We would like to thank members at our institute (Texas Biomedical Research Institute) for their efforts in keeping our facilities fully operational and safe during the COVID-19 pandemic. We would also like to thank our Institutional Biosafety Committee (IBC) and spell (IACUC) for reviewing our protocols in a time-efficient manner.We thank Dr. Thomas Moran at the Icahn School of Medicine at Mount Sinai for providing the SARS-CoV cross-reactive 1C7C7 nucleocapsid (N) protein monoclonal antibody. SARS-CoV-2 research in the Martinez-Sobrido&#39;s laboratory is currently supported by the NIAID/NIH grants RO1AI161363-01, RO1AI161175-01A1, and R43AI165089-01; the Department of Defense (DoD) grants W81XWH2110095 and W81XWH2110103; the San Antonio Partnership for Precision Therapeutic; the Texas Biomedical Research Institute Forum; the University of Texas Health Science Center at San Antonio; the San Antonio Medical Foundation; and by the Center for Research on Influenza Pathogenesis and Transmission (CRIPT), a NIAID-funded Center of Excellence for Influenza Research and Response (CEIRR, contract # 75N93021C00014).

Protocols involving K18 hACE2 transgenic mice were approved by the Texas Biomedical Research Institute (TBRI) Institutional Biosafety Committee (IBC) and the Institutional Animal Care and Use Committee (IACUC). All experiments follow the recommendations in the Guide for the Care and Use of Laboratory Animals of the National Research Council40. The appropriate Personal Protection Equipment (PPE) is required when working with mice.
1. Use of K18 hACE2 transgenic mice
<ol>
	<li>Purchase and maintain 4-6-week-old female B6.Cg-Tg(K18-ACE2)2Prlmn/J mice (K18 hACE2 transgenic mice) in a biosafety level (BSL)-2 animal care facility under specific pathogen-free conditions.
	<ol>
		<li>After arrival at the BSL2 facilities, allow the animals to acclimate for 7 days and transfer them to the BSL-3 animal facility for infections and other experimental procedures.</li>
		<li>Following IACUC protocols, place 4 mice per cage. To ensure that the animal is deceased, after mice infection with rSARS-CoV-2 and in vivo imaging, euthanize the animals with a lethal dose of Fatal-Plus (&#62;100 mg/kg).</li>
	</ol>
	</li>
</ol>
2. Biosafety
NOTE: In this manuscript, rSARS-CoV-2 is generated using the BAC-based reverse genetic systems for SARS-CoV-2 USA-WA1/2020 strain, as previously described37. All in vivo procedures involving rSARS-CoV-2/Nluc or rSARS-CoV-2/Venus infections must be performed in a biological safety cabinet under BSL-3 conditions.
<ol>
	<li>Clean the biosafety cabinet with 2% Wexicide and 70% Ethanol disinfectant sequentially before and after performing all the experimental procedures described in this article.</li>
	<li>Sterilize all dissection material (scissors, dissecting forceps, etc.) and the homogenizer before and after each use.</li>
	<li>Clean the isolation chamber and disinfect using MB10 tablets before and after each use according to the manufacturer&#39;s instruction.</li>
	<li>Discard all biological material produced during the procedures following IBC and IACUC guidelines.</li>
</ol>
3. In vivo characterization of rSARS-CoV-2
<ol>
	<li>Mouse infections
	<ol>
		<li>Place female 4-6-week-old K18 hACE2 transgenic mice in labeled cages, identify the mice in each cage using an ear punch code and place 4 mice per cage. Use a group of mice for body weight and survival and another group of animals for viral titration and imaging.</li>
		<li>Before infection, shave mice chest on the ventral side from the pectoral nipple to the inguinal nipple area to facilitate the bioluminescence signal.</li>
		<li>Prepare the rSARS-CoV-2 inoculum with 105 plaque-forming units (PFU)/mouse under sterile conditions in a total volume of 50 &#181;L using sterile 1x phosphate buffer saline (PBS). 
		NOTE: Calculate the amount of rSARS-CoV-2 to be used in the viral dilution with the formula: virus needed = (105 PFU per mouse / 50 &#181;L) x final volume) / stock viral titer.</li>
		<li>Keep the virus inoculum chilled on ice.</li>
		<li>Use the mock-infected (1x PBS) and rSARS-CoV-2/WT-infected mice as internal controls. Place the mock-infected mice in a separate cage than rSARS-CoV-2-infected mice.</li>
		<li>Anesthetize the mice using 5% isoflurane gaseous sedation in an anesthesia chamber and maintain with 3% isoflurane.</li>
		<li>Once postural reaction and righting reflex are confirmed, place the mouse in the dorsal recumbency position.</li>
		<li>Scruff the neck of the mouse between the index finger and thumb and hold the tail against the palm of the hand with the pinky finger to hold the animal in a dorsal position.</li>
		<li>Place the pipette tip containing 50 &#181;L of the virus inoculum in the nostril and slowly eject the solution. Ensure that the virus inoculum is inhaled and there is no reflux by observing the inoculum drop disappearing.</li>
	</ol>
	</li>
	<li>Bioluminescence monitoring K18 hACE2 transgenic mice infected with rSARS-CoV-2/Nluc (Figure 1 and Figure 2) 
	NOTE: This experiment follows the schematic representation and uses the viruses displayed in Figure 1. An isoflurane anesthesia attachment is required for the in vivo imaging system (IVIS). See Table of Materials for details instruments and systems required.
	<ol>
		<li>Initiate the imaging software and set up the parameters, click image mode to Bioluminescence, open filter, and set the exposure time to auto.</li>
		<li>Upon initializing the IVIS machine, place the mice in the isolation chamber while still inside the biosafety cabinet. Induce mice with isoflurane at a 5% concentration. Once loss of the postural reaction and righting reflex is confirmed, maintain with 3% isoflurane.</li>
		<li>Once mice are anesthetized, remove them from the isolation chamber and retro-orbitally administer the luciferase substrate diluted 1:10 in 1x PBS (final volume 100 &#181;L/mouse) with a 25 G needle.</li>
		<li>After luciferase substrate administration, place the mice back in the isolation chamber with their chests facing up and nasal cavity inside the manifold cone to keep the animal anesthetized during the imaging procedure.</li>
		<li>Transfer the isolation chamber to the IVIS machine, and instantaneously after closing the IVIS imager door, select Acquire in the software program to initialize (Figure 2A).</li>
		<li>To analyze bioluminescence images acquired, utilize the ROI (region of interest) tool in the software to designate the precise signal and measure the flux (Figure 2B).</li>
		<li>Click on Measure and allow the system to begin assessing the bioluminescence in photons to provide the absolute photon emission comparable to the output measurements provided by the various parameters.</li>
		<li>Image mice at 1-, 2-, 4- and 6-days post-infection.</li>
		<li>After&#160;imaging&#160;place mice back into cage.</li>
	</ol>
	</li>
	<li>Fluorescence analysis in K18 hACE2 transgenic mice infected with rSARS-CoV-2/Venus (Figure 3 and Figure 4) 
	NOTE: This experiment follows the schematic representation and rSARS-CoV-2 shown in Figure 3. See Table of Materials for details instruments and systems required.
	<ol>
		<li>Initiate the imaging software and set up the parameters, set excitation (500 nm) and emission filters (530 nm), click image mode to Fluorescence and set the exposure time to auto.</li>
		<li>Intraperitoneally euthanize the mice using a lethal dose of Fatal-Plus (&#62;100 mg/kg). Following euthanasia, disinfect the incision site with 70% ethanol.</li>
		<li>Using tweezers, pull the skin, make an incision from the sternum to the abdomen and cut the incision from the sides with scissors. Cut the hepatic vein to minimize the amount of blood in the lungs and avoid high background signals during imaging.</li>
		<li>Using scissors, cut the sternum and open the ribcage. Next, snip the end of the trachea with scissors and remove the lungs with tweezers.</li>
		<li>Place the excised lungs in a 6-well plate containing 2 mL of 1x PBS and rinse to remove excess blood. Minimize the possibility of contamination between samples by disinfecting and cleaning surgery tools between samples using 70% ethanol.</li>
		<li>After initializing the IVIS machine, place the lungs in a black tray and separate the tissues from each other.</li>
		<li>Place the tray inside the isolation chamber inside the biosafety cabinet, and then transfer the isolation chamber to the IVIS. Close the door and click on Acquire to initiate the imaging system (Figure 4A).</li>
		<li>To analyze fluorescence, utilize the ROI tool and draw ROIs around each of the individual lungs. Measure each ROI manually and then use the average radiant efficiency values given and subtract from those of the mock-infected mice (Figure 4B).</li>
		<li>Once imaging is complete, place the tissues on ice for same-day analysis or in a cryotube for dry ice freezing to store at -80 &#176;C for later processing.</li>
	</ol>
	</li>
	<li>Lung bright field imaging and pathology scoring of K18 hACE2 transgenic mice infected with rSARS-CoV-2/Nluc (Figure 2A-C) and rSARS-CoV-2/Venus (Figure 4A-C)
	<ol>
		<li>After imaging bioluminescence of mice infected with rSARS-CoV-2/Nluc, rSARS-CoV-2/WT, and mock-infected, return the mice to their cages. Proceed with euthanasia and the ex vivo bright field imaging of mice lungs (Figure 2A).</li>
		<li>After imaging ex vivo fluorescence of lungs of infected mice, take bright-field images of the lungs (Figure 4A).</li>
		<li>Analyze the gross lesions on the surface of the lung using ImageJ (Figures 2C and 4C).</li>
		<li>Open the lung image to be analyzed in ImageJ.</li>
		<li>Calculate the ratio of pixel to cm, use the Straight tool and measure the actual length of the image.</li>
		<li>After selecting, click on Analyze &#62; Measure to calculate the length of pixels for the length.</li>
		<li>Click on Analysis &#62; Set Scale and input the numbers calculated from the previous step.</li>
		<li>Use the Freehand Selections tool and select the entire lung surface. Click on Analyze &#62; Measure to measure total lung area.</li>
		<li>Click on Edit &#62; Selection &#62; Make Inverse to select the rest of the lung area, then press delete or backspace to remove the background.</li>
		<li>Remove the selected area, then click on Image &#62; Adjust &#62; Color Threshold.</li>
		<li>To select pathologic lesion area, adjust Brightness to a minimum (between 1 to 50) and a maximum (between 50 to 200), depending on the levels of congestion and hemorrhages present.</li>
		<li>Once pathologic lesions are selected, click on Select at the bottom of the threshold color panel, then click on Analyze &#62; Measure to measure pathologic areas.</li>
		<li>Calculate the percentage of gross lesions with the formula: % of pathologic area = (measurement of pathologic area/total lung surface) x 100.</li>
	</ol>
	</li>
	<li>Viral titrations (Figure 2D and Figure 4D)
	<ol>
		<li>Upon imaging, complete the mice euthanasia and collect lungs, brain, and nasal mucosa.</li>
		<li>Place the lungs, brain, and nasal mucosa into separate sterile tissue homogenizers and add 1 mL of cold 1x PBS.</li>
		<li>Homogenize the samples by centrifuging at 21,500 x g for 10 min to pellet cell debris. Collect and transfer the supernatants into a new sterile tube and discard the pellet.</li>
		<li>If viral titrations are performed the same day, store the supernatants at 4 &#176;C. Alternatively, freeze the supernatant of the homogenized samples at -80 &#176;C until being evaluated later.</li>
		<li>Utilizing the supernatants obtained from the tissue homogenates make 10-fold serial dilutions and infect confluent monolayers of Vero E6 cells with 1 mL of each dilution of the supernatant (6-well plate format, 1.2 &#215; 106 cells/well, triplicates).</li>
		<li>Let the virus adsorb for 1 h at 37 &#176;C in a humidified 5% CO2 incubator.</li>
		<li>After viral adsorption, wash the cells with 1 mL of 1x PBS and incubate in 2 mL of post-infection media containing 1% Agar in the humidified 5% CO2 incubator at 37 &#176;C for 72 h.</li>
		<li>After the incubation, inactivate the plates in 10% neutral buffered formalin for 24 h at 4 &#176;C, ensure the entire plate is submerged.</li>
		<li>Take plates out of BSL3 and wash the cells three times with 1 mL of 1x PBS and permeabilize with 1 mL of 0.5% Triton X-100 for 10 min at room temperature (RT).</li>
		<li>Block the cells with 1 mL of 2.5% bovine serum albumin (BSA) in 1x PBS for 1 h at 37 &#176;C, followed by incubation in 1 mL of 1 &#181;g/mL of the SARS-CoV nucleocapsid (N) protein cross-reactive monoclonal antibody (1C7C7), diluted in 2.5% BSA for 1 h at 37 &#176;C.</li>
		<li>Wash the cells three times with 1 mL of 1x PBS and develop the plaques using the ABC kit and DAB Peroxidase Substrate kit according to the manufacturers&#39; instructions.</li>
		<li>Calculate the viral titers as PFU/mL. 
		&#8203;NOTE: Calculate with the formula PFU/mL = dilution factor x number of plaques x (1 mL/inoculum volume).</li>
	</ol>
	</li>
	<li>Nluc activity in tissues of K18 hACE2 transgenic mice infected with rSARS-CoV-2/Nluc (Figure 2E)
	<ol>
		<li>Quantify the presence of Nluc in the organ homogenates from mock, rSARS-CoV-2/WT, and rSARS-CoV-2/Nluc infected K18 hACE2 transgenic mice using a luciferase assay following the manufacturers&#39; instructions.</li>
	</ol>
	</li>
	<li>Evaluation of morbidity and mortality (Figure 2F, G and Figure 4E, F)
	<ol>
		<li>Intranasally infect 4-6-week-old female K18 hACE2 transgenic mice with 105 PFU of rSARS-CoV-2/WT, rSARS-CoV-2/Venus, rSARS-CoV-2/Nluc, or mock-infected as described in section 3.1.</li>
		<li>Monitor and weigh the mice over 12 days at the same time to minimize the weight variation due to food ingestion. Euthanize the mice that lose 25% of their initial body weight since they have reached a humane endpoint and note these mice as succumbing to viral infection.</li>
		<li>After 12 days, euthanize the mice that survive viral infection and calculate the % of body weight change and survival.</li>
	</ol>
	</li>
</ol>

<ol>
	<li>V'Kovski, P., Kratzel, A., Steiner, S., Stalder, H., Thiel, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Coronavirus+biology+and+replication:+implications+for+SARS-CoV-2.">Coronavirus biology and replication: implications for SARS-CoV-2.</a> Nature Reviews Microbiology. 19 (3), 155-170 (2021).</li><li>Pal, M., Berhanu, G., Desalegn, C., Kandi, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Severe+acute+respiratory+syndrome+coronavirus-2+(SARS-CoV-2):+An+update.">Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): An update.</a> Cureus. 12 (3), 7423 (2020).</li><li>Su, 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=Epidemiology,+genetic+recombination,+and+pathogenesis+of+coronaviruses.">Epidemiology, genetic recombination, and pathogenesis of coronaviruses.</a> Trends in Microbiology. 24 (6), 490-502 (2016).</li><li>Cui, J., Li, F., Shi, Z. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Origin+and+evolution+of+pathogenic+coronaviruses.">Origin and evolution of pathogenic coronaviruses.</a> Nature Reviews Microbiology. 17 (3), 181-192 (2019).</li><li>Lu, 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=Genomic+characterisation+and+epidemiology+of+2019+novel+coronavirus:+implications+for+virus+origins+and+receptor+binding.">Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding.</a> Lancet. 395 (10224), 565-574 (2020).</li><li>Evans, J. P., Liu, S. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+host+factors+in+SARS-CoV-2+entry.">Role of host factors in SARS-CoV-2 entry.</a> Journal of Biological Chemistry. 297 (1), 100847 (2021).</li><li>Petersen, 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=Comparing+SARS-CoV-2+with+SARS-CoV+and+influenza+pandemics.">Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics.</a> Lancet Infectious Diseases. 20 (9), 238-244 (2020).</li><li>Alfaraj, S. 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=Clinical+predictors+of+mortality+of+Middle+East+Respiratory+Syndrome+Coronavirus+(MERS-CoV)+infection:+A+cohort+study.">Clinical predictors of mortality of Middle East Respiratory Syndrome Coronavirus (MERS-CoV) infection: A cohort study.</a> Travel Medicine and Infectious Disease. 29, 48-50 (2019).</li><li>Harvey, W. 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=SARS-CoV-2+variants,+spike+mutations+and+immune+escape.">SARS-CoV-2 variants, spike mutations and immune escape.</a> Nature Reviews Microbiology. 19 (7), 409-424 (2021).</li><li>Dong, E., Du, H., Gardner, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=An+interactive+web-based+dashboard+to+track+COVID-19+in+real+time.">An interactive web-based dashboard to track COVID-19 in real time.</a> Lancet Infectious Diseases. 20 (5), 533-534 (2020).</li><li>Bar-On, Y. M., Flamholz, A., Phillips, R., Milo, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ARS-CoV-2+(COVID-19)+by+the+numbers.">ARS-CoV-2 (COVID-19) by the numbers.</a> Elife. 9, 57309 (2020).</li><li>Roussel, Y., 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=SARS-CoV-2:+fear+versus+data.">SARS-CoV-2: fear versus data.</a> International Journal of Antimicrobial Agents. 55 (5), 105947 (2020).</li><li>Scialo, F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SARS-CoV-2:+One+year+in+the+pandemic.+What+have+we+learned,+the+new+vaccine+era+and+the+threat+of+SARS-CoV-2+variants.">SARS-CoV-2: One year in the pandemic. What have we learned, the new vaccine era and the threat of SARS-CoV-2 variants.</a> Biomedicines. 9 (6), 611 (2021).</li><li>. Coronavirus (COVID-19) update: FDA authorizes additional monoclonal antibody for treatment of COVID-19 Available from: <a target="_blank" href="https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-additional-monoclonal-antibody-treatment-covid-19">https://www.fda.gov/news-events/press-announcements/coronavirus-covid-19-update-fda-authorizes-additional-monoclonal-antibody-treatment-covid-19</a> (2021)</li><li>Dougan, 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=Bamlanivimab+plus+Etesevimab+in+Mild+or+Moderate+Covid-19.">Bamlanivimab plus Etesevimab in Mild or Moderate Covid-19.</a> New England Journal of Medicine. 385 (15), 1382-1392 (2021).</li><li>Ledford, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=COVID+antibody+treatments+show+promise+for+preventing+severe+disease.">COVID antibody treatments show promise for preventing severe disease.</a> Nature. 591 (7851), 513-514 (2021).</li><li>Tuccori, 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=An+overview+of+the+preclinical+discovery+and+development+of+bamlanivimab+for+the+treatment+of+novel+coronavirus+infection+(COVID-19):+reasons+for+limited+clinical+use+and+lessons+for+the+future.">An overview of the preclinical discovery and development of bamlanivimab for the treatment of novel coronavirus infection (COVID-19): reasons for limited clinical use and lessons for the future.</a> Expert Opinion on Drug Discovery. , 1-12 (2021).</li><li>Phan, A. T., Gukasyan, J., Arabian, S., Wang, S., Neeki, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emergent+inpatient+administration+of+casirivimab+and+imdevimab+antibody+cocktail+for+the+treatment+of+COVID-19+pneumonia.">Emergent inpatient administration of casirivimab and imdevimab antibody cocktail for the treatment of COVID-19 pneumonia.</a> Cureus. 13 (5), 15280 (2021).</li><li>O'Brien, M. 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=Subcutaneous+REGEN-COV+antibody+combination+in+early+SARS-CoV-2+infection.">Subcutaneous REGEN-COV antibody combination in early SARS-CoV-2 infection.</a> medRxiv. , (2021).</li><li>Beigel, J. 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=Remdesivir+for+the+treatment+of+Covid-19+-+Final+report.">Remdesivir for the treatment of Covid-19 - Final report.</a> New England Journal of Medicine. 383 (19), 1813-1826 (2020).</li><li>Li, L., 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=Effect+of+convalescent+plasma+therapy+on+time+to+clinical+improvement+in+patients+with+severe+and+life-threatening+COVID-19:+A+randomized+clinical+trial.">Effect of convalescent plasma therapy on time to clinical improvement in patients with severe and life-threatening COVID-19: A randomized clinical trial.</a> Journal of the American Medical Association. 324 (5), 460-470 (2020).</li><li>Polack, F. 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=Safety+and+efficacy+of+the+BNT162b2+mRNA+Covid-19+vaccine.">Safety and efficacy of the BNT162b2 mRNA Covid-19 vaccine.</a> New England Journal of Medicine. 383 (27), 2603-2615 (2020).</li><li>Oliver, 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=The+advisory+committee+on+immunization+practices'+interim+recommendation+for+use+of+Pfizer-BioNTech+COVID-19+vaccine+-+United+States,+December+2020.">The advisory committee on immunization practices' interim recommendation for use of Pfizer-BioNTech COVID-19 vaccine - United States, December 2020.</a> Morbidity and Mortality Weekly Report. 69 (50), 1922-1924 (2020).</li><li>Oliver, 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=The+advisory+committee+on+immunization+practices'+interim+recommendation+for+use+of+Janssen+COVID-19+vaccine+-+United+States,+February+2021.">The advisory committee on immunization practices' interim recommendation for use of Janssen COVID-19 vaccine - United States, February 2021.</a> Morbidity and Mortality Weekly Report. 70 (9), 329-332 (2021).</li><li>Zhao, 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=Emission+spectra+of+bioluminescent+reporters+and+interaction+with+mammalian+tissue+determine+the+sensitivity+of+detection+in+vivo.">Emission spectra of bioluminescent reporters and interaction with mammalian tissue determine the sensitivity of detection in vivo.</a> Journal of Biomedical Optics. 10 (4), 41210 (2005).</li><li>Shaner, N. C., Steinbach, P. A., Tsien, R. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+guide+to+choosing+fluorescent+proteins.">A guide to choosing fluorescent proteins.</a> Nature Methods. 2 (12), 905-909 (2005).</li><li>Nogales, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+fluorescent+and+bioluminescent+bireporter+Influenza+A+Virus+to+evaluate+viral+infections.">A novel fluorescent and bioluminescent bireporter Influenza A Virus to evaluate viral infections.</a> Journal of Virology. 93 (10), 00032 (2019).</li><li>Nogales, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication-competent+fluorescent-expressing+influenza+B+virus.">Replication-competent fluorescent-expressing influenza B virus.</a> Virus Research. 213, 69-81 (2016).</li><li>Welsh, D. K., Noguchi, T. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cellular+bioluminescence+imaging.">Cellular bioluminescence imaging.</a> Cold Spring Harbor Protocols. 2012 (8), (2012).</li><li>Tran, V., Moser, L. A., Poole, D. S., Mehle, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Highly+sensitive+real-time+in+vivo+imaging+of+an+influenza+reporter+virus+reveals+dynamics+of+replication+and+spread.">Highly sensitive real-time in vivo imaging of an influenza reporter virus reveals dynamics of replication and spread.</a> Journal of Virology. 87 (24), 13321-13329 (2013).</li><li>Schoggins, J. 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=Dengue+reporter+viruses+reveal+viral+dynamics+in+interferon+receptor-deficient+mice+and+sensitivity+to+interferon+effectors+in+vitro.">Dengue reporter viruses reveal viral dynamics in interferon receptor-deficient mice and sensitivity to interferon effectors in vitro.</a> Proceedings of the National Academy of Sciences of the United States of America. 109 (36), 14610-14615 (2012).</li><li>Luker, G. D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Noninvasive+bioluminescence+imaging+of+herpes+simplex+virus+type+1+infection+and+therapy+in+living+mice.">Noninvasive bioluminescence imaging of herpes simplex virus type 1 infection and therapy in living mice.</a> Journal of Virology. 76 (23), 12149-12161 (2002).</li><li>Li, 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=Development+of+a+rapid+antiviral+screening+assay+based+on+eGFP+reporter+virus+of+Mayaro+virus.">Development of a rapid antiviral screening assay based on eGFP reporter virus of Mayaro virus.</a> Antiviral Research. 168, 82-90 (2019).</li><li>Kirui, J., Freed, E. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Generation+and+validation+of+a+highly+sensitive+bioluminescent+HIV-1+reporter+vector+that+simplifies+measurement+of+virus+release.">Generation and validation of a highly sensitive bioluminescent HIV-1 reporter vector that simplifies measurement of virus release.</a> Retrovirology. 17 (1), 12 (2020).</li><li>Shang, B., 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=Development+and+characterization+of+a+stable+eGFP+enterovirus+71+for+antiviral+screening.">Development and characterization of a stable eGFP enterovirus 71 for antiviral screening.</a> Antiviral Research. 97 (2), 198-205 (2013).</li><li>Zou, G., Xu, H. Y., Qing, M., Wang, Q. Y., Shi, P. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Development+and+characterization+of+a+stable+luciferase+dengue+virus+for+high-throughput+screening.">Development and characterization of a stable luciferase dengue virus for high-throughput screening.</a> Antiviral Research. 91 (1), 11-19 (2011).</li><li>Ye, C., 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=Rescue+of+SARS-CoV-2+from+a+single+bacterial+artificial+chromosome.">Rescue of SARS-CoV-2 from a single bacterial artificial chromosome.</a> mBio. 11 (5), 02168 (2020).</li><li>Avila-Perez, G., Park, J. G., Nogales, A., Almazan, F., Martinez-Sobrido, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Rescue+of+recombinant+Zika+virus+from+a+bacterial+artificial+chromosome+cDNA+clone.">Rescue of recombinant Zika virus from a bacterial artificial chromosome cDNA clone.</a> Journal of Visualized Experiments: JoVE. (148), e59537 (2019).</li><li>Chiem, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+bifluorescent-based+assay+for+the+identification+of+neutralizing+antibodies+against+SARS-CoV-2+variants+of+concern+in+vitro+and+in+vivo.">A bifluorescent-based assay for the identification of neutralizing antibodies against SARS-CoV-2 variants of concern in vitro and in vivo.</a> Journal of Virology. , (2021).</li><li>Committee for the update of the guide for the care and use of laboratory animals., Institute for laboratory animal research (U.S) &amp; National Academies Press (U.S.). <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Guide+for+the+care+and+use+of+laboratory+animals.+8th+edn.">Guide for the care and use of laboratory animals. 8th edn.</a> National Research Council (US). , (2011).</li><li>Ye, C., 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=Analysis+of+SARS-CoV-2+infection+dynamic+in+vivo+using+reporter-expressing+viruses.">Analysis of SARS-CoV-2 infection dynamic in vivo using reporter-expressing viruses.</a> Proceedings of the National Academy of Sciences of the United States of America. 118 (41), (2021).</li></ol>

The authors declare that the research was conducted in the absence of any commercial, financial and non-financial, or personal conflict of interest in relation to the work described.

This protocol demonstrates the feasibility of using these rSARS-CoV-2 expressing reporter genes to monitor viral infections in vivo. Both reporter-expressing recombinant viruses provide an excellent tool for studying SARS-CoV-2 infections in vivo. The described ex vivo (rSARS-CoV-2/Venus) and in vivo (rSARS-CoV-2/Nluc) imaging systems represent an excellent option to understand the dynamics of SARS-CoV-2 infection, viral pathogenesis and to identify infected cells/organs at different t...

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped, positive-sense, single-stranded RNA virus that belongs to the Betacoronavirus lineage in the Coronaviridae family1. This viral family is divided into Alpha-, Beta-, Gamma-, and Delta-coronavirus1. Alpha- and Betacoronaviruses mainly infect mammals, whereas Gamma- and Deltacoronavirus infect almost exclusively birds2. To date, seven coronaviruses (CoV) have crossed species barriers and emerged as human coronaviruses (HCoV): two alpha-CoVs (HCoV-229E and HCoV-NL63) and five beta-CoVs (HCoV-OC43, HCoV-HKU1, SARS-CoV, Middle East respiratory syndrome coronavirus [MERS-CoV], and SARS-CoV-2)3,4,5,6. SARS-CoV, MERS-CoV, and SARS-CoV-2 are highly pathogenic, causing severe lower respiratory tract infection7. Prior to the emergence of SARS-CoV-2, there were two epidemic outbreaks caused by CoVs: SARS-CoV in Guangdong Providence, China, from 2002-2003, with a case fatality rate (CFR) of about 9.7%; and MERS-CoV in the Middle East from 2012 to present, with a CFR of about 34%7,8. SARS-CoV-2 has an overall CFR between 3.4%-49%, with underlying conditions contributing to a higher CFR8,9. Since its discovery in December 2019, in Wuhan, China, SARS-CoV-2 has been responsible for over 242 million human infections and more than 4.9 million human deaths worldwide7,10,11,12. Notably, since late 2020, new SARS-CoV-2 variants of concern (VoC) and variants of interest (VoI) have impacted virus characteristics, including transmission and antigenicity9,13, and the overall direction of the COVID-19 pandemic. For the treatment of SARS-CoV-2 infections, there is currently only one United States (U.S.) Food and Drug Administration (FDA) therapeutic antiviral (remdesivir) and one Emergency Use Authorization (EUA) drug (baricitinib, to be administered in combination with remdesivir)14. There are also 6 approved EUA monoclonal antibodies: REGEN-COV (casirivimab and imdevimab, administered together), sotrovimab, tocilizumab, and bamlanivimab and etesevimab administered together15,16,17,18,19. There is currently only one FDA-approved prophylactic vaccine, Pfizer-BioNTech, and two other prophylactic vaccines (Moderna and Janssen) have been EUA approved20,21,22,23,24. However, with the uncontrolled infection rate and the emergence of VoC and VoI, SARS-CoV-2 still poses a threat to human health. Therefore, new approaches are urgently needed to identify efficient prophylactics and therapeutics to control SARS-CoV-2 infection and the still ongoing COVID-19 pandemic.
Studying SARS-CoV-2 requires laborious techniques and secondary approaches to identify the presence of the virus in infected cells and/or validated animal models of infection. The use of reverse genetics has allowed for the generation of recombinant viruses to answer important questions in the biology of viral infections. For instance, reverse genetics techniques have provided means to uncover and understand the mechanisms of viral infection, pathogenesis, and disease. Likewise, reverse genetics approaches have paved the way to engineer recombinant viruses lacking viral proteins to understand their contribution in viral pathogenesis. In addition, reverse genetics techniques have been used to generate recombinant viruses expressing reporter genes for in vitro and in vivo applications, including identifying prophylactic and/or therapeutic approaches for the treatment of viral infections. Fluorescent and bioluminescent proteins are the most commonly used reporter genes due to their sensitivity, stability, and easy detection based on the improvement of new technologies25,26. In vitro, fluorescent proteins have been shown to serve as a better option for the localization of viruses in infected cells, while luciferases are more convenient for quantification studies27,28,29. In vivo, luciferases are preferred over fluorescent proteins for whole animal imaging, while fluorescent proteins are preferred for the identification of infected cells or ex vivo imaging30,31,32. The use of reporter-expressing recombinant viruses has served as a powerful tool for the study of viruses in many families, including, among others, flaviviruses, enteroviruses, alphaviruses, lentiviruses, arenaviruses, and influenza viruses28,33,34,35,36.
To overcome the need for secondary approaches to study SARS-CoV-2 and characterize real-time SARS-CoV-2 infection in vivo, we have generated replication-competent recombinant (r)SARS-CoV-2 that expresses bioluminescent (nanoluciferase, Nluc) or fluorescent (Venus) proteins using our previously described bacterial artificial chromosomes(BAC)-based reverse genetics, which are maintained as a single copy in E. coli in order to minimize toxicity of virus sequences during its propagation in bacteria37,38. Notably, rSARS-CoV-2/Nluc and rSARS-CoV-2/Venus showed rSARS-CoV-2/WT-like pathogenicity in vivo. The high level of Venus expression from rSARS-CoV-2/Venus allowed detecting viral infection in the lungs of infected K18 hACE2 transgenic mice using an in vivo imaging system (IVIS)39. The levels of Venus expression correlated well with viral titers detected in the lungs, demonstrating the feasibility of using Venus expression as a valid surrogate of SARS-CoV-2 infection. Using rSARS-CoV-2/Nluc, we were able to track the dynamics of viral infection in real-time and longitudinally assess SARS-CoV-2 infection in vivo using the same IVIS approach in K18 hACE2 transgenic mice.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.5% Triton X-100</td>
			<td>J.T.Baker</td>
			<td>X198-07</td>
			<td>Store at room temperature (RT)</td>
		</tr>
		<tr>
			<td>1% DEAE-Dextran</td>
			<td>MP Biomedicals</td>
			<td>195133</td>
			<td></td>
		</tr>
		<tr>
			<td>10% Formalin solution, neutral buffered</td>
			<td>Sigma-Aldrich</td>
			<td>HT501128</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Oxoid</td>
			<td>LP0028</td>
			<td></td>
		</tr>
		<tr>
			<td>24-well Cell Culture Plate</td>
			<td>Greiner Bio-one</td>
			<td>662160</td>
			<td></td>
		</tr>
		<tr>
			<td>5% Sodium bicarbonate</td>
			<td>Sigma Aldrich</td>
			<td>S-5761</td>
			<td></td>
		</tr>
		<tr>
			<td>6-well Cell Culture Plate</td>
			<td>Greiner Bio-one</td>
			<td>657160</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well Cell Culture Plate</td>
			<td>Greiner Bio-one</td>
			<td>655-180</td>
			<td></td>
		</tr>
		<tr>
			<td>African green monkey kidney epithelial cells (Vero E6)</td>
			<td>ATCC</td>
			<td>CRL-1586</td>
			<td></td>
		</tr>
		<tr>
			<td>Ami HT</td>
			<td>Spectral Instruments Imaging</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Aura Imaging Software 3.2.0</td>
			<td>Spectral Instruments Imaging</td>
			<td></td>
			<td>Image analysis software</td>
		</tr>
		<tr>
			<td>Bovine Serum Albumin (BSA), 35%</td>
			<td>Sigma-Aldrich</td>
			<td>A9647</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Cell culture grade water</td>
			<td>Corning</td>
			<td>25-055-CV</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s modified Eagle&#8217;s medium (DMEM)</td>
			<td>Corning Cellgro</td>
			<td>15-013-CV</td>
			<td>Store at 4 &#176;C</td>
		</tr>
		<tr>
			<td>Anesthesia gas machine</td>
			<td>Veterinary Anesthesia Systems, Inc.</td>
			<td>VAS 2001R</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>Seradigm</td>
			<td>1500-050</td>
			<td>Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Four- to six-week-old female K18-hACE2 transgenic mice</td>
			<td>The Jackson Laboratory</td>
			<td>34860</td>
			<td></td>
		</tr>
		<tr>
			<td>Graphpad Prism Version 9.1.0</td>
			<td>GraphPad</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Isoflurane</td>
			<td>Baxter</td>
			<td>1001936040</td>
			<td>Store at RT</td>
		</tr>
		<tr>
			<td>MARS Data Analysis Software</td>
			<td>BMG LABTECH</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>MB10 tablets</td>
			<td>QUIP Laboratories</td>
			<td>MBTAB1.5</td>
			<td>Store at RT</td>
		</tr>
		<tr>
			<td>Nano-Glo Luciferase Assay Reagent</td>
			<td>Promega</td>
			<td>N1110</td>
			<td>This reagent is used to measure Nluc activity. Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>Nunc MicroWell 96-Well Microplates</td>
			<td>ThermoFisher Scientific</td>
			<td>269620</td>
			<td></td>
		</tr>
		<tr>
			<td>Nunc MicroWell 96-Well Microplates</td>
			<td>ThermoFisher Scientific</td>
			<td>269620</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin/Streptomycin/L-Glutamine (PSG) 100x</td>
			<td>Corning</td>
			<td>30-009-CI</td>
			<td>Store at -20 &#176;C</td>
		</tr>
		<tr>
			<td>PHERAstar FSX</td>
			<td>BMG LABTECH</td>
			<td>PHERAstar FSX</td>
			<td></td>
		</tr>
		<tr>
			<td>Precelleys Evolution homogenizer</td>
			<td>Bertin Instruments</td>
			<td>P000062-PEVO0-A</td>
			<td></td>
		</tr>
		<tr>
			<td>Soft tissue homogenizing CK14 &#8211; 7 mL</td>
			<td>Bertin Instruments</td>
			<td>P000940-LYSK0-A</td>
			<td></td>
		</tr>
		<tr>
			<td>T75 EasYFlask</td>
			<td>ThermoFisher Scientific</td>
			<td>156499</td>
			<td></td>
		</tr>
		<tr>
			<td>VECTASTAIN ABC-HRP Kit, Peroxidase</td>
			<td>Vector Laboratories</td>
			<td>PK-4002</td>
			<td>ABC kit and DAB Peroxidase Substrate kit</td>
		</tr>
	</tbody>
</table>

live imaging and quantification of viral infection in k18 hace2 transgenic mice using reporter-expressing recombinant sars-cov-2

The coronavirus disease 2019 (COVID-19) pandemic has been caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date, SARS-CoV-2 has been responsible for over 242 million infections and more than 4.9 million deaths worldwide. Similar to other viruses, studying SARS-CoV-2 requires the use of experimental methods to detect the presence of virus in infected cells and/or in animal models. To overcome this limitation, we generated replication-competent recombinant (r)SARS-CoV-2 that expresses bioluminescent (nanoluciferase, Nluc) or fluorescent (Venus) proteins. These reporter-expressing rSARS-CoV-2 allow tracking viral infections in vitro and in vivo based on the expression of Nluc and Venus reporter genes. Here the study describes the use of rSARS-CoV-2/Nluc and rSARS-CoV-2/Venus to detect and track SARS-CoV-2 infection in the previously described K18 human angiotensin-converting enzyme 2 (hACE2) transgenic mouse model of infection using in vivo imaging systems (IVIS). This rSARS-CoV-2/Nluc and rSARS-CoV-2/Venus show rSARS-CoV-2/WT-like pathogenicity and viral replication in vivo. Importantly, Nluc and Venus expression allow us to directly track viral infections in vivo and ex vivo, in infected mice. These rSARS-CoV-2/Nluc and rSARS-CoV-2/Venus represent an excellent option to study the biology of SARS-CoV-2 in vivo, to understand viral infection and associated COVID-19 disease, and to identify effective prophylactic and/or therapeutic treatments to combat SARS-CoV-2 infection.

rSARS-CoV-2/Nluc infection in K18 hACE2 transgenic mice (Figures 1 and 2) 
Figure 1A shows a schematic representation of the rSARS-CoV-2/WT (top) and rSARS-CoV-2/Nluc (bottom) used to assess infections in vivo. Figure 1B shows the schematic flow chart applied to assess rSARS-CoV-2/Nluc infection dynamics in K18 hACE2 transgenic mice. Four-to-six-week-old female K18 hACE2 transgenic mic...

Watch this Scientific Journal Video about Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2 at JoVE.com

Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2

This protocol describes the dynamics of viral infections using luciferase- and fluorescence-expressing recombinant (r)SARS-CoV-2 and an in vivo imaging systems (IVIS) in K18 hACE2 transgenic mice to overcome the need of secondary approaches required to study SARS-CoV-2 infections in vivo.

The coronavirus disease 2019 (COVID-19) pandemic has been caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To date, SARS-CoV-2 has ...

live-imaging-quantification-viral-infection-k18-hace2-transgenic-mice

Universidad de Cartagena UDEC

Research

JoVE Journal

Immunology and Infection

2.6K Views.  Texas Biomedical Research Institute. This protocol describes the dynamics of viral infections using luciferase- and fluorescence-expressing recombinant (r)SARS-CoV-2 and an in vivo imaging systems (IVIS) in K18 hACE2 transgenic mice to overcome the need of secondary approaches required to study SARS-CoV-2 infections in vivo.

Video: Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2

In vivo Imaging of Transgenic Leishmania Parasites in a Live Host

Distinct species of Leishmania, a protozoan parasite of the family Trypanosomatidae, typically cause different human disease manifestations. The most common forms of disease are visceral leishmaniasis (VL) and cutaneous leishmaniasis (CL). Mouse models of leishmaniasis are widely used, but quantification of parasite burdens during murine disease requires mice to be euthanized at various times after infection. Parasite loads are then measured either by microscopy, limiting dilution assay, or qPCR amplification of parasite DNA. The in vivo imaging system (IVIS) has an integrated software package that allows the detection of a bioluminescent signal associated with cells in living organisms. Both to minimize animal usage and to follow infection longitudinally in individuals, in vivo models for imaging Leishmania spp. causing VL or CL were established. Parasites were engineered to express luciferase, and these were introduced into mice either intradermally or intravenously. Quantitative measurements of the luciferase driving bioluminescence of the transgenic Leishmania parasites within the mouse were made using IVIS. Individual mice can be imaged multiple times during longitudinal studies, allowing us to assess the inter-animal variation in the initial experimental parasite inocula, and to assess the multiplication of parasites in mouse tissues. Parasites are detected with high sensitivity in cutaneous locations. Although it is very likely that the signal (photons/second/parasite) is lower in deeper visceral organs than the skin, but quantitative comparisons of signals in superficial versus deep sites have not been done. It is possible that parasite numbers between body sites cannot be directly compared, although parasite loads in the same tissues can be compared between mice. Examples of one visceralizing species (L. infantum chagasi) and one species causing cutaneous leishmaniasis (L. mexicana) are shown. The IVIS procedure can be used for monitoring and analyzing small animal models of a wide variety of Leishmania species causing the different forms of human leishmaniasis.

In vivo Imaging of Transgenic Leishmania Parasites in a Live Host

An in vivo imaging system is used to generate quantitative measurements of murine infection with the Trypanosomatid protozoan Leishmania. This is a non-invasive and non-lethal method for detecting parasites expressing luciferase within many tissues throughout the course of chronic Leishmania spp. infection.

Distinct species of Leishmania, a protozoan parasite of the family Trypanosomatidae, typically cause different human disease manifestations. The most ...

Production and Titering of Recombinant Adeno-associated Viral Vectors

In recent years recombinant adeno-associated viral vectors (AAV) have become increasingly valuable for in vivo studies in animals, and are also currently being tested in human clinical trials. Wild-type AAV is a non-pathogenic member of the parvoviridae family and inherently replication-deficient. The broad transduction profile, low immune response as well as the strong and persistent transgene expression achieved with these vectors has made them a popular and versatile tool for in vitro and in vivo gene delivery. rAAVs can be easily and cheaply produced in the laboratory and, based on their favourable safety profile, are generally given a low safety classification. Here, we describe a method for the production and titering of chimeric rAAVs containing the capsid proteins of both AAV1 and AAV2. The use of these so-called chimeric vectors combines the benefits of both parental serotypes such as high titres stocks (AAV1) and purification by affinity chromatography (AAV2). These AAV serotypes are the best studied of all AAV serotypes, and individually have a broad infectivity pattern. The chimeric vectors described here should have the infectious properties of AAV1 and AAV2 and can thus be expected to infect a large range of tissues, including neurons, skeletal muscle, pancreas, kidney among others. The method described here uses heparin column purification, a method believed to give a higher viral titer and cleaner viral preparation than other purification methods, such as centrifugation through a caesium chloride gradient. Additionally, we describe how these vectors can be quickly and easily titered to give accurate reading of the number of infectious particles produced.

Recombinant adeno-associated virus (rAAVs) vectors are becoming increasingly valuable for in vivo studies in animals. We describe how rAAVs can be produced in the laboratory and how these vectors can be titered to give an accurate reading of the number of infectious particles produced.

In recent years recombinant adeno-associated viral vectors (AAV) have become increasingly valuable for in vivo studies in animals, and are also currently ...

4D Multimodality Imaging of Citrobacter rodentium Infections in Mice

This protocol outlines the steps required to longitudinally monitor a bioluminescent bacterial infection using composite 3D diffuse light imaging tomography with integrated &mu;CT (DLIT-&mu;CT) and the subsequent use of this data to generate a four dimensional (4D) movie of the infection cycle. To develop the 4D infection movies and to validate the DLIT-&mu;CT imaging for bacterial infection studies using an IVIS Spectrum CT, we used infection with bioluminescent C. rodentium, which causes self-limiting colitis in mice. In this protocol, we outline the infection of mice with bioluminescent C. rodentium and non-invasive monitoring of colonization by daily DLIT-&mu;CT imaging and bacterial enumeration from feces for 8 days.
The use of the IVIS Spectrum CT facilitates seamless co-registration of optical and &mu;CT scans using a single imaging platform. The low dose &mu;CT modality enables the imaging of mice at multiple time points during infection, providing detailed anatomical localization of bioluminescent bacterial foci in 3D without causing artifacts from the cumulative radiation. Importantly, the 4D movies of infected mice provide a powerful analytical tool to monitor bacterial colonization dynamics in vivo.

4D Multimodality Imaging of Citrobacter rodentium Infections in Mice

Multi-modality imaging is a valuable approach for studying bacterial colonization in small animal models. This protocol outlines infection of mice with bioluminescent Citrobacter rodentium and the longitudinal monitoring of bacterial colonization using composite 3D diffuse light imaging tomography with &mu;CT imaging to create a 4D movie of C. rodentium infection.

This protocol outlines the steps required to  longitudinally monitor a bioluminescent bacterial infection using composite 3D diffuse light imaging ...

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Enveloped viruses utilize membrane glycoproteins on their surface to mediate entry into host cells. Three-dimensional structural analysis of these glycoprotein &#8216;spikes&#8217; is often technically challenging but important for understanding viral pathogenesis and in drug design. Here, a protocol is presented for viral spike structure determination through computational averaging of electron cryo-tomography data. Electron cryo-tomography is a technique in electron microscopy used to derive three-dimensional tomographic volume reconstructions, or tomograms, of pleomorphic biological specimens such as membrane viruses in a near-native, frozen-hydrated state. These tomograms reveal structures of interest in three dimensions, albeit at low resolution. Computational averaging of sub-volumes, or sub-tomograms, is necessary to obtain higher resolution detail of repeating structural motifs, such as viral glycoprotein spikes. A detailed computational approach for aligning and averaging sub-tomograms using the Jsubtomo software package is outlined. This approach enables visualization of the structure of viral glycoprotein spikes to a resolution in the range of 20-40 &#197; and study of the study of higher order spike-to-spike interactions on the virion membrane. Typical results are presented for Bunyamwera virus, an enveloped virus from the family Bunyaviridae. This family is a structurally diverse group of pathogens posing a threat to human and animal health.

An approach is presented for determining structures of viral membrane glycoprotein complexes using a combination of electron cryo-tomography and sub-tomogram averaging with the computational package Jsubtomo.

Enveloped viruses utilize membrane glycoproteins on their surface to mediate entry into host cells. Three-dimensional structural analysis of these ...

Quantification of Atherosclerosis in Mice

Cardiovascular disease is the main cause of death in the world. The underlying cause in most cases is atherosclerosis, which is in part a chronic inflammatory disease. Experimental atherosclerosis studies have elucidated the role of cholesterol and inflammation in the disease process. This has led to successful clinical trials with pharmaceutical agents that reduce clinical manifestations of atherosclerosis. Careful and well-controlled experiments in mouse models of the disease could further elucidate the pathogenesis of the disease, which is not fully understood. Standardized lesion analysis is important to reduce experimental variability and increase reproducibility. Determining lesion size in aortic root, aortic arch, and brachiocephalic artery are common endpoints in experimental atherosclerosis. This protocol provides a technical description for evaluation of atherosclerosis at all these sites in a single mouse. The protocol is particularly useful when material is limited, as is frequently the case when genetically modified animals are being characterized.

Murine models of atherosclerosis are useful tools to investigate pathogenic pathways on a molecular level, but require standardized quantification of lesion development. This protocol describes an optimized method to determine lesion size in the major arterial vessels including the aortic root, aortic arch, and brachiocephalic artery.

Cardiovascular disease is the main cause of death in the world. The underlying cause in most cases is atherosclerosis, which is in part a chronic ...

A Luciferase-fluorescent Reporter Influenza Virus for Live Imaging and Quantification of Viral Infection

Influenza A viruses (IAVs) cause human respiratory disease that is associated with significant health and economic consequences. As with other viruses, studying IAV requires the use of laborious secondary approaches to detect the presence of the virus in infected cells and/or in animal models of infection. This limitation has been recently circumvented with the generation of recombinant IAVs expressing easily traceable fluorescent or bioluminescent (luciferase) reporter proteins. However, researchers have been forced to select fluorescent or luciferase reporter genes due to the restricted capacity of the IAV genome for including foreign sequences. To overcome this limitation, we have generated a recombinant replication-competent bi-reporter IAV (BIRFLU) stably expressing both a fluorescent and a luciferase reporter gene to easily track IAV infections in vitro and in vivo. To this end, the viral non-structural (NS) and hemagglutinin (HA) viral segments of influenza A/Puerto Rico/8/34 H1N1 (PR8) were modified to encode the fluorescent Venus and the bioluminescent Nanoluc luciferase proteins, respectively. Here, we describe the use of BIRFLU in a mouse model of IAV infection and the detection of both reporter genes using an in vivo imaging system. Notably, we have observed a good correlation between the expressions of both reporters and viral replication. The combination of cutting-edge techniques in molecular biology, animal research and imaging technologies, provides researchers the unique opportunity to use this tool for influenza research, including the study of virus-host interactions and dynamics of viral infections. Importantly, the feasibility to genetically alter the viral genome to express two foreign genes from different viral segments opens up opportunities to use this approach for: (i) the development of novel IAV vaccines, (ii) the generation of recombinant IAVs that can be used as vaccine vectors for the treatment of other human pathogen infections.

Influenza A viruses (IAVs) are contagious respiratory pathogens that cause annual epidemics and occasional pandemics. Here, we describe a protocol to track viral infections in vivo using a novel recombinant luciferase and fluorescence-expressing bi-reporter IAV (BIRFLU). This approach provides researchers with an excellent tool to study IAV in vivo.

Influenza A viruses (IAVs) cause human respiratory disease that is associated with significant health and economic consequences. As with other viruses, ...

Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice

Recurrent urinary tract infections (rUTI) caused by uropathogenic Escherichia coli (UPEC) are common and costly. Previous articles describing models of UTI in male and female mice have illustrated the procedures for bacterial inoculation and enumeration in urine and tissues. During an initial bladder infection in C57BL/6 mice, UPEC establish latent reservoirs inside bladder epithelial cells that persist following clearance of UPEC bacteriuria. This model builds on these studies to examine rUTI caused by the emergence of UPEC from within latent bladder reservoirs. The urogenital bacterium Gardnerella vaginalis is used as the trigger of rUTI in this model because it is frequently present in the urogenital tracts of women, especially in the context of vaginal dysbiosis that has been associated with UTI. In addition, a method for in situ bladder fixation followed by scanning electron microscopy (SEM) analysis of bladder tissue is also described, with potential application to other studies involving the bladder.

Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice

A mouse model of uropathogenic E. coli (UPEC) transurethral inoculation to establish latent intracellular bladder reservoirs and subsequent bladder exposure to G. vaginalis to induce recurrent UPEC UTI is demonstrated. Also demonstrated are the enumeration of bacteria, urine cytology, and in situ bladder fixation and processing for scanning electron microscopy.

Recurrent urinary tract infections (rUTI) caused by uropathogenic Escherichia coli (UPEC) are common and costly. Previous articles describing models of ...

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

This manuscript provides a protocol for in situ hybridization chain reaction (HCR) coupled with immunofluorescence to visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in cell line&#160;and three-dimensional (3D) cultures of human airway epithelium. The method allows highly specific and sensitive visualization of viral RNA by relying on HCR initiated by probe localization. Split-initiator probes help amplify the signal by fluorescently labeled amplifiers, resulting in negligible background fluorescence in confocal microscopy. Labeling amplifiers with different fluorescent dyes facilitates the simultaneous recognition of various targets. This, in turn, allows the mapping of the infection in tissues to better understand viral pathogenesis and replication at the single-cell level. Coupling this method with immunofluorescence may facilitate better understanding of host-virus interactions, including alternation of the host epigenome and immune response pathways. Owing to sensitive and specific HCR technology, this protocol can also be used as a diagnostic tool. It is also important to remember that the technique may be modified easily to enable detection of any RNA, including non-coding RNAs and RNA viruses that may emerge in the future.

Here, we describe a simple method that combines RNA fluorescence in situ&#160;hybridization (RNA-FISH) with immunofluorescence to visualize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA. This protocol may increase understanding of the molecular characteristics of SARS-CoV-2 RNA-host interactions at a single-cell level.

This manuscript provides a protocol for in situ hybridization chain reaction (HCR) coupled with immunofluorescence to visualize severe acute respiratory ...

Detection of SARS-CoV-2 Neutralizing Antibodies using High-Throughput Fluorescent Imaging of Pseudovirus Infection

As the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, it has become evident that the presence of neutralizing antibodies against the virus may provide protection against future infection. Thus, as the creation and translation of effective COVID-19 vaccines continues at an unprecedented speed, the development of fast and effective methods to measure neutralizing antibodies against SARS-CoV-2 will become increasingly important to determine long-term protection against infection for both previously infected and immunized individuals. This paper describes a high-throughput protocol using vesicular stomatitis virus (VSV) pseudotyped with the SARS-CoV-2 spike protein to measure the presence of neutralizing antibodies in convalescent serum from patients who have recently recovered from COVID-19. The use of a replicating pseudotyped virus eliminates the necessity for a containment level 3 facility required for SARS-CoV-2 handling, making this protocol accessible to virtually any containment level 2 lab. The use of a 96-well format allows for many samples to be run at the same time with a short turnaround time of 24 h.

The protocol described here outlines a fast and effective method for measuring neutralizing antibodies against the SARS-CoV-2 spike protein by evaluating the ability of convalescent serum samples to inhibit infection by an enhanced green fluorescent protein-labeled vesicular stomatitis virus pseudotyped with spike glycoprotein.

As the COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to evolve, it has become evident that the ...

A Rapid, Multiplex Dual Reporter IgG and IgM SARS-CoV-2 Neutralization Assay for a Multiplexed Bead-Based Flow Analysis System

The COVID-19 pandemic has underscored the need for rapid high-throughput methods for sensitive and specific serological detection of infection with novel pathogens, such as SARS-CoV-2. Multiplex serological testing can be particularly useful because it can simultaneously analyze antibodies to multiple antigens that optimizes pathogen coverage, and controls for variability in the organism and the individual host response. Here we describe a SARS-CoV-2 IgG 3-plex fluorescent microsphere-based assay that can detect both IgM and IgG antibodies to three major SARS-CoV-2 antigens-the spike (S) protein, spike angiotensin-converting enzyme-2 (ACE2) receptor-binding domain (RBD), and nucleocapsid (Nc). The assay was shown to have comparable performance to a SARS-CoV-2 reference assay for IgG in serum obtained at &#8805;21 days from symptom onset but had higher sensitivity with samples collected at &#8804;5 days from symptom onset. Further, using soluble ACE2 in a neutralization assay format, inhibition of antibody binding was demonstrated for S and RBD.

A flow analysis system for bead-based multiplexed assays which provides a two-reporter readout was used for the development of multiplex serological and antibody neutralization assays that can simultaneously measure neutralizing IgG and IgM antibodies for SARS-CoV-2.

The COVID-19 pandemic has underscored the need for rapid high-throughput methods for sensitive and specific serological detection of infection with novel ...

Live Imaging and Quantification of Viral Infection in K18 hACE2 Transgenic Mice Using Reporter-Expressing Recombinant SARS-CoV-2

Summary

Explore More Videos

Chapters in this video

In vivo Imaging of Transgenic Leishmania Parasites in a Live Host

Production and Titering of Recombinant Adeno-associated Viral Vectors

4D Multimodality Imaging of Citrobacter rodentium Infections in Mice

Averaging of Viral Envelope Glycoprotein Spikes from Electron Cryotomography Reconstructions using Jsubtomo

Quantification of Atherosclerosis in Mice

A Luciferase-fluorescent Reporter Influenza Virus for Live Imaging and Quantification of Viral Infection

Recurrent Escherichia coli Urinary Tract Infection Triggered by Gardnerella vaginalis Bladder Exposure in Mice

Visualization of SARS-CoV-2 using Immuno RNA-Fluorescence In Situ Hybridization

Detection of SARS-CoV-2 Neutralizing Antibodies using High-Throughput Fluorescent Imaging of Pseudovirus Infection

A Rapid, Multiplex Dual Reporter IgG and IgM SARS-CoV-2 Neutralization Assay for a Multiplexed Bead-Based Flow Analysis System