a leading cause of epidemic and sporadic gastroenteritis worldwide. Because most infections are either spread directly via the ...

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins

The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and cellular proteins by mass spectrometry. Although proteins that interact with viral genomes play major roles in determining the outcome of infection, a comprehensive analysis of viral genome associated proteins was not previously feasible. Here we demonstrate a method that enables the direct purification of HSV-1 genomes from infected cells. Replicating viral DNA is selectively labeled with modified nucleotides that contain an alkyne functional group. Labeled DNA is then specifically and irreversibly tagged via the covalent attachment of biotin azide via a copper(I)-catalyzed azide-alkyne cycloaddition or click reaction. Biotin-tagged DNA is purified on streptavidin-coated beads and associated proteins are eluted and identified by mass spectrometry. This method enables the selective targeting and isolation of HSV-1 replication forks or whole genomes from complex biological environments. Furthermore, adaptation of this approach will allow for the investigation of various aspects of herpesviral infection, as well as the examination of the genomes of other DNA viruses.

The goal of this protocol is to specifically tag and selectively isolate viral DNA from infected cells for the characterization of viral genome associated proteins.