We thank the Clinical Microbiology Service staff of the Memorial Sloan-Kettering Cancer Center for help in collecting clinical specimens. This study was supported in part by a research agreement between MSKCC and Alere Scarborough (SK2013-0262).

ETHICS STATEMENT: The use of left-over clinical specimens is approved and follows the guidelines of the Memorial Sloan Kettering Cancer Center Institutional Review Board.
1. Before Running the Assay
NOTE: The Influenza A and B assay is approved for nasopharyngeal swab specimens and for nasopharyngeal swabs stored in viral transport media. Swabs are included in the kit and should be used for optimal performance. However, rayon, foam, flocked swabs or polyester nasal swabs can also be used to collect nasal swab samples.
<ol>
	<li>To collect a nasal swab sample, insert the swab into the nostril that has the most visible drainage or that is most congested. With gentle rotation, push the swab into the nostril until resistance is met and rotate several times against the nasal wall before slowly removing from the nostril. Store the swabs and transport them in vials containing 3 ml of viral transport media (VTM). 
	NOTE: Careful attention to appropriate specimen collection must be taken as inadequate specimen collection may yield erroneous results. 
	NOTE: Swab specimens should be tested as soon as possible after collection. However, they may be stored at room temperature for up to 2 hr or refrigerated at 2-8 &#176;C for up to 24 hr if testing is not immediately available. Freshly collected specimens are ideal for optimal test performance. Improper sample handling, storage, and/or transport may yield erroneous results. 
	NOTE: As a precautionary measure, individuals performing this test should treat all specimens as potentially infectious by following universal precautions when handling specimens.</li>
	<li>Bring all samples to room temperature prior to testing. 
	NOTE: All test components are for a single use only and should not be used to perform multiple tests. Do not mix kit components from different lot numbers. Do not use kit reagents past their expiration date.</li>
	<li>Bring the blue sample receiver to room temperature prior to testing. The orange test base can be tested without the need to warm to room temperature.</li>
	<li>Leave all test pieces in the foil wrapping until immediately before use. Turn on the instrument by pressing the power button on the side of the instrument. Enter the user-ID and press &#39;OK.&#39;</li>
</ol>
2. Running the Test
<ol>
	<li>To begin the test process, touch &#39;Run Test&#39; on the instrument screen. Enter the patient ID by using on-screen keyboard or barcode scanner and press &#39;OK.&#39; Open the lid and insert the Orange test base into the Orange test base holder.</li>
	<li>Confirm that the correct test is displayed on the screen and press &#39;OK.&#39; Insert the blue sample receiver into the blue sample receiver holder. 
	NOTE: Do not open the sample receiver before placing in the instrument as this will prevent the elution buffer from reaching the correct operating temperature and may impact test performance.</li>
	<li>Wait for the sample receiver to warm up. When prompted by the instrument, remove the foil seal and place the patient swab to be tested into the sample receiver. 
	NOTE: When removing the foil, place two fingers on the edge of the Sample Receiver to ensure that it stays in place.</li>
	<li>Vigorously mix the swab in the liquid for 10 sec, pressing the swab head against the side the sample receiver as you mix it to help dislodge the specimen from the swab. Press &#39;OK&#39; to proceed. If testing swabs stored in viral transport medium, vortex the VTM for 10 sec then add 200 &#181;l to the sample receiver.</li>
	<li>Press the white transfer cartridge into the blue sample receiver. Continue pressing on the sample receiver until the orange indicator rises.</li>
	<li>Lift and then connect the transfer cartridge to the test base. Observe the orange indicator descend once the cartridge transfer is attached correctly. Close the Lid and do not open until the &#34;Test Complete&#34; message appears on the screen.</li>
</ol>
3. Quality Control
<ol>
	<li>Touch &#39;Run QC Test&#39; on the home screen. Select the QC Test to be Run. Confirm the test type to match the QC sample intended for testing by touching &#39;OK&#39; and following the on screen prompts to complete testing.</li>
</ol>
4. Result Interpretation
<ol>
	<li>After the test run is complete, observe the results of the test displayed on the screen with interpretations for the presence of Influenza A, B, unknown subtypes. For invalid results repeat the test.</li>
</ol>
5. Maintenance and Cleaning
<ol>
	<li>Clean the instrument and the surrounding bench area daily with 70% ethanol or 10% bleach solution. Spray the cleaning solution on a damp, lint-free cloth to clean. Do not pour the solutions directly on the instrument.</li>
</ol>

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<li>Agrawal, A. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comparative+evaluation+of+real-time+PCR+and+conventional+RT-PCR+during+a+2+year+surveillance+for+influenza+and+respiratory+syncytial+virus+among+children+with+acute+respiratory+infections+in+Kolkata%2C+India%2C+reveals+a+distinct+seasonality+of+infection%5BTitle%5D)+AND+%22Journal+of+Medical+Microbiology%22%5BJournal%5D)">Comparative evaluation of real-time PCR and conventional RT-PCR during a 2 year surveillance for influenza and respiratory syncytial virus among children with acute respiratory infections in Kolkata, India, reveals a distinct seasonality of infection.</a> Journal of Medical Microbiology. 58 (12), 1616-1622 (2009).</li>
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<li>Dale, S. E., Mayer, C., Mayer, M. C., Menegus, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Analytical+and+clinical+sensitivity+of+the+3M+rapid+detection+influenza+A%2BB+assay%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Analytical and clinical sensitivity of the 3M rapid detection influenza A+B assay.</a> J Clin Microbiol. 46 (11), 3804-3807 (2008).</li>
<li>van Doorn, H. R., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Clinical+validation+of+a+point-of-care+multiplexed+in+vitro+immunoassay+using+monoclonal+antibodies+%28the+MSD+influenza+test%29+in+four+hospitals+in+Vietnam%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Clinical validation of a point-of-care multiplexed in vitro immunoassay using monoclonal antibodies (the MSD influenza test) in four hospitals in Vietnam.</a> J Clin Microbiol. 50 (5), 1621-1625 (2012).</li>
<li>Hurt, A. C., Alexander, R., Hibbert, J., Deed, N., Barr, I. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Performance+of+six+influenza+rapid+tests+in+detecting+human+influenza+in+clinical+specimens%5BTitle%5D)+AND+%22Journal+of+Clinical+Virology%22%5BJournal%5D)">Performance of six influenza rapid tests in detecting human influenza in clinical specimens.</a> Journal of Clinical Virology. 39 (2), 132-135 (2007).</li>
<li>Fiore, A. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Antiviral+agents+for+the+treatment+and+chemoprophylaxis+of+influenza+---+recommendations+of+the+Advisory+Committee+on+Immunization+Practices+%28ACIP%29%5BTitle%5D)+AND+%22MMWR+Recomm+Rep%22%5BJournal%5D)">Antiviral agents for the treatment and chemoprophylaxis of influenza --- recommendations of the Advisory Committee on Immunization Practices (ACIP).</a> MMWR Recomm Rep. 60 (1), 1-24 (2011).</li>
<li>Harper, S. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Seasonal+influenza+in+adults+and+children--diagnosis%2C+treatment%2C+chemoprophylaxis%2C+and+institutional+outbreak+management%3A+clinical+practice+guidelines+of+the+Infectious+Diseases+Society+of+America%5BTitle%5D)+AND+%22Clin+Infect+Dis%22%5BJournal%5D)">Seasonal influenza in adults and children--diagnosis, treatment, chemoprophylaxis, and institutional outbreak management: clinical practice guidelines of the Infectious Diseases Society of America.</a> Clin Infect Dis. 48 (8), 1003-1032 (2009).</li>
<li>Hannoun, C., Tumova, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Survey+on+influenza+laboratory+diagnostic+and+surveillance+methods+in+Europe%5BTitle%5D)+AND+%22European+Journal+of+Epidemiology%22%5BJournal%5D)">Survey on influenza laboratory diagnostic and surveillance methods in Europe.</a> European Journal of Epidemiology. 16 (3), 217-222 (2000).</li>
<li>Leonardi, G. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Rapid+identification+of+2009+H1N1+influenza+A+virus+using+fluorescent+antibody+methods%5BTitle%5D)+AND+%22Am+J+Clin+Pathol%22%5BJournal%5D)">Rapid identification of 2009 H1N1 influenza A virus using fluorescent antibody methods.</a> Am J Clin Pathol. 134 (6), 910-914 (2010).</li>
<li>Chartrand, C., Leeflang, M. M. G., Minion, J., Brewer, T., Pai, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Accuracy+of+Rapid+Influenza+Diagnostic+TestsA+Meta-analysis%5BTitle%5D)+AND+%22Annals+of+Internal+Medicine%22%5BJournal%5D)">Accuracy of Rapid Influenza Diagnostic TestsA Meta-analysis.</a> Annals of Internal Medicine. 156 (7), 500-511 (2012).</li>
<li>Lee, G. C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Evaluation+of+a+rapid+diagnostic+test%2C+NanoSign%28R%29+Influenza+A%2FB+Antigen%2C+for+detection+of+the+2009+pandemic+influenza+A%2FH1N1+viruses%5BTitle%5D)+AND+%22Virol+J%22%5BJournal%5D)">Evaluation of a rapid diagnostic test, NanoSign(R) Influenza A/B Antigen, for detection of the 2009 pandemic influenza A/H1N1 viruses.</a> Virol J. 7, 244(2010).</li>
<li>Tang, Y. W., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Clinical+accuracy+of+a+PLEX-ID+flu+device+for+simultaneous+detection+and+identification+of+influenza+viruses+A+and+B%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Clinical accuracy of a PLEX-ID flu device for simultaneous detection and identification of influenza viruses A and B.</a> J Clin Microbiol. 51 (1), 40-45 (2013).</li>
<li>Bandt, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Economic+high-throughput-identification+of+influenza+A+subtypes+from+clinical+specimens+with+a+DNA-oligonucleotide+microarray+in+an+outbreak+situation%5BTitle%5D)+AND+%22Molecular+and+Cellular+Probes%22%5BJournal%5D)">Economic high-throughput-identification of influenza A subtypes from clinical specimens with a DNA-oligonucleotide microarray in an outbreak situation.</a> Molecular and Cellular Probes. 26 (1), 6-10 (2012).</li>
<li>Pierce, V. M., Elkan, M., Leet, M., McGowan, K. L., Hodinka, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comparison+of+the+Idaho+Technology+FilmArray+system+to+real-time+PCR+for+detection+of+respiratory+pathogens+in+children%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Comparison of the Idaho Technology FilmArray system to real-time PCR for detection of respiratory pathogens in children.</a> J Clin Microbiol. 50 (2), 364-371 (2012).</li>
<li>Teo, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((VereFlu%E2%84%A2%3A+an+integrated+multiplex+RT-PCR+and+microarray+assay+for+rapid+detection+and+identification+of+human+influenza+A+and+B+viruses+using+lab-on-chip+technology%5BTitle%5D)+AND+%22Archives+of+Virology%22%5BJournal%5D)">VereFlu™: an integrated multiplex RT-PCR and microarray assay for rapid detection and identification of human influenza A and B viruses using lab-on-chip technology.</a> Archives of Virology. 156 (8), 1371-1378 (2011).</li>
<li>Babady, N. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Comparison+of+the+Luminex+xTAG+RVP+Fast+assay+and+the+Idaho+Technology+FilmArray+RP+assay+for+detection+of+respiratory+viruses+in+pediatric+patients+at+a+cancer+hospital%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Comparison of the Luminex xTAG RVP Fast assay and the Idaho Technology FilmArray RP assay for detection of respiratory viruses in pediatric patients at a cancer hospital.</a> J Clin Microbiol. 50 (7), 2282-2288 (2012).</li>
<li>Chidlow, G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Duplex+real-time+reverse+transcriptase+PCR+assays+for+rapid+detection+and+identification+of+pandemic+%28H1N1%29+2009+and+seasonal+influenza+A%2FH1%2C+A%2FH3%2C+and+B+viruses%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Duplex real-time reverse transcriptase PCR assays for rapid detection and identification of pandemic (H1N1) 2009 and seasonal influenza A/H1, A/H3, and B viruses.</a> J Clin Microbiol. 48 (3), 862-866 (2010).</li>
<li>Bell, J. J., Selvarangan, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Evaluation+of+the+Alere+I+influenza+A%26B+nucleic+acid+amplification+test+by+use+of+respiratory+specimens+collected+in+viral+transport+medium%5BTitle%5D)+AND+%22J+Clin+Microbiol%22%5BJournal%5D)">Evaluation of the Alere I influenza A&B nucleic acid amplification test by use of respiratory specimens collected in viral transport medium.</a> J Clin Microbiol. 52 (11), 3992-3995 (2014).</li>
<li>Nie, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/pubmed?term=((Evaluation+of+Alere+i+Influenza+A%26B+for+Rapid+Detection+of+Influenza+Viruses+A+and+B%5BTitle%5D)+AND+%22Journal+of+Clinical+Microbiology%22%5BJournal%5D)">Evaluation of Alere i Influenza A&B for Rapid Detection of Influenza Viruses A and B.</a> Journal of Clinical Microbiology. 52 (9), 3339-3344 (2014).</li>
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</ol>

The authors have nothing to disclose.

Influenza viruses are significant world-wide causes of morbidity and mortality. Rapid and accurate diagnosis of influenza is one of the major keys to managing flu outbreaks during respiratory season. Other antigen-based tests are rapid and easy to perform; however, they have low sensitivities13. On the other hand, traditional molecular tests have improved sensitivity, but require more experienced laboratory technologists to perform and are more costly. The Influenza A and B assay described in this study and protocol is a CLIA-waived, rapid molecular test for Influenza A and B. The technology is based on an isothermal-amplification for the detection and differentiation of influenza viruses A and B. We show representative results to demonstrate the performance of the influenza A and B assay on a panel of archived, frozen NPS VTM samples was evaluated as compared to another molecular-based respiratory panel assay.
The samples that were determined to be &#34;equivocal&#34; or &#34;untypeable&#34; by the RP test had the lowest sensitivity by the Influenza A and B assay. In addition, discordant results were observed more frequently for specimens with higher CT values in RP assays, suggesting that the lower detection rate by the assay was associated with the lower viral titers. The assay had an improved performance for the detection on influenza virus B over influenza virus A detection with a 90.2% sensitivity and 98.1% specificity. The results here are consistent with previously published literature26,27,28.
This study has two important limitations. First, samples were stored in VTM for testing on the platform. However, at the time the samples were tested, the platform did not have FDA approval for this sample type. Therefore, the dilution into VTM, may have reduced the detection of low-titer VTM samples. Second, the specimens that were tested with the Influenza A and B assay had been stored at -70 &#176;C for 6 to 9 months prior to testing whereas the RP testing was done on fresh specimens immediately after they were received. It is possible that freezing the specimens further reduced influenza detection in the samples.
The influenza A &#38; B assay has few steps and is simple to perform. However, there are two key steps that must be completed appropriately and that users can troubleshoot if they experience errors. First, when initially setting up the assay, the transfer cartridge must be connected to the test base until they click into place. If these two pieces are not secured appropriately, the run will fail and will need to be repeated from the beginning. Second, the instrument needs to warm up for 2 min prior to adding the sample. After this warm up time, users have 30 sec to add the sample, connect the transfer cartridge to the test base, and close the lid. If the time passes before this step is complete, the instrument will fail the run and the sample set up will have to be repeated from the beginning.
The limitations of the assay include slightly increased hands-on time and lower sensitivity compared to the respiratory panel and does not subtype influenza A. Further, the only specimen types that can be used with the assay are nasopharyngeal swabs or the NPS that are stored in viral transport media; the performance of the assay for any other specimen type, such as lower respiratory specimens, has not been evaluated. It is important to note that all of the steps in this protocol are critical. Any modifications or deviation from the protocol as written may result in lower performance or of the assay and must be assessed by the user. The benefit of the technology is that the instrument has a small footprint, only takes 15 min to perform and, even though the technology is based on molecular methods, does not require special training or qualifications to perform. The Influenza A and B assay evaluated in this study has the potential to serve as an alternative to RIDTs for the diagnosis of influenza. The system has the advantage of a short total test time, has a small footprint and is easy to use. Overall, the design of the instrument is suitable for point-of-care testing.

Influenza virus infections result in a significant amount of morbidity and mortality each year1,2,3. Uncomplicated influenza is characterized by constitutional and respiratory symptoms such as fever, myalgia, headache, and non-productive cough4,5. Older individuals, young children, immunocompromised patients, and patients with underlying comorbidities are at a higher risk for serious complications such as pneumonia, myocarditis, central nervous system disease, or death6,7.
Influenza infection is unique from other respiratory viruses in that prompt administration of antiviral therapy within 48 h of symptom onset can reduce the disease severity and length8. Rapid identification of influenza has also been shown to reduce the use of unnecessary antibiotics9,10. Further, hospitalized patients with influenza infections must be placed in isolated rooms with appropriate infection control precautions. However, respiratory illnesses caused by non-influenza viruses can be difficult to clinically distinguish from influenza. For this reason, rapid and accurate diagnostic testing for influenza is very important for clinical patient management.
Several assays are available for the detection and identification of influenza viruses. Rapid influenza antigen detection tests (RIDTs) are widely used in clinical practice as point-of-care tests because they are simple to use and provide results within 15 to 30 min11,12; however, their sensitivities vary widely (10-80%) depending on the manufacturer and the population being tested, and the influenza type and subtype13,14,15. Direct fluorescence assays (DFAs) provide superior sensitivities over RIDTs, but the processing time is greater (~3 hr) and must be completed by skilled technologists16,17. Viral culture has been the gold standard for influenza diagnostics and has improved sensitivity over both RIDTs and DFAs18. However, influenza viral culture can take anywhere from 2-14 d to complete, diminishing its utility in aiding patient management19. Lastly, nucleic acid amplification tests (NAAT) have replaced culture techniques as the new gold standard in influenza diagnostics. NAAT are considered to have the greatest sensitivity for detecting influenza in a few hours. However, NAAT are the most expensive assays and require specialized equipment and technologists to perform5,20,21,22,23,24,25.
The influenza A and B assay described here is the first CLIA-waived molecular rapid flu test that is readily available. This assay works by employing a Nicking Endonuclease Amplification Reaction (NEAR) that uses isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes. This assay differentiates influenza A from B, requires 2 min to set up and process one sample, and requires a total of 15 min to complete.
Here, we present the protocol for the Influenza A &#38; B assay. In addition, we provide a sample data set comparing the performance of the Influenza A and B assay on archived nasopharyngeal swab (NPS) specimens stored in viral transport medium (VTM) to another respiratory pathogen panel assay.

<table><tbody><tr><td>Alere i Instrument</td><td>Alere</td><td>NAT-000 (Global), NAT-024 (US)</td><td></td></tr><tr><td>Alere i Influenza A &amp;amp; B 24 Test Kit</td><td>Alere</td><td>425-000 (Global), 425-024 (US)</td><td></td></tr><tr><td>Alere i Barcode Scanner</td><td>Alere</td><td>EQ001001</td><td></td></tr><tr><td>Alere Universal Printer</td><td>Alere</td><td>55115 (Global), alereiprinter&amp;nbsp;(US)</td><td></td></tr><tr><td>200 &amp;micro;l precision pipette</td><td></td><td></td><td></td></tr><tr><td>200 &amp;micro;l disposable pipette tips</td><td></td><td></td><td></td></tr><tr><td>Viral transport medium</td><td>Remel</td><td>M4-RT</td><td></td></tr></tbody></table>

rapid molecular detection and differentiation of influenza viruses a and b

Influenza is a contagious respiratory illness caused by influenza viruses A and B in humans and causes a significant amount of morbidity and mortality every year. The Influenza A and B assay was the first CLIA-waived molecular rapid flu test available. The Influenza A and B test works by employing isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes. Here, the performance of the Influenza A and B assay on frozen, archived nasopharyngeal swab (NPS) specimens stored in viral transport medium (VTM) were compared to a respiratory panel assay.
The performance of the Influenza A and B assay was evaluated by comparing the results to the respiratory panel reference method. The sensitivity for total influenza virus A was 67.5% (95% CI (CI), 56.6-78.5) and the specificity was 86.9% (CI, 71.0-100). For influenza virus B testing, the sensitivity and specificity were 90.2% (CI, 68.5-100) and 98.8% (CI, 68.5-100), respectively.
This system has the advantage of a significantly shorter test time than any other currently available molecular assay and the simple, pipette-free procedure runs on a fully integrated, closed, small-footprint system. Overall, the Influenza A and B assay evaluated in this study has the potential to serve as a point-of-care rapid influenza diagnostic test.

In this study, archived NPS specimens were collected from inpatients presenting with influenza-like symptoms at Memorial Sloan-Kettering Cancer Center (MSKCC) during an influenza outbreak between December 15, 2012 and March 1, 2013. The NPS specimens were submitted in 3 ml of VTM and tested as part of routine clinical practice with a molecular assay that detects a panel of respiratory viruses (RP), including Influenza A, A-1, A-3, and B. During the study period, 3,675 NPS specimens were submitted to the MSKCC clinical laboratory for testing. Of those specimens, 45, 425, 37, and 77 tested positive for influenza viruses A-1, A-3, A-un-subtypable (A-u), and B, respectively with the RP. A total of 360 positive specimens, 40 samples from each of the influenza subtypes, and 37 A-u. In addition, 1-2 negative samples that arrived to the laboratory immediately before or after each of the positive specimens were chosen for subsequent testing with the influenza A and B assay.
In total, the Influenza A and B assay detected 79 influenza virus A, 37 influenza virus B, 240 negative, and 4 invalid results (failure of internal controls) (Table 1). There were 46 discrepant results with 44 samples positive on RP only and two positive on the Influenza A and B assay only. A third molecular-based influenza assay was performed on the 44 discordant specimens which detected 33/43 (8 influenza virus A, 21 A-u, and 2 influenza virus B) that were positive by the RP and 0/1 positive (influenza virus A) by the Influenza A and B assay. An agreement between two or more assays was considered an accurate identification.
The overall Influenza A and B assay sensitivity for total influenza virus A was 67.5% (95% CI (CI), 56.6-78.5). The sensitivity for the influenza A subtypes was A-1, 84.6% (CI, 58.5-100), A-3, 90.2% (CI, 62.8-100), and A-u, 21.9% (CI, 19.6-24.1). The overall specificity for the influenza virus A was 86.9% (CI, 71.0-100). For influenza virus B testing, the sensitivity and specificity were 90.2% (CI, 68.5-100) and 98.8% (CI, 68.5-100), respectively.
Overall, the mean CT values in specimens with discordant results were significantly higher than those obtained for concordant results (16.4 &#177; 0.48 vs. 25.7 &#177; 0.51; p &#62;0.000) (Figure 1).
<img alt="Figure 1" src="/files/ftp_upload/54312/54312fig1.jpg" /> 
Figure 1: Average CT values determined by RP assay for samples that were positive and negative, respectively by the assay for each influenza subtype. Error bars represent standard deviation. **, p &#60;0.01; ***, p &#60;0.001. <a href="https://cloudflare-jove-com.remotexs.ntu.edu.sg/files/ftp_upload/54312/54312fig1large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Table 1" src="/files/ftp_upload/54312/54312table1.jpg" /> 
Table 1: Performance of the Influenza A&#38;B on VTM specimens compared to reference results.

Watch this Scientific Journal Video about Rapid Molecular Detection and Differentiation of Influenza Viruses A and B at JoVE.com

Rapid Molecular Detection and Differentiation of Influenza Viruses A and B

We describe a rapid, molecular-based Influenza A and B assay. The Influenza assay detects each target within 15 min by employing isothermal amplification with influenza-specific primers followed by target detection with molecular beacon probes. The Influenza A and B assay is user-friendly and required minimal hands-on time to perform.

Influenza is a contagious respiratory illness caused by influenza viruses A and B in humans and causes a significant amount of morbidity and mortality ...

rapid-molecular-detection-differentiation-influenza-viruses

Nanyang Technological University

Research

JoVE Journal

Immunology and Infection

15.7K Views.  Memorial Sloan Kettering Cancer Center.  We beschrijven een snelle, moleculair-gebaseerde Influenza A en B assay. De Influenza test detecteert elk doel binnen 15 minuten door het gebruik van isotherme amplificatie met influenza-specifieke primers, gevolgd door detectie van targets met moleculaire beacon sondes. De Influenza A en B test is gebruiksvriendelijk en vereist een minimale hands-on tijd om te presteren. 

Video: Rapid Molecular Detection and Differentiation of Influenza Viruses A and B

Generation of Recombinant Influenza Virus from Plasmid DNA

Efforts by a number of influenza research groups have been pivotal in the development and improvement of influenza A virus reverse genetics. Originally established in 1999 1,2 plasmid-based reverse genetic techniques to generate recombinant viruses have revolutionized the influenza research field because specific questions have been answered by genetically engineered, infectious, recombinant influenza viruses. Such studies include virus replication, function of viral proteins, the contribution of specific mutations in viral proteins in viral replication and/or pathogenesis and, also, viral vectors using recombinant influenza viruses expressing foreign proteins 3.

Rescue of influenza A viruses from plasmid DNA is a basic and essential experimental technique that allows influenza researchers to generate recombinant viruses to study multiple aspects in the biology of influenza virus, and to be used as potential vectors or vaccines.

Efforts by a number of influenza research groups have been pivotal in the development and improvement of influenza A virus reverse genetics. Originally ...

ampliPHOX Colorimetric Detection on a DNA Microarray for Influenza

DNA microarrays have emerged as a powerful tool for pathogen detection.1-5 For instance, many examples of the ability to type and subtype influenza virus have been demonstrated.6-11 The identification and subtyping of influenza on DNA microarrays has applications in both public health and the clinic for early detection, rapid intervention, and minimizing the impact of an influenza pandemic. Traditional fluorescence is currently the most commonly used microarray detection method. However, as microarray technology progresses towards clinical use,1 replacing expensive instrumentation with low cost detection technology exhibiting similar performance characteristics to fluorescence will make microarray assays more attractive and cost-effective.
The ampliPHOX colorimetric detection technology is intended for research applications, and has a limit of detection within one order of magnitude of traditional fluorescence11, with a main advantage being an approximate ten-fold lower instrument cost compared to the confocal microarray scanners required for fluorescence microarray detection. Another advantage is the compact size of the instrument which allows for portability and flexibility, unlike traditional fluorescence instruments. Because the polymerization technology is not as inherently linear as fluorescence detection, however, it is best suited for lower density microarray applications in which a yes/no answer for the presence of a certain sequence is desired, such as for pathogen detection arrays. Currently the maximum spot density compatible with ampliPHOX detection is &tilde;1800 spots/array. Because of the spot density limitations, higher density microarrays are not suitable for ampliPHOX detection.
Here, we present ampliPHOX colorimetric detection technology as a method of signal amplification on a low density microarray developed for the detection and characterization of influenza viruses (FluChip). Although this protocol uses the FluChip (a DNA microarray) as one specific application of ampliPHOX detection, any microarray incorporating biotinylated target can be labeled and detected in a similar manner. The microarray design and biotinylation of the target to be captured are the responsibility of the user. Once the biotinylated target has been captured on the array, ampliPHOX detection can be performed by first tagging the array with a streptavidin-label conjugate (ampliTAG). Upon light exposure using the ampliPHOX Reader instrument, polymerization of a monomer solution (ampliPHY) occurs only in regions containing ampliTAG-labeled targets. The polymer formed can be subsequently stained with a non-toxic solution to improve visual contrast, followed by imaging and analysis using a simple software package (ampliVIEW). The entire FluChip assay from un-extracted sample to result can be performed in about 6 hours, and the ampliPHOX detection steps described above can be completed in about 30 min.

ampliPHOX colorimetric detection technology is presented as an inexpensive alternative to fluorescence detection for microarrays. Based on photopolymerization, ampliPHOX produces solid polymer spots visible to the naked eye in just a few minutes. Results are then imaged and automatically interpreted with a simple yet powerful software package.

DNA microarrays have emerged as a powerful tool for pathogen detection.1-5  For instance, many examples of the ability to type and subtype influenza virus ...

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

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

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

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

Rapid Diagnosis of Avian Influenza Virus in Wild Birds: Use of a Portable rRT-PCR and Freeze-dried Reagents in the Field

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory flyways. Sampling of wild birds for avian influenza virus (AIV) is often conducted in remote regions, but results are often delayed because of the need to transport samples to a laboratory equipped for molecular testing. Real-time reverse transcriptase polymerase chain reaction (rRT-PCR) is a molecular technique that offers one of the most accurate and sensitive methods for diagnosis of AIV. The previously strict lab protocols needed for rRT-PCR are now being adapted for the field. Development of freeze-dried (lyophilized) reagents that do not require cold chain, with sensitivity at the level of wet reagents has brought on-site remote testing to a practical goal.
Here we present a method for the rapid diagnosis of AIV in wild birds using an rRT-PCR unit (Ruggedized Advanced Pathogen Identification Device or RAPID, Idaho Technologies, Salt Lake City, UT) that employs lyophilized reagents (Influenza A Target 1 Taqman; ASAY-ASY-0109, Idaho Technologies). The reagents contain all of the necessary components for testing at appropriate concentrations in a single tube: primers, probes, enzymes, buffers and internal positive controls, eliminating errors associated with improper storage or handling of wet reagents. The portable unit performs a screen for Influenza A by targeting the matrix gene and yields results in 2-3 hours. Genetic subtyping is also possible with H5 and H7 primer sets that target the hemagglutinin gene.
The system is suitable for use on cloacal and oropharyngeal samples collected from wild birds, as demonstrated here on the migratory shorebird species, the western sandpiper (Calidrus mauri) captured in Northern California. Animal handling followed protocols approved by the Animal Care and Use Committee of the U.S. Geological Survey Western Ecological Research Center and permits of the U.S. Geological Survey Bird Banding Laboratory. The primary advantage of this technique is to expedite diagnosis of wild birds, increasing the chances of containing an outbreak in a remote location. On-site diagnosis would also prove useful for identifying and studying infected individuals in wild populations. The opportunity to collect information on host biology (immunological and physiological response to infection) and spatial ecology (migratory performance of infected birds) will provide insights into the extent to which wild birds can act as vectors for AIV over long distances.

This study describes diagnosis of avian influenza in wild birds using a portable rRT-PCR system. The method takes advantage of freeze-dried reagents to screen wild birds in a non-laboratory setting, typical of an outbreak scenario. Use of molecular tools provides accurate and sensitive alternatives for rapid diagnosis.

Wild birds have been implicated in the spread of highly pathogenic avian influenza (HPAI) of the H5N1 subtype, prompting surveillance along migratory ...

High-throughput Detection Method for Influenza Virus

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

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

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

Microfluidic Chip Fabrication and Method to Detect Influenza

Fast and effective diagnostics play an important role in controlling infectious disease by enabling effective patient management and treatment. Here, we present an integrated microfluidic thermoplastic chip with the ability to amplify influenza A virus in patient nasopharyngeal (NP) swabs and aspirates. Upon loading the patient sample, the microfluidic device sequentially carries out on-chip cell lysis, RNA purification and concentration steps within the solid phase extraction (SPE), reverse transcription (RT) and polymerase chain reaction (PCR) in RT-PCR chambers, respectively. End-point detection is performed using an off-chip Bioanalyzer (Agilent Technologies, Santa Clara, CA). For peripherals, we used a single syringe pump to drive reagent and samples, while two thin film heaters were used as the heat sources for the RT and PCR chambers. The chip is designed to be single layer and suitable for high throughput manufacturing to reduce the fabrication time and cost. The microfluidic chip provides a platform to analyze a wide variety of virus and bacteria, limited only by changes in reagent design needed to detect new pathogens of interest.

An integrated microfluidic thermoplastic chip has been developed for use as a molecular diagnostic. The chip performs nucleic acid extraction, reverse transcriptase, and PCR. Methods for fabricating and running the chip are described.

Fast  and effective diagnostics play an important role in controlling infectious  disease by enabling effective patient management and treatment. Here, we ...

Bioengineering

Fluorescence-based Neuraminidase Inhibition Assay to Assess the Susceptibility of Influenza Viruses to The Neuraminidase Inhibitor Class of Antivirals

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against currently circulating strains. In addition to their use in treating seasonal influenza, the NA inhibitors have been stockpiled by a number of countries for use in the event of a pandemic. It is therefore important to monitor the susceptibility of circulating influenza viruses to this class of antivirals. There are different types of assays that can be used to assess the susceptibility of influenza viruses to the NA inhibitors, but the enzyme inhibition assays using either a fluorescent substrate or a chemiluminescent substrate are the most widely used and recommended. This protocol describes the use of a fluorescence-based assay to assess influenza virus susceptibility to NA inhibitors. The assay is based on the NA enzyme cleaving the 2&#8242;-(4-Methylumbelliferyl)-&#945;-D-N-acetylneuraminic acid (MUNANA) substrate to release the fluorescent product 4-methylumbelliferone (4-MU). Therefore, the inhibitory effect of an NA inhibitor on the influenza virus NA is determined based on the concentration of the NA inhibitor that is required to reduce 50% of the NA activity, given as an IC50 value.

We describe the use of a phenotypic fluorescence-based neuraminidase inhibition assay to assess the susceptibility of influenza A and B viruses to the neuraminidase inhibitor class of antivirals.

The neuraminidase (NA) inhibitors are the only class of antivirals approved for the treatment and prophylaxis of influenza that are effective against ...

Influenza A Virus Studies in a Mouse Model of Infection

Influenza viruses cause over 500,000 deaths worldwide1 and are associated with an annual cost of 12 - 14 billion USD in the United States alone considering direct medical and hospitalization expenses and work absenteeism2. Animal models are crucial in Influenza A virus (IAV) studies to evaluate viral pathogenesis, host-pathogen interactions, immune responses, and the efficacy of current and/or novel vaccine approaches as well as antivirals. Mice are an advantageous small animal model because their immune system is evolutionarily similar to that found in humans, they are available from commercial vendors as genetically identical subjects, there are multiple strains that can be exploited to evaluate the genetic basis of infections, and they are relatively inexpensive and easy to manipulate. To recapitulate IAV infection in humans via the airways, mice are first anesthetized prior to intranasal inoculation with infectious IAVs under proper biosafety containment. After infection, the pathogenesis of IAVs is determined by monitoring daily the morbidity (body weight loss) and mortality (survival) rate. In addition, viral pathogenesis can also be evaluated by assessing virus replication in the upper (nasal mucosa) or lower (lungs) respiratory tract of infected mice. Humoral responses upon IAV infection can be rapidly evaluated by non-invasive bleeding and secondary antibody detection assays aimed at detecting the presence of total or neutralizing antibodies. Here, we describe the common methods used to infect mice intranasally (i.n) with IAV and evaluate pathogenesis, humoral immune responses and protection efficacy.

Influenza A viruses (IAVs) are important human respiratory pathogens. To understand the pathogenicity of IAVs and to perform preclinical testing of novel vaccine approaches, animal models mimicking human physiology are required. Here, we describe techniques to evaluate IAV pathogenesis, humoral responses and vaccine efficacy using a mouse model of infection.

Influenza viruses cause over 500,000 deaths worldwide1 and are associated with an annual cost of 12 - 14 billion USD in the United States alone ...

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

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

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

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

Multiplex RT-qPCR Assay for Respiratory Virus Detection

Development of Multiplex Real-Time RT-qPCR Assays for the Detection of SARS-CoV-2, Influenza A/B, and MERS-CoV

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) is a serious threat to the general public&#39;s health. During influenza seasons, the spread of SARS-CoV-2 and other respiratory viruses may cause a population-wide burden of respiratory disease that is difficult to manage. For that, the respiratory viruses SARS-CoV-2, Influenza A, Influenza B, and Middle East respiratory syndrome (MERS-CoV) will need to be carefully watched over in the upcoming fall and winter seasons, particularly in the case of SARS-CoV-2, Influenza A, and Influenza B, which share similar epidemiological factors like susceptible populations, mode of transmission, and clinical syndromes. Without target-specific assays, it can be challenging to differentiate among cases of these viruses owing to their similarities. Accordingly, a sensitive and targeted multiplex assay that can easily differentiate between these viral targets will be useful for healthcare practitioners. In this study, we developed a real-time reverse transcriptase-PCR-based assay utilizing an in-house developed R3T one-step RT-qPCR kit for simultaneous detection of SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV. With as few as 10 copies of their synthetic RNAs, we can successfully identify SARS-CoV-2, Influenza A, Influenza B, and MERS-CoV targets simultaneously with 100% specificity. This assay is found to be accurate, reliable, simple, sensitive, and specific. The developed method can be used as an optimized SARS-CoV-2, Influenza A, Influenza B, and SARS-CoV-2, MERS-CoV diagnostic assay in hospitals, medical centers, and diagnostic laboratories as well as for research purposes.

Author Spotlight: Advancements in Multiplex Detection of Respiratory Viruses 

We present two probe-based in-house one-step RT-qPCR kits for common respiratory viruses. The first assay is for SARS-CoV-2 (N), Influenza A (H1N1 and H3N2), and Influenza B. The second is for SARS-Cov-2 (N) and MERS (UpE and ORF1a). These assays can be successfully implemented in any specialized laboratory.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that causes Coronavirus disease 2019 (COVID-19) is a serious threat to the general ...

Rapid Molecular Detection and Differentiation of Influenza Viruses A and B

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