This work was supported in part by the Scripps Microarray Core Facility, and a contract from the Centers for Disease Control (J.C.P.). RPdV is a recipient of a Rubicon and VENI grant from the Netherlands Organization for Scientific Research (NWO). The Consortium for Functional Glycomics (http://www.functionalglycomics.org/) funded by NIGMS grant GM62116 (J.C.P.) provided several glycans used in this study. This is publication 29113 from The Scripps Research Institute.

NOTE: All steps are carried out at room temperature unless otherwise indicated.&#160;
1. Array Construction
<ol>
	<li>Glycan Preparation and Plate Setup
	<ol>
		<li>Prepare a stock of printing buffer. First make 500 ml of a 150 mM stock solution of dibasic sodium phosphate. Also make 50 ml of a 150 mM stock solution of monobasic sodium phosphate solution. In a flask, using a magnetic stir bar and pH meter, slowly titrate the dibasic sodium phosphate solution with the monobasic solution until a pH of 8.5 is reached. Add Tween-20 to 0.005%.</li>
		<li>Prepare the glycan samples. Dilute PAA conjugated glycans, (diLacNAc (Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;-PAA), 3SLNLN (Neu5Ac&#945;2-3Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;-PAA) and 6SLNLN (Neu5Ac&#945;2-6Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;-PAA (Figure 1A)) are to be diluted to 100&#181;g/ml in printing buffer from step1.1.1. Monovalent glycans, diLacNAc (Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;-(CH2)3NH2, 3SLNLN (Neu5Ac&#945;2-3Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;--(CH2)3NH2) and 6SLNLN (Neu5Ac&#945;2-6Gal&#946;1-4GlcNAc&#946;1-3Gal&#946;1-4GlcNAc&#946;--(CH2)3NH2)) to 100&#181;M in printing buffer from step 1.1.1. Finally, prepare the amine-functionalized dyes, to use as grid markers/landing lights. Dye marker spots are printed at 1 &#181;M. 
		NOTE: Atto488-NHS dye is used in our prints. However, any amine-functionalized dye, readable by the slide scanner is appropriate for this purpose.</li>
		<li>Transfer 10 &#181;l of each glycan sample to 384-well microtiter plates, used for the printing robot. Store unused glycans in printing buffer solution at -20 &#176;C in sealed tubes. Tansfer 10 &#181;l of the dye marker to the printing plate. &#160;</li>
	</ol>
	</li>
	<li>Printing 
	NOTE: All steps that concern touching or moving the slides must be done with gloves.
	<ol>
		<li>Place arrayer pins in the printing head according to the correct configuration of the layout. For this layout use one pin to print all samples and arrays. Print the glycans in blocks of six, skipping one feature (a feature is defined as single spot of a certain compound), on each side, such that spots of the same sample are not printed exactly beside each other. 
		NOTE: The end user must decide the configuration. &#160;</li>
		<li>Remove slides from bags, open boxes, and remove any dust particles or small pieces of plastic that might be on their surfaces by blowing ultra-high purity Nitrogen gas on each slide. Place the desired number of slides, coated side up, on the arrayer stage.</li>
		<li>Program the arrayer, use the parameters of 27 spots per visit to the source plate, using 3 &#34;pre-spots&#34; onto poly-L-lysine coated slides, to remove excess liquid at the tip of the printing pins
		<ol>
			<li>Turn on MPU (Main Power Unit) and Climate Control Unit. Open Tiling Analysis software on computer.</li>
			<li>Select layout to the print. Select Options &#8594; Pin Tool to be used for printing the array 1 x 1 print tool - 1 single pin. Select the Target tab &#8594; Tool Array Definition &#8594; Print Pattern and add the pitch (spot-to-spot distance), number of rows and columns to accommodate the samples to be printed, and the printing pattern of the samples (for this array an 8 x 8 printing pattern is used at 340 &#181;m pitch for 7 total samples).</li>
			<li>Select Target &#8594; Slide Layout and program the block-to-block distance to allow printing of each replicate array into the 48-well (4 x 12) slide template. Select Source and add the number of source pickups (1 for each sample when using 1 pin) (for this print 7 source pickups will be used to accommodate 6 sample wells and 1 dye marker well). 
			NOTE: The source dialogue should turn GREEN to show that the number of source visits matches the samples to be printed in the print pattern.</li>
			<li>Select Target&#160;&#8594; Adapter Plate and Slide Layout and adjust the slide number (5 slides are printed at a time for this print with 1 pre-spotting slide).</li>
			<li>Release the tray by clicking the T1 button to activate the tray and add the desired number of slides to the tray, paying close attention to the locations of the pre-spotting slide (BLUE) and &#34;real&#34; slides.</li>
			<li>Place plain glass slides on all remaining vacuum ports to block the vacuum and click OK to activate the vacuum. Check that all slides are held in place and click OK to return the tray to the home position.</li>
			<li>Load the printing plate into the plate holder and ensure the rack is set correctly in place. Click GO and allow the printing process to proceed.</li>
		</ol>
		</li>
		<li>Print the remaining 24 spots in replicates of 6 spots per array (4 arrays/source visit).</li>
		<li>Load the 384-well plates into the printer and begin printing. Maintain relative humidity, while printing, throughout the print between 55 and 65%. The printer stops after printing 5 slides. &#160; 
		NOTE: While the microarray in this assay is printed in a specific 8 x 8 pattern, different microarray printing robots will require equipment specific programming to achieve the desired layout. It is up to the end user to determine the most appropriate pattern given their equipments&#8217; specifications.</li>
	</ol>
	</li>
	<li>Humidification/Immobilizing 
	NOTE: Once the slides have finished printing, they undergo a temporary immobilization step, also called humidifying. Humidifying post-print helps to homogenize the sample attachment by re-wetting the spots and ensuring complete blocking.
	<ol>
		<li>Put slides in a 100% humidity chamber immediately after printing for a period of 30 min. Construct the chamber by placing very wet paper towels flat in the bottom of a large glass dish, placing the slides on some sort of rack, such as a test tube rack, print side up, and sealing with plastic wrap to trap in the moisture.</li>
		<li>Number slides with an alcohol/solvent resistant marking pen and store in a desiccation box. Desiccate overnight.</li>
	</ol>
	</li>
	<li>Numbering, Blocking, and Storage
	<ol>
		<li>Prepare the blocking buffer&#160;&#8211; 50 mM ethanolamine in 50 mM borate buffer. First, dissolve boric acid, in ddH2O, to a final concentration of 50 mM in a flask containing a magnetic stir bar. Stir the solution vigorously on a stirring plate until all solid has dissolved. While constantly stirring, add the appropriate amount of ethanolamine from a 16.54 M stock solution to reach the desired 50 mM concentration. Add concentrated sodium hydroxide to adjust to a final pH of 9.2.</li>
		<li>Immerse the printed slides in the blocking buffer solution for 1 hr.</li>
		<li>Following 1 hr, rinse the slides in ddH2O to remove any excess traces of blocking buffer. Dispose blocking buffer in an appropriate waste container.</li>
		<li>Transfer the slides to glass staining holders and spin dry. Dry arrays by placing them in a centrifuge equipped with swinging plate holders, at a speed of 10 x g for 5 min.</li>
		<li>Once the slides are dry, they can be incubated immediately or stored. Storage conditions are -20 &#176;C in a sealed plastic bag. &#160;</li>
	</ol>
	</li>
</ol>
2. Analyzing Glycan Binding Proteins
<ol>
	<li>Prepare a humidified chamber in which the arrays to be hybridized will fit. A simple chamber consists of a Pyrex dish, layered on the bottom with dampened paper towels and a rack, upon which the slides will rest.</li>
	<li>Use biotinylated lectins SNA (Sambuca nigra agglutinin) and ECA (Erythrina cristagalli agglutinin) at 10 &#956;g/ml + 2 &#181;g/ml of Streptavidin-555 dye, in probing buffer (PBS + 0.01% Tween-20). For HA (A/Vietnam/1203/04 H5N1 and A/KY/07 H1N1, in this example), use a starting concentration of 20 &#956;g/ml pre-complexed, as previously described 34. Briefly, make a HA:Mouse-&#945;-Strep:Goat-&#945;-Mouse-Alexa647 mixture in blocking buffer (PBS + 3%BSA + 0.01% Tween-20), at a 4:2:1 molar ratio. 
	NOTE: The array is probed with lectins to ascertain that glycans are immobilized and detectable (Figure 1B).</li>
	<li>Transfer the glycan binding protein-antibody mix solution of 20 &#181;l to a 384-well plate and incubate on ice for 30 min. Serially dilute lectin and HA samples 1:1, in their appropriate buffer, 8 times, by mixing 10 &#181;l of sample with 10 &#181;l of buffer.</li>
	<li>Pipette 8 &#181;l of the sample onto the micro-well surface and incubate in the sealed humidification (100% RH) chamber for 90 min.</li>
	<li>Wash the slides one at a time by holding the edges and dipping them four times in a mixture of PBS and 0.05% Tween, then four times in PBS, and finally four times in deionized H2O. Using the same drying protocol described in the blocking step, spin the arrays dry in a centrifuge for 5 min at 10 x g.</li>
</ol>
3. Scanning and Data Analyses 
NOTE: The glycan microarrays can be scanned at different settings, depending on the microarray scanner&#8217;s manufacturer. By varying the laser power and resolution, the instrument can produce an image with as many signals as possible within its dynamic range (Figure 1C).
<ol>
	<li>Use a fluorescent slide scanner and scan the arrays immediately after incubation with the glycan binding proteins. Take care to ensure the slide is correctly inserted into the scanning instrument.
	<ol>
		<li>Open scanning software. Click start to open the program. Connect to scanner: Scanner &#8594; Connect or green button in the Scanner navigation panel menu.</li>
		<li>Open autoloader door of the scanner. Place slides in slots in autoloader in specific order. Close autoloader door. Click &#34;read loader&#34; in the Tools navigation panel to auto detect slides in the scanner.</li>
		<li>Set scan parameter: Scanner &#8594; Scan parameters appropriate to the experiment (e.g. 635 laser power high, detection gain 50%). Scan slides: Scanner&#160;&#8594; scan. Select path by creating a folder to save the scan images and name individual scans. Do this prior to the actual scanning. Repeat for each individual slide. Click OK to start scanning.</li>
	</ol>
	</li>
	<li>Use the scanner software to set up the instrument and scan the slides. Set scanner to iteratively scan at low laser power (5 mW) with increasing gain settings of 25%, 50% and 75%. &#160; 
	NOTE: The settings can be tested and optimized, but keep in mind that each scan can possibly lower the fluorescence output of the dyes due to photobleaching.
	<ol>
		<li>Open data acquisition and analysis software such as Mapix software. Click start to open the program. Open scan image: File&#160;&#8594; open image. Open GAL file: Analyze&#160;&#8594; open grid and select the appropriate GAL file.</li>
		<li>Enter blocks mode: Image &#8594; blocks mode to move the grid. Use the grid markers to set the grid to the appropriate location on the slide. Adjust individual blocks as necessary to match the printed array.</li>
		<li>Enter spots mode: Image &#8594; spots mode to adjust location and size of individual spots within the block. Once all blocks and spots are adjusted and in place, measure signal intensities by Analyze&#160;&#8594; photometric calculations. Save the output file.</li>
	</ol>
	</li>
	<li>Once the slides have finished scanning, images are analyzed for binding signals with the image-processing program installed (Figure 1D-G). For image analysis, load a GAL (Array List) file over the scanned TIFF image. 
	NOTE: The GAL file contains both the spot layout pattern and identities of each spot location. GAL files for arrays are created by the printer software using a tab-delimited text file that contains the identities of the samples and their location in the 384-well source plate.</li>
	<li>Use the grid marker/landing lights printed on the microarrays to properly place the GAL grid. Individual spots may need to be moved individually, but a well-printed array will generally allow blocks within the grid to be placed with ease. Following grid placement, collect spot intensities by the software and saved as a tab-delimited text file (.txt). &#160;
	<ol>
		<li>Using spreadsheet program, open the output file from the scanner. Open the appropriate macro file from the folder location. Click View &#8594; Macro &#8594; RunMacro. &#160; 
		NOTE: The pre-written will copy the raw output data, remove unnecessary rows and columns, sort the data by sample, calculate the average mean signal minus background values and plot the resultant values in to an spread-sheet worksheet containing the graphs for each of the six samples tested on the array.</li>
	</ol>
	</li>
</ol>

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C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glycan+microarrays+for+decoding+the+glycome.">Glycan microarrays for decoding the glycome.</a> Annu Rev Biochem. 80, 797-823 (2011).</li><li>Song, 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=A+sialylated+glycan+microarray+reveals+novel+interactions+of+modified+sialic+acids+with+proteins+and+viruses.">A sialylated glycan microarray reveals novel interactions of modified sialic acids with proteins and viruses.</a> J Biol Chem. 286 (36), 31610-31622 (2011).</li><li>Gulati, S., 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=Human+H3N2+Influenza+Viruses+Isolated+from+1968+To+2012+Show+Varying+Preference+for+Receptor+Substructures+with+No+Apparent+Consequences+for+Disease+or+Spread.">Human H3N2 Influenza Viruses Isolated from 1968 To 2012 Show Varying Preference for Receptor Substructures with No Apparent Consequences for Disease or Spread.</a> PLoS One. 8 (6), (2013).</li><li>Stevens, J., Blixt, O., Paulson, J. C., Wilson, I. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Glycan+microarray+technologies:+tools+to+survey+host+specificity+of+influenza+viruses.">Glycan microarray technologies: tools to survey host specificity of influenza viruses.</a> Nat Rev Microbiol. 4 (11), 857-864 (2006).</li><li>de Vries, R. 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=Evolution+of+the+hemagglutinin+protein+of+the+new+pandemic+H1N1+influenza+virus:+maintaining+optimal+receptor+binding+by+compensatory+substitutions.">Evolution of the hemagglutinin protein of the new pandemic H1N1 influenza virus: maintaining optimal receptor binding by compensatory substitutions.</a> J Virol. 87 (24), 13868-13877 (2013).</li><li>Yang, H., 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=Structure+and+receptor+binding+preferences+of+recombinant+human+A(H3N2)+virus+hemagglutinins.">Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins.</a> Virology. 477, 18-31 (2015).</li><li>de Vries, R. 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=The+influenza+A+virus+hemagglutinin+glycosylation+state+affects+receptor-binding+specificity.">The influenza A virus hemagglutinin glycosylation state affects receptor-binding specificity.</a> Virology. 403 (1), 17-25 (2010).</li></ol>

The authors have nothing to disclose

Assessing IAV receptor specificity is an important step in analyzing pandemic potential of avian viruses. Sialic acid recognition by the virus is linked to several biological properties such as binding to and release from the cell. Knowledge of which amino-acid mutations are necessary for avian viruses to achieve &#945;2-6 binding and cross the species barrier enables pandemic preparedness. Several assays are used to determine receptor specificity; however, all have their drawbacks, including only measuring avidity and n...

Wild waterfowl are the natural reservoir for IAV, but IAV is able to cross the species barrier to poultry and mammals, including, humans. Avian IAVs recognize &#945;2-3 linked sialic acids (avian-type receptors), whereas human viruses bind &#945;2-6 linked sialic acids (human-type receptors). To be able to efficiently replicate and transmit between humans an avian IAV needs to bind to human-type receptors 1.
IAVs are divided based on serology that characterizes the antigenicity of their hemagglutinin (HA) and neuraminidase (NA) envelope glycoproteins. HA binds to sialic acids, whereas NA is the receptor-destroying enzyme at the other end of the viral lifecycle and cleaves sialic acid 2. All human infecting viruses, including H1N1, H2N2 and H3N2, have an avian origin 3. Over the last two of decades several avian to human crossovers have occurred, with H5N1, H7N7, and H7N9 being the most well-known; however, other subtypes have infected humans more sporadically (H6N1, H7N1, H7N2, H9N2, H10N7, H10N8) 4. Fortunately, it seems that none of these viruses have been able to fully adapt to human-type &#945;2-6-linked sialic acid receptors 5-8. Adaptation of avian or other zoonotic viruses to accommodate replication and transmission in human hosts could have a devastating effect on human health. Therefore, prior knowledge of how these viruses are evolving to bind human-type receptors will help world-wide surveillance of emerging influenza viruses.
Determination of receptor preference was first elucidated using erythrocytes of different species and remains a favored assay among flu researchers 9-12. The demonstration that avian viruses recognize &#945;2-3 sialic acid and human viruses &#945;2-6 linked sialic acid was originally based on an assay using hemagglutination of erythrocytes enzymatically engineered to contain each of the linkages 13,14. Although the readout is hemagglutination, a standard assay for virologists, the underlying glycan structures are not defined, only the terminal linkage. Additionally, the limited availability of the sialyltransferases, used to re-sialylate the cells, have limited the use of this assay 15-18. Subsequently, other methods of determining receptor-binding preferences were introduced using sialylated glycan structures linked to poly-acrylamide (PAA) or poly-glutamate (PGA) structures in plate-based assays 19,20. Several variations are possible in coating either the glycans or viruses to microtiter plates, each of which results in a robust, reliable and very sensitive ELISA-type assay 21-23. Alternatively, biotin-linked glycans can replace PAA/PGA and can be conjugated to streptavidin-coated plates 2,24. Although some specific sera may be required, ELISAs are standard and several glycans linked to PAA are readily commercially and non-commercially available (Consortium for Functional Glycomics (http://www.functionalglycomics.org)).
Glycan microarray technologies have emerged as an invaluable tool to determine receptor specificity, as multiple different glycans are spotted, and binding to a wide array of different structures can be assessed within a single assay 25-29. The binding of IAV to these structures provides a better understanding of the glycan structures that IAV preferentially recognizes 30-33. Glycan microarrays require small amounts of sample volume to perform a binding assay and only uses minute amounts of glycan per spot (2 nl). However, these arrays are typically used only to evaluate specificity of glycans receptors. Analysis of multiple viruses, or hemagglutinin proteins, at multiple concentration ranges can be prohibitive due to the number of slides required. Furthermore, to date, no relative avidity assay has been developed using glycan array techniques.
To combine the low sample requirement afforded by glycan microarray techniques and the sensitivity of PAA-linked glycans in ELISA-based assays, we sought to develop a multi-well glycan array that would allow for high-throughput analysis with similar or better resolution as compared to the traditional ELISA-based assay. Simultaneously, we wanted to minimize the amount of biologicals and reporter chemicals consumed. The ultimate result is a miniaturized avidity assay, specifically developed for monitoring IAV specificity and is equally applicable to assess other glycan binding proteins. Using a glass slide separated into 48 micro-wells by a Teflon mask, 6 different glycans are spotted in 6 replicates per well. The microarray platform affords the same trends in receptor binding seen in the macro ELISA format with several advantages. These include (I) printing of compound in 6 replicates, using minimal sample, versus the coating of several rows in a plate, using 100 &#181;l per well; (II) multiple different compounds analyzed simultaneously in a single well, including controls; (III) a massive decrease in incubation volume and; (IV) a larger dynamic range using a fluorescent readout. A single slide can be calculated to be equivalent to 18x 96-well plates.
With the following protocol, any lab capable of fabricating and analyzing spotted microarrays should be able to manufacture this miniaturized ELISA format.

<table><tbody><tr><td>NEXTERION&amp;reg; Slide H MPX-48&amp;nbsp;</td><td>Schott</td><td>1091525</td><td>Microwell slides</td></tr><tr><td>ProScanArray Plus&amp;nbsp;</td><td>PerkinElmer</td><td>discontinued</td><td>confocal microarray scanner</td></tr><tr><td>Innoscan 1100AL Scanner/Mapix Software</td><td>Innopsys</td><td>-</td><td>confocal microarray scanner</td></tr><tr><td>MicroGrid II&amp;nbsp;</td><td>Digilab</td><td>-</td><td>microaray printer</td></tr><tr><td>SNA</td><td>Vector Labs</td><td>B-1305&amp;nbsp;</td><td>Plant Lectin</td></tr><tr><td>ECA</td><td>Vector Labs</td><td>B-1145&amp;nbsp;</td><td>Plant Lectin</td></tr><tr><td>Anti-Strep Antibody</td><td>IBA</td><td>2-1509-001&amp;nbsp;</td><td>Anitbody for HA binding</td></tr><tr><td>Anti-Mouse Alexa-647</td><td>Life</td><td>A-21235</td><td>Anitbody for HA binding</td></tr><tr><td>Tween-20</td><td>Sigma</td><td>P2287&amp;nbsp;</td><td>detergent</td></tr><tr><td>di-basic Sodium Phosphate</td><td>Sigma</td><td>255793</td><td>printing buffer component</td></tr><tr><td>mono-basic Sodium phosphate</td><td>Sigma</td><td>229903&amp;nbsp;</td><td>printing buffer component</td></tr><tr><td>poly-l-lysine solution</td><td>Sigma</td><td>P8920&amp;nbsp;</td><td>pre-spotting slide component</td></tr><tr><td>sodium hydroxide</td><td>Sigma</td><td>221465</td><td>pre-spotting slide component</td></tr><tr><td>ethanol</td><td>Sigma</td><td>493546</td><td>pre-spotting slide component</td></tr><tr><td>phosphate buffered saline</td><td>Corning</td><td>46-013-CM</td><td>incubation/washing buffer</td></tr><tr><td>SMP4B pins</td><td>Telechem</td><td>SMP4B</td><td>printing pin</td></tr><tr><td>Compressed Nitrogen (Grade5)</td><td>Praxair</td><td>UN1066</td><td>general dusting/drying tool</td></tr><tr><td>Boric Acid</td><td>Sigma</td><td>B6768-500G</td><td>Slide blocking reagent</td></tr><tr><td>ethanolamine</td><td>Sigma</td><td>E9508-500ML</td><td>Slide blocking reagent</td></tr><tr><td>Atto 488</td><td>AttoTec</td><td>AD 488-91</td><td>Gridmarker on array</td></tr><tr><td>PAA-LNLN</td><td>Consortium for Functional Glycomics</td><td>PA368</td><td>Spotted glycans</td></tr><tr><td>PAA-3SLNLN</td><td>Consortium for Functional Glycomics</td><td>PA362</td><td>Spotted glycans</td></tr><tr><td>PAA-6SLNLN</td><td>Consortium for Functional Glycomics</td><td>PA343</td><td>Spotted glycans</td></tr><tr><td>LNLN</td><td>Consortium for Functional Glycomics</td><td>Te98</td><td>Spotted glycans</td></tr><tr><td>3SLNLN</td><td>Consortium for Functional Glycomics</td><td>Te175</td><td>Spotted glycans</td></tr><tr><td>6SLNLN</td><td>Consortium for Functional Glycomics</td><td>Te176</td><td>Spotted glycans</td></tr><tr><td>384-well microtiter plate</td><td>Matrix TechCorp</td><td>4361</td><td>Printing plate</td></tr><tr><td>VWR lab marker</td><td>VWR</td><td>52877-150</td><td>Slide Numbering</td></tr><tr><td>Wheaton slide staining dish</td><td>Sigma</td><td>Z103969-1EA</td><td>Blocking and Drying</td></tr></tbody></table>

a miniaturized glycan microarray assay for assessing avidity and specificity of influenza a virus hemagglutinins

Influenza A virus (IAV) hemagglutinins recognize sialic acids on the cell surface as functional receptors to gain entry into cells. Wild waterfowl are the natural reservoir for IAV, but IAV can cross the species barrier to poultry, swine, horses and humans. Avian viruses recognize sialic acid attached to a penultimate galactose by a &#945;2-3 linkage (avian-type receptors) whereas human viruses preferentially recognize sialic acid with a &#945;2-6 linkage (human-type receptors). To monitor if avian viruses are adapting to human type receptors, several methods can be used. Glycan microarrays with diverse libraries of synthetic sialosides are increasingly used to evaluate receptor specificity. However, this technique is not used for measuring avidities. Measurement of avidity is typically achieved by evaluating the binding of serially diluted hemagglutinin or virus to glycans adsorbed to conventional polypropylene 96-well plates. In this assay, glycans with &#945;2-3 or &#945;2-6 sialic acids are coupled to biotin and adsorbed to streptavidin plates, or are coupled to polyacrylamide (PAA) which directly adsorb to the plastic. We have significantly miniaturized this assay by directly printing PAA-linked sialosides and their non PAA-linked counterparts on micro-well glass slides. This set-up, with 48 arrays on a single slide, enables simultaneous assays of 6 glycan binding proteins at 8 dilutions, interrogating 6 different glycans, including two non-sialylated controls. This is equivalent to 18x 96-well plates in the traditional plate assay. The glycan array format decreases consumption of compounds and biologicals and thus greatly enhances efficiency.

Printing, Scanning &#38; Data analyses
To ensure proper printing, it is vital to have the correct alignment of the spotted grid within the teflon mask, which delineates each array on the slide. During printing, due to the nature of the teflon coating, spots cannot be seen by the naked eye on the MPX slides. Attention is paid then to the appearance of the pre-spots on the poly-L-Lysine coated slides. Directly after printing, each...

Watch this Scientific Journal Video about A Miniaturized Glycan Microarray Assay for Assessing Avidity and Specificity of Influenza A Virus Hemagglutinins at JoVE.com

A Miniaturized Glycan Microarray Assay for Assessing Avidity and Specificity of Influenza A Virus Hemagglutinins

Using a printed glycan microarray strategy, a conventional 96-well plate assay was miniaturized for analysis of influenza A virus hemagglutinin avidity and specificity for sialic acid containing receptors.

Influenza A virus (IAV) hemagglutinins recognize sialic acids on the cell surface as functional receptors to gain entry into cells. Wild waterfowl are the ...

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Universidad de Cartagena UDEC

Research

JoVE Journal

Immunology and Infection

7.9K Views.  The Scripps Research Institute. Using a printed glycan microarray strategy, a conventional 96-well plate assay was miniaturized for analysis of influenza A virus hemagglutinin avidity and specificity for sialic acid containing receptors.

Video: A Miniaturized Glycan Microarray Assay for Assessing Avidity and Specificity of Influenza A Virus Hemagglutinins

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 ...

High-throughput Detection Method for Influenza Virus

Influenza virus is a respiratory pathogen that causes a high degree of morbidity and mortality every year in multiple parts of the world. Therefore, precise diagnosis of the infecting strain and rapid high-throughput screening of vast numbers of clinical samples is paramount to control the spread of pandemic infections. Current clinical diagnoses of influenza infections are based on serologic testing, polymerase chain reaction, direct specimen immunofluorescence and cell culture 1,2.
Here, we report the development of a novel diagnostic technique used to detect live influenza viruses. We used the mouse-adapted human A/PR/8/34 (PR8, H1N1) virus 3 to test the efficacy of this technique using MDCK cells 4. MDCK cells (104 or 5 x 103 per well) were cultured in 96- or 384-well plates, infected with PR8 and viral proteins were detected using anti-M2 followed by an IR dye-conjugated secondary antibody. M2 5 and hemagglutinin 1 are two major marker proteins used in many different diagnostic assays. Employing IR-dye-conjugated secondary antibodies minimized the autofluorescence associated with other fluorescent dyes. The use of anti-M2 antibody allowed us to use the antigen-specific fluorescence intensity as a direct metric of viral quantity. To enumerate the fluorescence intensity, we used the LI-COR Odyssey-based IR scanner. This system uses two channel laser-based IR detections to identify fluorophores and differentiate them from background noise. The first channel excites at 680 nm and emits at 700 nm to help quantify the background. The second channel detects fluorophores that excite at 780 nm and emit at 800 nm. Scanning of PR8-infected MDCK cells in the IR scanner indicated a viral titer-dependent bright fluorescence. A positive correlation of fluorescence intensity to virus titer starting from 102-105 PFU could be consistently observed. Minimal but detectable positivity consistently seen with 102-103 PFU PR8 viral titers demonstrated the high sensitivity of the near-IR dyes. The signal-to-noise ratio was determined by comparing the mock-infected or isotype antibody-treated MDCK cells.
Using the fluorescence intensities from 96- or 384-well plate formats, we constructed standard titration curves. In these calculations, the first variable is the viral titer while the second variable is the fluorescence intensity. Therefore, we used the exponential distribution to generate a curve-fit to determine the polynomial relationship between the viral titers and fluorescence intensities. Collectively, we conclude that IR dye-based protein detection system can help diagnose infecting viral strains and precisely enumerate the titer of the infecting pathogens.

This method describes the use of Infrared dye based imaging system for detection of H1N1 in bronchioalveolar lavage (BAL) fluid of infected mice at a high sensitivity. This methodology can be performed in a 96- or 384-well plate, requires &lt;10 &mu;l volume of test material and has the potential for concurrent screening of multiple pathogens.

Influenza virus is a respiratory pathogen that causes a high degree of morbidity and mortality every year in multiple parts of the world. Therefore, ...

Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional methods to measure NA inhibiting (NI) antibody titers are not practical for routine serology. This protocol describes the enzyme-linked lectin assay (ELLA), a practical alternative method to measure NI titers that is performed in 96 well plates coated with a large glycoprotein substrate, fetuin. NA cleaves terminal sialic acids from fetuin, exposing the penultimate sugar, galactose. Peanut agglutinin (PNA) is a lectin with specificity for galactose and therefore the extent of desialylation can be quantified using a PNA-horseradish peroxidase conjugate, followed by addition of a chromogenic peroxidase substrate. The optical density that is measured is proportional to NA activity. To measure NI antibody titers, serial dilutions of sera are incubated at 37 &#176;C O/N on fetuin-coated plates with a fixed amount of NA. The reciprocal of the highest serum dilution that results in &#8805;50% inhibition of NA activity is designated as the NI antibody titer. The ELLA provides a practical format for routine evaluation of human antibody responses following influenza infection or vaccination.

We describe the enzyme-linked lectin assay (ELLA) for measuring influenza neuraminidase (NA)-inhibition antibody titers in sera. The assay uses peanut agglutinin to quantify galactose residues that become accessible when NA removes sialic acid from fetuin-coated, 96-well plates.

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional ...

Optimization of a Quantitative Micro-neutralization Assay

The micro-neutralization (MN) assay is a standard technique for measuring the infectivity of the influenza virus and the inhibition of virus replication. In this study, we present the protocol of an imaging-based MN assay to quantify the true antigenic relationships between viruses. Unlike typical plaque reduction assays that rely on visible plaques, this assay quantitates the entire infected cell population of each well. The protocol matches the virus type or subtype with the selection of cell lines to achieve maximum infectivity, which enhances sample contrast during imaging and image processing. The introduction of quantitative titration defines the amount of input viruses of neutralization and enables the results from different experiments to be comparable. The imaging setup with a flatbed scanner and free downloadable software makes the approach high throughput, cost effective, user friendly, and easy to deploy in most laboratories. Our study demonstrates that the improved MN assay works well with the current circulating influenza A(H1N1)pdm09, A(H3N2), and B viruses, without being significantly influenced by amino acid substitutions in the neuraminidase (NA) of A(H3N2) viruses. It is particularly useful for the characterization of viruses that either grow to low HA titer and/or undergo an abortive infection resulting in an inability to form plaques in cultured cells.

This study describes an imaging-based micro-neutralization assay to analyze the antigenic relationships between viruses. The protocol employs a flatbed scanner and has four steps, including titration, titration quantitation, neutralization, and neutralization quantitation. The assay works well with current circulating influenza A(H1N1)pdm09, A(H3N2), and B viruses.

The micro-neutralization (MN) assay is a standard technique for measuring the infectivity of the influenza virus and the inhibition of virus replication. ...

A Method to Assess Fc-mediated Effector Functions Induced by Influenza Hemagglutinin Specific Antibodies

Antibodies play a crucial role in coupling the innate and adaptive immune responses against viral pathogens through their antigen binding domains and Fc-regions. Here, we describe how to measure the activation of Fc effector functions by monoclonal antibodies targeting the influenza virus hemagglutinin with the use of a genetically engineered Jurkat cell line expressing an activating type 1 Fc-Fc&#947;R. Using this method, the contribution of specific Fc-Fc&#947;R interactions conferred by immunoglobulins can be determined using an in vitro assay.

We describe a method to measure the activation of Fc-mediated effector functions by antibodies that target the influenza virus hemagglutinin. This assay can also be adapted to assess the ability of monoclonal antibodies or polyclonal sera targeting other viral surface glycoproteins to induce Fc-mediated immunity.

Antibodies play a crucial role in coupling the innate and adaptive immune responses against viral pathogens through their antigen binding domains and ...

An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers

Antibody titers are commonly used as surrogate markers for serological protection against influenza and other pathogens. Detailed knowledge of antibody production pre- and post-vaccination is required to understand vaccine-induced immunity. This article describes a reliable point-by-point protocol to determine influenza-specific antibody titers. The first protocol describes a method to specify the antigen amounts required for hemagglutination, which standardizes the concentrations for subsequent usage in the second protocol (hemagglutination assay, HA assay). The second protocol describes the quantification of influenza-specific antibody titers against different viral strains by using a serial dilution of human serum or cell culture supernatants (hemagglutination inhibition assay, HI assay).
As an applied example, we show the antibody response of a healthy cohort, which received a trivalent inactivated influenza vaccine. Additionally, the cross-reactivity between the different influenza viruses is shown and methods to minimize cross-reactivity by using different types of animal red blood cells (RBCs) are explained. The discussion highlights advantages and disadvantages of the presented assays and how the determination of influenza-specific antibody titers can improve the understanding of vaccine-related immunity.

An Optimized Hemagglutination Inhibition HI Assay to Quantify Influenza-specific Antibody Titers

The presented protocols describe how to perform a hemagglutination inhibition assay to quantify influenza-specific antibody titers from serum samples of influenza vaccine recipients. The first assay determines optimal viral antigen concentrations by hemagglutination. The second assay quantifies influenza-specific antibody titers by hemagglutination inhibition.

Antibody titers are commonly used as surrogate markers for serological protection against influenza and other pathogens. Detailed knowledge of antibody ...

Medicine

Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes

The influenza virus remains a significant cause of mortality worldwide due to the limited effectiveness of currently available vaccines. A key challenge to the development of universal influenza vaccines is high antigenic diversity resulting from antigenic drift. Overcoming this challenge requires novel research tools to measure the breadth of serum antibodies directed against many virus strains across different antigenic subtypes. Here, we present a protocol for analyzing the breadth of serum antibodies against diverse influenza virus strains using a protein microarray of influenza antigens.
This influenza antigen microarray is constructed by printing purified hemagglutinin and neuraminidase antigens onto a nitrocellulose-coated membrane using a microarray printer. Human sera are incubated on the microarray to bind antibodies against the influenza antigens. Quantum-dot-conjugated secondary antibodies are used to simultaneously detect IgG and IgA antibodies binding to each antigen on the microarray. Quantitative antibody binding is measured as fluorescence intensity using a portable imager. Representative results are shown to demonstrate assay reproducibility in measuring subtype-specific and cross-reactive influenza antibodies in human sera.
Compared to traditional methods such as ELISA, the influenza antigen microarray provides a high throughput multiplexed approach capable of testing hundreds of sera for multiple antibody isotypes against hundreds of antigens in a short time frame, and thus has applications in sero-surveillance and vaccine development. A limitation is the inability to distinguish binding antibodies from neutralizing antibodies.

We present a protocol for using a protein microarray constructed by printing influenza antigens onto nitrocellulose-coated slides to simultaneously probe serum for multiple antibody isotypes against over 250 antigens from different virus strains, thus allowing measurement of the breadth of serum antibodies across virus subtypes.

The influenza virus remains a significant cause of mortality worldwide due to the limited effectiveness of currently available vaccines. A key challenge ...

The Hemagglutination Inhibition Assay to Detect Serum Antibodies Against a Target Antigen

Source: Kaufmann, L. et al., <a href="https://appjove.unicartagenaproxy.elogim.com/v/55833">An Optimized Hemagglutination Inhibition (HI) Assay to Quantify Influenza-specific Antibody Titers.</a> J. Vis. Exp. (2017)
The video demonstrates a hemagglutination inhibition assay for detecting serum antibodies against specific antigens. Confirmation of hemagglutination inhibition in the test well and hemagglutination in the control well is achieved through distinct visual patterns. This assay plays a crucial role in assessing immune response, vaccine effectiveness, and studying viral infections in virology and immunology.

All procedures involving human participants have been performed in compliance with the institutional, national, and international guidelines for human ...

JoVE Encyclopedia of Experiments

Immunology

Immunodiagnostics

Specialized Assays

An Assay to Measure Influenza Neuraminidase Inhibition Antibody Titers

Source: Gao, J., et al. <a href="https://appjove.unicartagenaproxy.elogim.com/v/54573">Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay.</a> J. Vis. Exp. (2016).
This video demonstrates an assay measuring influenza neuraminidase (NA) inhibiting antibody titers in a serum sample. A serum sample containing antibodies against NA is added to a fetuin-coated microwell plate. Upon adding the virus, the antibodies prevent viral NA from cleaving fetuin and exposing its galactose moiety. A peroxidase-conjugated lectin is then added, which binds to the exposed galactose. The NA-inhibiting antibody titer is determined using a colorimetric test, where a peroxidase substrate gets cleaved by the immobilized lectin-conjugated peroxidase to produce color.

All procedures involving sample collection have been performed in accordance with the institute&#39;s IRB guidelines.
1. Preparation of Reagents and ...

Antibody-Based Technologies

Characterization and Functional Analysis

Viral Antigen Microarray Assay to Detect Antibody Isotypes in Serum Against Viral Antigen

Source: Khan, S., et al., <a href="https://appjove.unicartagenaproxy.elogim.com/v/59973">Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes.</a> J. Vis. Exp. (2019)
In this video, we demonstrate the process for detecting antibody isotypes in multiple human serum samples using a microarray slide printed with antigenic subtypes of influenza virus strains.

Source: Khan, S., et al., Use of an Influenza Antigen Microarray to Measure the Breadth of Serum Antibodies Across Virus Subtypes. J. Vis. Exp. (2019)
In ...