We thank the laboratorians, epidemiologists, and affiliates with public health departments for sample submissions to the Centers for Disease Control and Prevention. The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the Centers for Disease Control and Prevention. Use of trade names and commercial sources are for identification only and do not imply endorsement by the Centers for Disease Control and Prevention.

While the IHC protocol was performed on formalin-fixed tissues, which inactivates RABV if present, appropriate biosafety protocols should be properly followed. All biosafety procedures are described in the Biosafety in Microbiological and Biomedical Laboratories (BMBL) 5th Edition (https://www.cdc.gov/biosafety/publications/bmbl5/index.htm), including wearing proper personal protective equipment (PPE), and vaccination requirement as described12. In addition, proper containment and handling of hazardous chemicals (like formalin, AEC and xylene), should be followed (e.g., fume hoods).
1. Formalin fixation of tissues
<ol>
	<li>Place 3-5 mm brain tissues collected after necropsy13 into 10% phosphate buffered formalin solution (1:20 to 1:50 tissue/formalin ratio) for 24-72 h. 
	CAUTION: Formalin is a toxic fixative.</li>
	<li>Record the approximate tissue weight (size), tissue type (brain areas) and volume of formalin. It is important for laboratories to document and maintain records on fixation times.</li>
	<li>For longer tissue storage after formalin fixation and prior to processing, place the tissue in 70% ethanol.</li>
</ol>
2. Tissue processing
<ol>
	<li>Following the specimen fixation, dissect the tissue to include the important brain areas e.g., cross sections of the brainstem, cerebellum (3 lobes), or the hippocampus (both hippocampi) each cut 3 to 5 mm thick and placed into processing cassettes.</li>
	<li>Process the tissue cassettes for paraffin wax infiltration, embedded into paraffin blocks and sectioned (3 to 6 &#181;m) on a microtome.</li>
</ol>
3. Preparation of Materials / Staining dishes
<ol>
	<li>Set up the staining dish14 (Table of Materials) as shown in Figure 1. Fill each dish with 250 mL of the solution.</li>
	<li>Preparation of the 3-Amino-9-ethylcarbizole (AEC) substrate stock solution
	<ol>
		<li>Dissolve one 20 mg tablet of 3-amino 9-ethylcarbazole (AEC) into 5 mL of N,N, dimethylformamide using a glass pipette. 
		CAUTION: AEC is a carcinogen.</li>
	</ol>
	</li>
	<li>Preparation of the protease (e.g., Pronase) stock solution for the antigen retrieval
	<ol>
		<li>Dissolve 7 mg of the protease in 200 mL of PBS.</li>
	</ol>
	</li>
	<li>Preparation of the rinse buffer PBS-T
	<ol>
		<li>Add 10 mL of Tween 80 to 990 mL of PBS. Mix it well to form a homogenous solution.</li>
	</ol>
	</li>
</ol>
4. Deparaffinization and tissue rehydration
<ol>
	<li>Make 5 &#181;m paraffin section using a microtome, float it on a water bath at 38 &#730;C and collect on to glass slides. Label the slides with a reagent resistant pen/marker.</li>
	<li>Place the slides onto a tray and melt in a 55-60 &#730;C oven for 1 h. Do not raise the temperature above 60 &#730;C as it can destroy the viral antigen.</li>
	<li>Remove slides from the oven and immediately deparaffinize in 3 consecutive xylene rinses of 5 min each in the dishes 1, 2 and 3.</li>
	<li>Rehydrate the sections on the slide by sequential immersions in decreasing dilution of ethanol to deionized water: (4 through 11 is a dip rinse) dish 4: xylene/100% ethanol (1:1); dish 5: 100% ethanol; dish 6: 100% ethanol; dish 7: 95% ethanol; dish 8: 95% ethanol; dish 9: 80% ethanol; dish 10: 70% ethanol; dish 11: deionized water (Figure 1. Dish set-up). 
	CAUTION: Xylene is a hazardous chemical and work should be conducted in a fume hood.</li>
</ol>
5. Proteolytic antigen retrieval
<ol>
	<li>Treat slides with the protease (2.5 &#181;g/mL of PBS) for 30 min for proteolytic antigen retrieval in dish 12.</li>
	<li>Then rinse in PBS-T for 10 min (dish 13).</li>
	<li>Treat with 3% hydrogen peroxide for 10 min (dish 14).</li>
	<li>Again, wash with PBS-T for 10 min (dish 15).</li>
</ol>
6. Staining procedure
<ol>
	<li>Handle slides one at a time keeping the remaining slides submerged in the buffer (do not remove the whole slide holder - keep slides wet). Remove one slide and blot off excess buffer (using a paper towel) from around the tissue section being careful not to disturb the tissue section. Incubate slides in a humidity chamber, made by placing moistened paper towels, on the lab bench top14 at room temperature with normal goat serum (blocking) for 15 min.</li>
	<li>Incubate with the optimal pre-determined dilution primary anti-rabies antibody (1:250 dilution of mouse anti-rabies serum, unpublished) (positive control) and negative control antibodies at room temperature same as above (step 6.1.) for 60 min with no washes in between.</li>
	<li>After 60 min, wash with PBS-T for 10 min (dish 16).</li>
	<li>Incubate with the biotinylated antibody (species specific) in a humidity chamber at room temperature for 15 min (handling same as step 6.1.).</li>
	<li>Wash with PBS-T for 10 min (dish 16).</li>
	<li>Incubate with Streptavidin-HRP complex in a humidity chamber at room temperature for 15 min (handling same as 6.1.).</li>
	<li>Wash with PBS-T for 10 min (dish 16).</li>
	<li>Incubate with peroxidase substrate, amino-ethylcarbazole (AEC), in a humidity chamber at room temperature for 10 min. Make AEC just prior to use. To do so, add 1 mL of AEC stock solution to 14 mL of 0.1M acetate buffer, pH 5.2. Add 0.15 mL of 3% H2O2. Filter the mixture just before use (0.45 &#181;m filter). 
	NOTE: The working solution of AEC is only stable for 2-3 h. The AEC stock solution can be stored in the refrigerator for longer periods.</li>
	<li>Wash in deionized water 10 min (dish 17)</li>
	<li>Counterstained with Gill&#39;s Hematoxylin diluted 1:2 with deionized water for 2 min (dish 18).</li>
	<li>Rinse off excess Hematoxylin with deionized water dip rinse (dish 19 and 20).</li>
	<li>Rinse in Scott&#39;s Tap water 30 s (bluing solution) dish 21.</li>
	<li>Wash in deionized water 10 min (dish 22)</li>
	<li>Remove slides one at a time - mount with water-soluble mounting medium.</li>
	<li>Read slides on a light microscope.</li>
</ol>

<ol>
	<li>Rupprecht, C., Kuzmin, I., Meslin, F. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Lyssaviruses+and+rabies:+current+conundrums,+concerns,+contradictions+and+controversies.">Lyssaviruses and rabies: current conundrums, concerns, contradictions and controversies.</a> F1000Research. 6, 184 (2017).</li><li>Fooks, A. R., 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=Current+status+of+rabies+and+prospects+for+elimination.">Current status of rabies and prospects for elimination.</a> Lancet. 384 (9951), 1389-1399 (2014).</li><li>Finke, S., Brzozka, K., Conzelmann, K. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tracking+fluorescence-labeled+rabies+virus:+enhanced+green+fluorescent+protein-tagged+phosphoprotein+P+supports+virus+gene+expression+and+formation+of+infectious+particles.">Tracking fluorescence-labeled rabies virus: enhanced green fluorescent protein-tagged phosphoprotein P supports virus gene expression and formation of infectious particles.</a> Journal of Virology. 78 (22), 12333-12343 (2004).</li><li>WHO. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=WHO+Expert+Consulation+on+Rabies,+Third+Report.">WHO Expert Consulation on Rabies, Third Report.</a> WHO Technical Report Series. 1012, 1 (2018).</li><li>Goldwasser, R. A., Kissling, R. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fluorescent+antibody+staining+of+street+and+fixed+rabies+virus+antigens.">Fluorescent antibody staining of street and fixed rabies virus antigens.</a> Proceedings of the Society for Experimental Biology and Medicine. 98 (2), 219-223 (1958).</li><li>Lembo, T., 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=Evaluation+of+a+direct,+rapid+immunohistochemical+test+for+rabies+diagnosis.">Evaluation of a direct, rapid immunohistochemical test for rabies diagnosis.</a> Emerging Infectious Diseases. 12 (2), 310-313 (2006).</li><li>Fekadu, M., Greer, P. W., Chandler, F. W., Sanderlin, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Use+of+the+avidin-biotin+peroxidase+system+to+detect+rabies+antigen+in+formalin-fixed+paraffin-embedded+tissues.">Use of the avidin-biotin peroxidase system to detect rabies antigen in formalin-fixed paraffin-embedded tissues.</a> Journal of Virological Methods. 19 (2), 91-96 (1988).</li><li>Hamir, A. N., Moser, G., Rupprecht, C. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+five+year+(1985-1989)+retrospective+study+of+equine+neurological+diseases+with+special+reference+to+rabies.">A five year (1985-1989) retrospective study of equine neurological diseases with special reference to rabies.</a> Journal of Comparative Pathology. 106 (4), 411-421 (1992).</li><li>Inoue, 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=Cross-reactive+antigenicity+of+nucleoproteins+of+lyssaviruses+recognized+by+a+monospecific+antirabies+virus+nucleoprotein+antiserum+on+paraffin+sections+of+formalin-fixed+tissues.">Cross-reactive antigenicity of nucleoproteins of lyssaviruses recognized by a monospecific antirabies virus nucleoprotein antiserum on paraffin sections of formalin-fixed tissues.</a> Pathology International. 53 (8), 525-533 (2003).</li><li>Webster, J. D., Miller, M. A., Dusold, D., Ramos-Vara, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+prolonged+formalin+fixation+on+diagnostic+immunohistochemistry+in+domestic+animals.">Effects of prolonged formalin fixation on diagnostic immunohistochemistry in domestic animals.</a> Journal of Histochemistry and Cytochemistry. 57 (8), 753-761 (2009).</li><li>Feiden, 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=Immunohistochemical+staining+of+rabies+virus+antigen+with+monoclonal+and+polyclonal+antibodies+in+paraffin+tissue+sections.">Immunohistochemical staining of rabies virus antigen with monoclonal and polyclonal antibodies in paraffin tissue sections.</a> Zentralblatt fur Veterinarmedizin Reihe B. 35 (4), 247-255 (1988).</li><li>Manning, S. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Human+rabies+prevention--United+States,+2008:+recommendations+of+the+Advisory+Committee+on+Immunization+Practices.">Human rabies prevention--United States, 2008: recommendations of the Advisory Committee on Immunization Practices.</a> Morbidity and Mortality Weekly Reports Recommendations and Reports. 57, 1-28 (2008).</li><li>WHO. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Laboratory techniques in rabies. 1, 67-72 (2018).</li><li>Patrick, E. M., 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=Enhanced+Rabies+Surveillance+Using+a+Direct+Rapid+Immunohistochemical+Test.">Enhanced Rabies Surveillance Using a Direct Rapid Immunohistochemical Test.</a> Journal of Visualized Experiments. (146), (2019).</li><li>Whitfield, S. G., 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+comparative+study+of+the+fluorescent+antibody+test+for+rabies+diagnosis+in+fresh+and+formalin-fixed+brain+tissue+specimens.">A comparative study of the fluorescent antibody test for rabies diagnosis in fresh and formalin-fixed brain tissue specimens.</a> Journal of Virology Methods. 95 (1-2), 145-151 (2001).</li><li>WHO. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Diagnostic procedures for antigen detection. , (2016).</li><li>Jarvis, J. A., Franke, M. A., Davis, A. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rabies+direct+fluorescent+antibody+test+does+not+inactivate+rabies+or+eastern+equine+encephalitis+viruses.">Rabies direct fluorescent antibody test does not inactivate rabies or eastern equine encephalitis viruses.</a> Journal of Virology Methods. 234, 52-53 (2016).</li></ol>

The authors have nothing to disclose.

Due to the high fatality rate of rabies after the symptom onset, the diagnosis of suspect animals for RABV infection is extremely critical for an appropriate post-exposure prophylactic treatment. Rabies diagnosis primarily depends on DFA, DRIT, and PCR-based techniques using fresh or frozen tissues. For testing of formalin-fixed tissues, the IHC test provides an alternative method for the sensitive and specific detection of RABV antigen. While the tissues fixed in formalin have proteins stabilized due to the modification of side chains like cross-linking, the samples need to be processed before the antigen detection. In this protocol, the epitopes were recovered through the partial proteolytic digestion by the protease (e.g., Pronase) to enable the binding of primary antibodies to the RNP complex. While mAbs reactive against N protein are predominantly relied on in DFA and DRIT, pAbs that are reactive against multiple epitopes on N protein would be preferred for an IHC test. In addition, the reactivity or pAbs could be broader against different RABV variants and against non-rabies lyssaviruses as compared to mAbs.
One of the major limitations of IHC test is the protocol involves several sequential steps and takes about 6 hours for completion. If the tissue needs to be fixed in formalin and embedded in paraffin blocks, it requires an additional 1 - 2 days before the tissue could be stained. Another limitation is the non-availability of commercial primary anti-rabies antibodies for the IHC test. However, IHC does provide an option to perform rabies diagnosis when only FF tissues are available for testing. The IHC test is particularly important for testing rabies cases if one half of the tissues are stored in formalin (and other unfixed tissues tested by DFA) and it was necessary to test complete cross section of the brainstem and other tissues, as required for diagnosis. Rabies antigen detection by IHC test can be utilized for human post-mortem brain samples for the diagnosis and / or retrospective analysis of suspect cases based on the clinical symptoms. While IHC was not approved as a primary or confirmatory test for rabies diagnosis, like DFA, the method detects antigen using rabies specific antibodies. Comparison of DFA using fresh/frozen vs FF tissues provided similar sensitivity and specificity15. Unless antibodies are directly conjugated to FITC (the requirement for DFA test), HRP labeled antibodies can be used in IHC for staining rabies antigen. The advantage with HRP based detection is the ability to use a light microscope for the observation. The current commercially available DFA reagents, FITC conjugated rabies specific antibodies (mAbs) does not detect antigen after formalin fixation due to the modification of epitopes. However, if FITC conjugated rabies specific pAbs are available, it can be used as a staining method, as recommended by World Health Organization16. In addition to antigen detection, FF tissues can be subjected to RNA isolation followed by PCR and sequencing using specific primers for confirming the presence of RABV genomic RNA.
The other advantages of formalin-fixed tissues include determination of histological changes by hematoxylin and eosin staining method. While the formalin treatment preserves protein, it completely inactivates most pathogens in the sample due to the extensive crosslinking of proteins and degradation or modification of nucleic acids. Thus, the method improves the safety of biological sample handling, shipping and testing compared to DFA. The acetone fixation step in DFA does not inactivate RABV and should be handled with appropriate PPE17. The samples after formalin fixation are stable and can be stored at ambient temperature, which is suited for low-resource areas where access to a cold storage is limited. Similarly, paraffin-embedded formalin-fixed tissues can be considered for the long-term storage at ambient temperatures without losing the antibody reactivity against proteins.

Rabies is an acute progressive encephalitis caused by the negative sense RNA viruses belonging to the genus lyssavirus1. Nearly 99% of all human deaths caused by the infection with rabies virus (RABV), the type member of the genus, is transmitted by dogs2. Rabies diagnosis of suspect animals relies on the detection of antigen (primarily viral encoded nucleoprotein, N protein) in complex with genomic RNA (ribonucleoprotein complex, RNP) in the brain tissue3. The antigen detection by the direct fluorescent antibody (DFA) test is considered the gold standard for rabies diagnosis4. The method utilizes fresh or fresh frozen brain material, a touch impression on a slide, fixation in acetone, staining using commercially available fluorescent isothiocyanate (FITC) labeled monoclonal or polyclonal antibodies (mAbs/pAbs) and read by the fluorescence microscopy5. The DFA test is rapid, sensitive, and specific for rabies antigen detection in fresh brain tissue. Recently, a direct rapid immunohistochemical test (DRIT), modified immunohistochemistry (IHC) technique, was demonstrated to exhibit similar sensitivity to DFA but offers the advantage of light microscopy for visualization6. While the detection method used in DRIT, is similar to IHC, the initial step utilizes fresh or frozen tissues to generate touch impressions of the sample followed by fixation in formalin.
IHC is a widely used technique to determine histological changes and detection of proteins using specific antibodies in formalin-fixed tissues embedded in paraffin blocks. IHC is an established alternative test for the rabies antigen detection in the tissue sections7. IHC has been particularly utilized for the diagnosis of retrospective cases that exhibited neurological diseases to determine the burden of rabies8. Paraffin-embedded formalin-fixed tissues preserve the proteins for the detection even after several years when stored at ambient temperature9. Formalin treatment modifies proteins by cross-linking and altering the amino acid side chains, which might make the epitopes no longer reactive against antibodies10. While the IHC test for rabies antigen detection involves either mAbs or pAbs, the latter is advantageous as multiple epitopes and divergent lyssaviruses can be detected11.
The standard steps involved in IHC are formalin fixation of tissues, embedding in paraffin blocks, sectioning of tissues, deparaffinization and hydration, epitope recovery, reactivity against primary and secondary antibodies, and the development using chromogenic substrates. This manuscript describes a detailed account of the protocol for rabies diagnosis. For rabies antigen detection, mouse serum immunized with RABV (pAbs) generated at the U.S. Centers for Disease Control and Prevention (CDC) Atlanta, Georgia, in combination with biotinylated anti-mouse secondary antibodies are utilized. Biotinylated Abs are detected by the addition of streptavidin-horseradish peroxidase (HRP) complex followed by the color development with amino-ethylcarbazole substrate.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>3% hydrogen peroxide</td>
			<td>Pharamacy brands</td>
			<td></td>
			<td>Off the shelf 3% H2O2</td>
		</tr>
		<tr>
			<td>3-Amino-9-ethylcarbazole (AEC)</td>
			<td>Millipore Sigma</td>
			<td>A6926</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetate Buffer pH 5.2</td>
			<td>Poly Scientific R&#38;D Corp.</td>
			<td>s140</td>
			<td></td>
		</tr>
		<tr>
			<td>Buffered Formalin 10% Phosphate Buffered</td>
			<td>Fisher Scientific</td>
			<td>SF100-4</td>
			<td>Certified</td>
		</tr>
		<tr>
			<td>Cover slips Corning</td>
			<td>Fisher Scientific</td>
			<td>12-553-471</td>
			<td>24 X 50 mm</td>
		</tr>
		<tr>
			<td>Ethanol 190 Proof</td>
			<td>Pharmco-AAPER</td>
			<td>111000190</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol 200 Proof</td>
			<td>Pharmco-AAPER</td>
			<td>111000200</td>
			<td></td>
		</tr>
		<tr>
			<td>Gill&#39;s hematoxylin formulation #2</td>
			<td>Fisher Scientific</td>
			<td>CS401-1D</td>
			<td></td>
		</tr>
		<tr>
			<td>HistoMark Biotin-Streptavidin Peroxidase Kit</td>
			<td>seracare</td>
			<td>71-00-18</td>
			<td>Mouse Primary Antibody&#160;</td>
		</tr>
		<tr>
			<td>ImmunoHistoMount</td>
			<td>Millipore Sigma</td>
			<td>i1161</td>
			<td>Mounting media</td>
		</tr>
		<tr>
			<td>N,N, Dimethyl formamide GR</td>
			<td>Fisher Scientific</td>
			<td>D119</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffered Saline&#160;</td>
			<td>HyClone</td>
			<td>RR14440.01</td>
			<td>01M, pH 7.2 (pH 7.2-7.6)</td>
		</tr>
		<tr>
			<td>Plan-APOCHROMAT 40X/0.95 Objective</td>
			<td>Multiple vendors</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Plan-APOCHROMATIC 20X/0.75 Objective</td>
			<td>Multiple vendors</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Pronase</td>
			<td>Millipore Sigma</td>
			<td>53702</td>
			<td>Protease, Streptomyces griseus</td>
		</tr>
		<tr>
			<td>Scott&#39;s Tap Water&#160;</td>
			<td>Poly Scientific R&#38;D Corp.</td>
			<td>s1887</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue-Tek Slide stain set</td>
			<td>Fisher Scientific</td>
			<td>50-294-72</td>
			<td></td>
		</tr>
		<tr>
			<td>TWEEN-80&#160;</td>
			<td>Millipore Sigma</td>
			<td>P1754</td>
			<td></td>
		</tr>
		<tr>
			<td>Xylene</td>
			<td>Fisher Scientific</td>
			<td>X3S-4</td>
			<td>Histological Grade</td>
		</tr>
		<tr>
			<td>Zeiss Axioplan 2 imaging - microscope</td>
			<td>Multiple vendors</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

immunohistochemistry test for the lyssavirus antigen detection from formalin-fixed tissues

One of the primary diagnostic modalities for rabies is the detection of viral ribonucleoprotein (RNP) complex (antigen) in the infected tissue samples. While the direct fluorescent antibody (DFA) test or the direct rapid immunohistochemical test (DRIT) are most commonly utilized for the antigen detection, both tests require fresh and/or frozen tissues for impressions on slides prior to the antigen detection using antibodies. If samples are collected and fixed in formalin, neither test is optimal for the antigen detection, however, testing can be performed by conventional immunohistochemistry (IHC) after embedding in paraffin blocks and sectioning. With this IHC method, tissues are stained with anti-rabies antibodies, sections are deparaffinized, antigen retrieved by partial proteolysis or other methods, and incubated with primary and secondary antibodies. Antigens are stained using horseradish peroxidase / amino ethyl carbazole and counterstained with hematoxylin for the visualization using a light microscope. In addition to the specific antigen detection, formalin fixation offers other advantages like the determination of histological changes, relaxed conditions for specimen storage and transport (under ambient temperatures), ability to test retrospective cases and improved biological safety through the inactivation of infectious agents.

Figure 2 demonstrates representative IHC staining results of positive and negative control samples in different brain tissues tested. Figure 2A,D,G represent positive samples at 200x, while Figure 2B,E,H correspond to 400x magnification, respectively. Figure 2A-C correspond to the brainstem; Figure 2D-F correspond to the cerebellum and Purkinje cells; and Figure 2G-I correspond to the hippocampus. Figure 2C,F,I are negative control samples. The magenta red staining demonstrates the color development using AEC substrate in the blue background (Hematoxylin counterstain) due to the reactivity of antibodies against rabies antigen. AEC is a peroxidase substrate, which upon oxidation reaction, catalyzed by HRP, results in water insoluble precipitate observable under a light microscope.
A positive result in IHC corresponds to magenta red staining in tissue sections. The staining of cytoplasmic inclusions and granular inclusions of varying size are indicative of samples positive for RABV infections. Samples are deemed negative if no specific red staining or only the blue background due to hematoxylin was observed. In addition to the positive staining, the distribution of inclusions could provide indirect quantification of levels of rabies antigen in the sample, which might correspond to the viral load of the tissue samples. Irrespective of the levels of distribution, any specific staining will classify the sample as positive for RABV antigen detection.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/60138/60138fig1.jpg" /> 
Figure 1: Flow chart indicating different steps for IHC testing. <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60138/60138fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/60138/60138fig2.jpg" /> 
Figure 2: Immunohistochemical staining of positive and negative rabies brain tissue. (A) Intracytoplasmic viral inclusions and rabies virus antigen detection in the brainstem 200x total magnification; (B) positive brainstem 400x; (C) brainstem negative control 200x; (D) rabies virus inclusions within the cerebellum 200x; (E) cerebellum and Purkinje cells 400x; (F) cerebellum negative control; (G) Viral inclusions within hippocampus 200x; (H) hippocampus 400x; hippocampus negative control 200x. The red stain indicates the presence of rabies virus antigen using the Streptavidin-biotin complex staining method (AEC substrate). Hematoxylin counterstain (blue). <a href="https://www-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/60138/60138fig2large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Immunohistochemistry Test for the Lyssavirus Antigen Detection from Formalin-Fixed Tissues at JoVE.com

Immunohistochemistry Test for the Lyssavirus Antigen Detection from Formalin-Fixed Tissues

Here, we present an immunohistochemistry test protocol for the detection of rabies virus antigen as an alternative diagnostic test for formalin-fixed tissues.

One of the primary diagnostic modalities for rabies is the detection of viral ribonucleoprotein (RNP) complex (antigen) in the infected tissue samples. ...

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Nanyang Technological University

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JoVE Journal

Immunology and Infection

4.1K Views.  Centers for Disease Control and Prevention. Here, we present an immunohistochemistry test protocol for the detection of rabies virus antigen as an alternative diagnostic test for formalin-fixed tissues.

Video: Immunohistochemistry Test for the Lyssavirus Antigen Detection from Formalin-Fixed Tissues

Detection of Infectious Virus from Field-collected Mosquitoes by Vero Cell Culture Assay

Mosquitoes transmit a number of distinct viruses including important human pathogens such as West Nile virus, dengue virus, and chickungunya virus. Many of these viruses have intensified in their endemic ranges and expanded to new territories, necessitating effective surveillance and control programs to respond to these threats. One strategy to monitor virus activity involves collecting large numbers of mosquitoes from endemic sites and testing them for viral infection. In this article, we describe how to handle, process, and screen field-collected mosquitoes for infectious virus by Vero cell culture assay. Mosquitoes are sorted by trap location and species, and grouped into pools containing &le;50 individuals. Pooled specimens are homogenized in buffered saline using a mixer-mill and the aqueous phase is inoculated onto confluent Vero cell cultures (Clone E6). Cell cultures are monitored for cytopathic effect from days 3-7 post-inoculation and any viruses grown in cell culture are identified by the appropriate diagnostic assays. By utilizing this approach, we have isolated 9 different viruses from mosquitoes collected in Connecticut, USA, and among these, 5 are known to cause human disease. Three of these viruses (West Nile virus, Potosi virus, and La Crosse virus) represent new records for North America or the New England region since 1999. The ability to detect a wide diversity of viruses is critical to monitoring both established and newly emerging viruses in the mosquito population.

We describe a method to process and screen field-collected mosquitoes for a diversity of viruses by Vero cell culture assay. By employing this technique, we have detected 9 different viruses from 4 taxonomic families in mosquitoes collected in Connecticut.

Mosquitoes transmit a number of distinct viruses including important human pathogens such as West Nile virus, dengue virus, and chickungunya virus. Many ...

Diagnosing Pulmonary Tuberculosis with the Xpert MTB/RIF Test

Tuberculosis (TB) due to Mycobacterium tuberculosis (MTB) remains a major public health issue: the infection affects up to one third of the world population1, and almost two million people are killed by TB each year.2 Universal access to high-quality, patient-centered treatment for all TB patients is emphasized by WHO's Stop TB Strategy.3 The rapid detection of MTB in respiratory specimens and drug therapy based on reliable drug resistance testing results are a prerequisite for the successful implementation of this strategy. However, in many areas of the world, TB diagnosis still relies on insensitive, poorly standardized sputum microscopy methods. Ineffective TB detection and the emergence and transmission of drug-resistant MTB strains increasingly jeopardize global TB control activities.2
Effective diagnosis of pulmonary TB requires the availability - on a global scale - of standardized, easy-to-use, and robust diagnostic tools that would allow the direct detection of both the MTB complex and resistance to key antibiotics, such as rifampicin (RIF). The latter result can serve as marker for multidrug-resistant MTB (MDR TB) and has been reported in &gt; 95% of the MDR-TB isolates.4, 5 The rapid availability of reliable test results is likely to directly translate into sound patient management decisions that, ultimately, will cure the individual patient and break the chain of TB transmission in the community.2
Cepheid's (Sunnyvale, CA, U.S.A.) Xpert MTB/RIF assay6, 7 meets the demands outlined above in a remarkable manner. It is a nucleic-acids amplification test for 1) the detection of MTB complex DNA in sputum or concentrated sputum sediments; and 2) the detection of RIF resistance-associated mutations of the rpoB gene.8 It is designed for use with Cepheid's GeneXpert Dx System that integrates and automates sample processing, nucleic acid amplification, and detection of the target sequences using real-time PCR and reverse transcriptase PCR. The system consists of an instrument, personal computer, barcode scanner, and preloaded software for running tests and viewing the results.9 It employs single-use disposable Xpert MTB/RIF cartridges that hold PCR reagents and host the PCR process. Because the cartridges are self-contained, cross-contamination between samples is eliminated.6 Current nucleic acid amplification methods used to detect MTB are complex, labor-intensive, and technically demanding. The Xpert MTB/RIF assay has the potential to bring standardized, sensitive and very specific diagnostic testing for both TB and drug resistance to universal-access point-of-care settings3, provided that they will be able to afford it. In order to facilitate access, the Foundation for Innovative New Diagnostics (FIND) has negotiated significant price reductions. Current FIND-negotiated prices, along with the list of countries eligible for the discounts, are available on the web.10

The Xpert MTB/RIF test integrates sample decontamination, hands-free operation, on-board sample processing, and ultra-sensitive hemi-nested PCR for the simultaneous detection of Mycobacterium tuberculosis and rifampicin resistance, either in expectorated sputum or concentrated sputum sediments, in approximately two hours. Testing is standardized and requires only moderate laboratory infrastructure and training.

Tuberculosis (TB) due to Mycobacterium tuberculosis (MTB) remains a major public health issue: the infection affects up to one third of the world ...

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Microdissection has been used for the examination of tissues at DNA, RNA, and protein levels for over a decade. Laser capture microscopy (LCM) is the most common microdissection technique used today. In this technique, a laser is used to focally melt a thermoplastic membrane that overlies a dehydrated tissue section1. The tissue section composite is then lifted and separated from the membrane. Although this technique can be used successfully for tissue examination, it is time consuming and expensive. Furthermore, the successful completion of procedures using this technique requires the use of a laser, thus limiting its use. A new more affordable and practical microdissection approach called mesodissection is a possible solution to the pitfalls of LCM. This technique employs the MESO-1/MeSectr system to mill the desired tissue from a slide mounted tissue sample while concurrently dispensing and aspirating fluid to recover the desired tissue sample into a consumable mill bit. Before the dissection process begins, the user aligns the formalin fixed paraffin embedded (FFPE) slide with a hematoxylin and eosin stained (H&#38;E) reference slide. Thereafter, the operator annotates the desired dissection area and proceeds to dissect the appropriate segment. The program generates an archived image of the dissection. The main advantage of mesodissection is the short duration needed to dissect a slide, taking an average of ten minutes from set up to sample generation in this experiment. Additionally, the system is significantly more cost effective and user friendly. A slight disadvantage is that it is not as precise as laser capture microscopy. In this article we demonstrate how mesodissection can be used to extract RNA from slides from FFPE granulomas caused by Mycobacterium tuberculosis (Mtb).

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Microdissection has been extensively employed for the examination of DNA, RNA, and protein within tissue. Laser capture microscopy (LCM) is the most commonly used method, but a new milling technique, mesodissection, is recently available. We demonstrate RNA extraction from mesodissected formalin fixed paraffin embedded tissue slides of Mycobacterium tuberculosis granulomas.

Microdissection has been used for the examination of tissues at DNA, RNA, and protein levels for over a decade. Laser capture microscopy (LCM) is the most ...

Detection of Human Leukocyte Antigen Biomarkers in Breast Cancer Utilizing Label-free Biosensor Technology

According to the American Cancer Society, more than 200,000 women will be diagnosed with invasive breast cancer each year and approximately 40,000 will die from the disease. The human leukocyte antigen (HLA) class I samples peptides derived from proteasomal degradation of cellular proteins and presents these fragments on the cell surface for interrogation by circulating cytotoxic T lymphocytes (CTL). Generation of T-cell receptor mimic (TCRm) monoclonal antibodies (mAbs) which recognize breast cancer specific peptide/HLA-A*02:01 complexes such as those derived from macrophage migration inhibitory factor (MIF19-27) and NY-ESO-1157-165 enable detection and destruction of breast cancer cells in the absence of an effective anti-tumor CTL response. Intact class I HLA/peptide complexes are shed by breast cancer cells and represent potentially relevant cancer biomarkers. In this work, a breakthrough biomarker screening system for cancer diagnostics incorporating T-cell receptor mimic monoclonal antibodies combined with a novel, label-free biosensor utilizing guided-mode resonance (GMR) sensor technology is presented. Detection of shed MIF/HLA-A*02:01 complexes in MDA-MB-231 cell supernatants, spiked human serum, and patient plasma is demonstrated. The impact of this work could revolutionize personalized medicine through development of companion disease diagnostics for targeted immunotherapies.

Intact class I HLA/peptide complexes are shed by cancer cells, representing a potential relevant cancer biomarker. Utilizing label-free sensor technology and T-cell receptor mimicking monoclonal antibodies, detection of shed MIF/HLA-A*02:01 complexes in MDA-MB-231 cell supernatants, spiked human serum, and patient plasma is demonstrated, enabling development of a novel cancer diagnostic platform.

According to the American Cancer Society, more than 200,000 women will be diagnosed with invasive breast cancer each year and approximately 40,000 will ...

Isolation of Leukocytes from the Murine Tissues at the Maternal-Fetal Interface

Immune tolerance in pregnancy requires that the immune system of the mother undergoes distinctive changes in order to accept and nurture the developing fetus. This tolerance is initiated during coitus, established during fecundation and implantation, and maintained throughout pregnancy. Active cellular and molecular mediators of maternal-fetal tolerance are enriched at the site of contact between fetal and maternal tissues, known as the maternal-fetal interface, which includes the placenta and the uterine and decidual tissues. This interface is comprised of stromal cells and infiltrating leukocytes, and their abundance and phenotypic characteristics change over the course of pregnancy. Infiltrating leukocytes at the maternal-fetal interface include neutrophils, macrophages, dendritic cells, mast cells, T cells, B cells, NK cells, and NKT cells that together create the local micro-environment that sustains pregnancy. An imbalance among these cells or any inappropriate alteration in their phenotypes is considered a mechanism of disease in pregnancy. Therefore, the study of leukocytes that infiltrate the maternal-fetal interface is essential in order to elucidate the immune mechanisms that lead to pregnancy-related complications. Described herein is a protocol that uses a combination of gentle mechanical dissociation followed by a robust enzymatic disaggregation with a proteolytic and collagenolytic enzymatic cocktail to isolate the infiltrating leukocytes from the murine tissues at the maternal-fetal interface. This protocol allows for the isolation of high numbers of viable leukocytes (&#62;70%) with sufficiently conserved antigenic and functional properties. Isolated leukocytes can then be analyzed by several techniques, including immunophenotyping, cell sorting, imaging, immunoblotting, mRNA expression, cell culture, and in vitro functional assays such as mixed leukocyte reactions, proliferation, or cytotoxicity assays.

Described herein is a protocol to isolate and analyze the infiltrating leukocytes of tissues at the maternal-fetal interface (uterus, decidua, and placenta) of mice. This protocol maintains the integrity of most cell surface markers and yields enough viable cells for downstream applications including flow cytometry analysis.

Immune tolerance in pregnancy requires that the immune system of the mother undergoes distinctive changes in order to accept and nurture the developing ...

Nasal Wipes for Influenza A Virus Detection and Isolation from Swine

Surveillance for influenza A viruses in swine is critical to human and animal health because influenza A virus rapidly evolves in swine populations and new strains are continually emerging. Swine are able to be infected by diverse lineages of influenza A virus making them important hosts for the emergence and maintenance of novel influenza A virus strains. Sampling pigs in diverse settings such as commercial swine farms, agricultural fairs, and live animal markets is important to provide a comprehensive view of currently circulating IAV strains. The current gold-standard ante-mortem sampling technique (i.e. collection of nasal swabs) is labor intensive because it requires physical restraint of the pigs. Nasal wipes involve rubbing a piece of fabric across the snout of the pig with minimal to no restraint of the animal. The nasal wipe procedure is simple to perform and does not require personnel with professional veterinary or animal handling training. While slightly less sensitive than nasal swabs, virus detection and isolation rates are adequate to make nasal wipes a viable alternative for sampling individual pigs when low stress sampling methods are required. The proceeding protocol outlines the steps needed to collect a viable nasal wipe from an individual pig.

The authors present a protocol to collect swine nasal wipes to detect and isolate influenza A viruses.

Surveillance for influenza A viruses in swine is critical to human and animal health because influenza A virus rapidly evolves in swine populations and ...

Generation of Two-color Antigen Microarrays for the Simultaneous Detection of IgG and IgM Autoantibodies

Autoantibodies, which are antibodies against self-antigens, are present in many disease states and can serve as markers for disease activity. The levels of autoantibodies to specific antigens are typically detected with the enzyme-linked immunosorbent assay (ELISA) technique. However, screening for multiple autoantibodies with ELISA can be time-consuming and requires a large quantity of patient sample. The antigen microarray technique is an alternative method that can be used to screen for autoantibodies in a multiplex fashion. In this technique, antigens are arrayed onto specially coated microscope slides with a robotic microarrayer. The slides are probed with patient serum samples and subsequently fluorescent-labeled secondary antibodies are added to detect binding of serum autoantibodies to the antigens. The autoantibody reactivities are revealed and quantified by scanning the slides with a scanner that can detect fluorescent signals. Here we describe methods to generate custom antigen microarrays. Our current arrays are printed with 9 solid pins and can include up to 162 antigens spotted in duplicate. The arrays can be easily customized by changing the antigens in the source plate that is used by the microarrayer. We have developed a two-color secondary antibody detection scheme that can distinguish IgG and IgM reactivities on the same slide surface. The detection system has been optimized to study binding of human and murine autoantibodies.

We describe here a method to generate customizable antigen microarrays that can be used for the simultaneous detection of serum IgG and IgM autoantibodies from humans and mice. These arrays allow for high-throughput and quantitative detection of antibodies against any antigens or epitopes of interest.

Autoantibodies, which are antibodies against self-antigens, are present in many disease states and can serve as markers for disease activity. The levels ...

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate and enrich these rare cells for studies of their phenotype and biology. Approaches are inevitably based on the principle that B cells recognize native antigen by virtue of cell surface receptors that are representative in specificity of antibodies that will eventually be secreted by their differentiated daughters. Perhaps the most obvious approach to the problem involves use of fluorochrome-conjugated antigens in conjunction with fluorescence-activated cell sorting (FACS). However, the utility of these methods is limited by cell frequency and the achievable rate of analysis and isolation by electronic sorting. A novel method to enrich rare antigen-specific B cells using magnetic nanoparticles that results in high yield enrichment of antigen-reactive B cells from large starting cell populations is described. This method enables improved monitoring of the phenotype and biology of antigen reactive cells before and following in vivo antigen encounter, such as after immunization or during development of autoimmunity.

A simple yet effective method that employs magnetic nanoparticles to detect and enrich antigen-reactive B cells for functional and phenotypic analysis is described.

B cells reactive with a specific antigen usually occur at a frequency of &lt;0.05% of lymphocytes. For decades researchers have sought methods to isolate ...

Isolation, Characterization, and Purification of Macrophages from Tissues Affected by Obesity-related Inflammation

Obesity promotes a chronic inflammatory state that is largely mediated by tissue-resident macrophages as well as monocyte-derived macrophages. Diet-induced obesity (DIO) is a valuable model in studying the role of macrophage heterogeneity; however, adequate macrophage isolations are difficult to acquire from inflamed tissues. In this protocol, we outline the isolation steps and necessary troubleshooting guidelines derived from our studies for obtaining a suitable population of tissue-resident macrophages from mice following 18 weeks of high-fat (HFD) or high-fat/high-cholesterol (HFHCD) diet intervention. This protocol focuses on three hallmark tissues studied in obesity and atherosclerosis including the liver, white adipose tissues (WAT), and the aorta. We highlight how dualistic usage of flow cytometry can achieve a new dimension of isolation and characterization of tissue-resident macrophages. A fundamental section of this protocol addresses the intricacies underlying tissue-specific enzymatic digestions and macrophage isolation, and subsequent cell-surface antibody staining for flow cytometric analysis. This protocol addresses existing complexities underlying fluorescent-activated cell sorting (FACS) and presents clarifications to these complexities so as to obtain broad range characterization from adequately sorted cell populations. Alternate enrichment methods are included for sorting cells, such as the dense liver, allowing for flexibility and time management when working with FACS. In brief, this protocol aids the researcher to evaluate macrophage heterogeneity from a multitude of inflamed tissues in a given study and provides insightful troubleshooting tips that have been successful for favorable cellular isolation and characterization of immune cells in DIO-mediated inflammation.

This protocol allows a researcher to isolate and characterize tissue-resident macrophages in various hallmark inflamed tissues extracted from diet-induced models of metabolic disorders.

Obesity promotes a chronic inflammatory state that is largely mediated by tissue-resident macrophages as well as monocyte-derived macrophages. ...

In Vivo Assay for Detection of Antigen-specific T-cell Cytolytic Function Using a Vaccination Model

Current methodologies for antigen-specific killing are limited to in vitro use or utilized in infectious disease models. However, there is not a protocol specifically intended to measure antigen-specific killing without an infection. This protocol is designed and describes methods to overcome these limitations by allowing for the detection of antigen-specific killing of a target cell by CD8+ T cells in vivo. This is accomplished by merging a vaccination model with a traditional CFSE-labeled target killing assay. This combination allows the researcher to assess the antigen-specific CTL potential directly and quickly as the assay is not dependent upon tumor growth or infection. In addition, the readout is based on flow cytometry and so should be readily accessible to most researchers. The major limitation of the study is identifying the timeline in vivo that is appropriate to the hypothesis being tested. Variations in antigen strength and mutations in the T cells that may result in differential cytolytic function need to be carefully assessed to determine the optimal time for cell harvest and assessment. The appropriate concentration of peptide for vaccination has been optimized for hgp10025-33 and OVA257-264, but further validation would be needed for other peptides that may be more appropriate to a given study. Overall, this protocol allows a quick assessment of killing function in vivo and can be adapted to any given antigen.

In Vivo Assay for Detection of Antigen-specific T-cell Cytolytic Function Using a Vaccination Model

The goal of this protocol is to allow for detection of in vivo antigen-specific killing of a target cell in a murine model.

Current methodologies for antigen-specific killing are limited to in vitro use or utilized in infectious disease models. However, there is not a protocol ...

Immunohistochemistry Test for the Lyssavirus Antigen Detection from Formalin-Fixed Tissues

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Rozdziały w tym wideo

Detection of Infectious Virus from Field-collected Mosquitoes by Vero Cell Culture Assay

Diagnosing Pulmonary Tuberculosis with the Xpert MTB/RIF Test

A Novel Microdissection Approach to Recovering Mycobacterium tuberculosis Specific Transcripts from Formalin Fixed Paraffin Embedded Lung Granulomas

Detection of Human Leukocyte Antigen Biomarkers in Breast Cancer Utilizing Label-free Biosensor Technology

Isolation of Leukocytes from the Murine Tissues at the Maternal-Fetal Interface

Nasal Wipes for Influenza A Virus Detection and Isolation from Swine

Generation of Two-color Antigen Microarrays for the Simultaneous Detection of IgG and IgM Autoantibodies

Detection and Enrichment of Rare Antigen-specific B Cells for Analysis of Phenotype and Function

Isolation, Characterization, and Purification of Macrophages from Tissues Affected by Obesity-related Inflammation

In Vivo Assay for Detection of Antigen-specific T-cell Cytolytic Function Using a Vaccination Model