{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T16:56:58Z","timestamp":1780333018876,"version":"3.54.1"},"reference-count":56,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T00:00:00Z","timestamp":1693526400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Public Health"],"abstract":"<jats:p>Standard multiplex RT-qPCR diagnostic tests use nasopharyngeal swabs to simultaneously detect a variety of infections, but commercially available kits can be expensive and have limited throughput. Previously, we clinically validated a saliva-based RT-qPCR diagnostic test for SARS-CoV-2 to provide low-cost testing with high throughput and low turnaround time on a university campus. Here, we developed a respiratory diagnostic panel to detect SARS-CoV-2, influenza A and B within a single saliva sample. When compared to clinical results, our assay demonstrated 93.5% accuracy for influenza A samples (43\/46 concordant results) with no effect on SARS-CoV-2 accuracy or limit of detection. In addition, our assay can detect simulated coinfections at varying virus concentrations generated from synthetic RNA controls. We also confirmed the stability of influenza A in saliva at room temperature for up to 5\u2009days. The cost of the assay is lower than standard nasopharyngeal swab respiratory panel tests as saliva collection does not require specialized swabs or trained clinical personnel. By repurposing the lab infrastructure developed for the COVID-19 pandemic, our multiplex assay can be used to provide expanded access to respiratory disease diagnostics, especially for community, school, or university testing applications where saliva testing was effectively utilized during the COVID-19 pandemic.<\/jats:p>","DOI":"10.3389\/fpubh.2023.1168551","type":"journal-article","created":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T08:27:25Z","timestamp":1693556845000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Repurposing a SARS-CoV-2 surveillance program for infectious respiratory diseases in a university setting"],"prefix":"10.3389","volume":"11","author":[{"given":"Kylie L.","family":"King","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rachel","family":"Ham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Austin","family":"Smothers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Isaac","family":"Lee","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tyler","family":"Bowie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Erika","family":"Teetsel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Congyue","family":"Peng","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Delphine","family":"Dean","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2023,9,1]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1016\/S2213-2600(18)30496-X","article-title":"Mortality, morbidity, and hospitalisations due to influenza lower respiratory tract infections, 2017: an analysis for the Global Burden of Disease Study 2017","volume":"7","author":"Troeger","year":"2019","journal-title":"Lancet Respir Med"},{"key":"ref2","volume-title":"Undergraduate student reference group data report fall 2019","year":"2020"},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1263","DOI":"10.1086\/429237\/2\/","article-title":"Colds and influenza-like illnesses in university students: impact on health, academic and work performance, and health care use","volume":"40","author":"Nichol","year":"2005","journal-title":"Clin Infect Dis"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1080\/07448481.2010.502197","article-title":"Influenza-like illness among university students: symptom severity and duration due to influenza virus infection compared to other etiologies","volume":"59","author":"Mullins","year":"2011","journal-title":"J Am Coll Heal"},{"key":"ref5","doi-asserted-by":"publisher","first-page":"1811","DOI":"10.1086\/649555\/2\/","article-title":"Notes from the field: outbreak of 2009 pandemic influenza A (H1N1) virus at a large public University in Delaware, April-May 2009","volume":"49","author":"Iuliano","year":"2009","journal-title":"Clin Infect Dis"},{"key":"ref6","doi-asserted-by":"publisher","first-page":"582","DOI":"10.1111\/irv.12563","article-title":"Human coronaviruses and other respiratory infections in young adults on a university campus: prevalence, symptoms, and shedding","volume":"12","author":"Davis","year":"2018","journal-title":"Influenza Other Respir Viruses"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"e2171","DOI":"10.1002\/rmv.2171","article-title":"The unique features of SARS-CoV-2 transmission: comparison with SARS-CoV, MERS-CoV and 2009 H1N1 pandemic influenza virus","volume":"31","author":"Wu","year":"2021","journal-title":"Rev Med Virol"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2334-10-106","article-title":"Age groups and spread of influenza: implications for vaccination strategy","volume":"10","author":"Hsieh","year":"2010","journal-title":"BMC Infect Dis"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"ofab618","DOI":"10.1093\/ofid\/ofaB618","article-title":"Circulation of non-SARS-CoV-2 respiratory pathogens and coinfection with SARS-CoV-2 amid the COVID-19 pandemic","volume":"9","author":"Uhteg","year":"2022","journal-title":"Infect Dis"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"1013","DOI":"10.15585\/mmwr.mm7029A1","article-title":"Changes in influenza and other respiratory virus activity during the COVID-19 pandemic \u2014 United States, 2020\u20132021","volume":"70","author":"Olsen","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"ref11","doi-asserted-by":"publisher","first-page":"39","DOI":"10.14745\/ccdr.v48i01a06","article-title":"National FluWatch mid-season report, 2021-2022: sporadic influenza activity returns","volume":"48","author":"Bancej","year":"2022","journal-title":"Can Commun Dis Rep"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"365","DOI":"10.15585\/mmwr.mm7110A1","article-title":"Interim estimates of 2021\u201322 seasonal influenza vaccine effectiveness \u2014 United States, February 2022","volume":"71","author":"Chung","year":"2022","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"ref13","year":"2023"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1712","DOI":"10.15585\/mmwr.mm7049E1","article-title":"Influenza A(H3N2) outbreak on a university campus \u2014 Michigan, October\u2013November 2021","volume":"70","author":"Delahoy","year":"2021","journal-title":"MMWR Morb Mortal Wkly Rep"},{"key":"ref15","volume-title":"Flu virus grips college campuses","author":"Whitford","year":"2021"},{"key":"ref16","doi-asserted-by":"publisher","first-page":"1210","DOI":"10.1111\/j.1539-6924.2010.01428.x","article-title":"The effect of mask use on the spread of influenza during a pandemic","volume":"30","author":"Brienen","year":"2010","journal-title":"Risk Anal"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e31955","DOI":"10.2196\/31955","article-title":"Mask use to curtail influenza in a post-COVID-19 world: modeling study","volume":"3","author":"Froese","year":"2022","journal-title":"JMIRx Med"},{"key":"ref18","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1186\/S12985-021-01594-0","article-title":"Influenza co-infection associated with severity and mortality in COVID-19 patients","volume":"18","author":"Alosaimi","year":"2021","journal-title":"Virol J"},{"key":"ref19","doi-asserted-by":"publisher","first-page":"e0009997","DOI":"10.1371\/journal.pntd.0009997","article-title":"Clinical and virological impact of single and dual infections with influenza A (H1N1) and SARS-CoV-2 in adult inpatients","volume":"15","author":"Zheng","year":"2021","journal-title":"PLoS Negl Trop Dis"},{"key":"ref20","doi-asserted-by":"publisher","first-page":"e2365","DOI":"10.1002\/rmv.2365","article-title":"Respiratory viral co-infections in patients with COVID-19 and associated outcomes: a systematic review and meta-analysis","volume":"33","author":"Krumbein","year":"2023","journal-title":"Rev Med Virol"},{"key":"ref21","doi-asserted-by":"publisher","first-page":"e0124822","DOI":"10.1128\/spectrum.01248-22","article-title":"Comparative performance of the luminex NxTAG respiratory pathogen panel, GenMark eSensor respiratory viral panel, and BioFire FilmArray respiratory panel","volume":"10","author":"Popowitch","year":"2022","journal-title":"Microbiol Spectr"},{"key":"ref22","doi-asserted-by":"publisher","first-page":"31","DOI":"10.4415\/ANN_23_01_05","article-title":"Diagnosis of respiratory syncytial virus (RSV) infection in children by respiratory panel utilized during the COVID-19 pandemic","volume":"59","author":"Petrocelli","year":"2023","journal-title":"Ann Ist Super Sanita"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"e02955-20","DOI":"10.1128\/JCM.02955-20","article-title":"Multicenter evaluation of the cepheid xpert xpress SARS-CoV-2\/Flu\/RSV test","volume":"59","author":"Mostafa","year":"2021","journal-title":"J Clin Microbiol"},{"key":"ref24","year":"2023"},{"key":"ref25","year":"2023"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.medj.2020.12.010","article-title":"SalivaDirect: a simplified and flexible platform to enhance SARS-CoV-2 testing capacity","volume":"2","author":"Vogels","year":"2021","journal-title":"Med"},{"key":"ref27","doi-asserted-by":"publisher","first-page":"858421","DOI":"10.3389\/fpubh.2022.858421","article-title":"Implementation of a rural community diagnostic testing strategy for SARS-CoV-2 in upstate South Carolina","volume":"10","author":"Plumb","year":"2022","journal-title":"Front Public Health"},{"key":"ref28","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1128\/JCM.39.1.196-200.2001\/ASSET\/76B6DCBA-92CD-43D7-8252-8D0B01867813","article-title":"Simultaneous detection of influenza viruses A and B using real-time quantitative PCR","volume":"39","author":"Van Elden","year":"2001","journal-title":"J Clin Microbiol"},{"key":"ref29","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1128\/JCM.01704-16","article-title":"Comparison between saliva and nasopharyngeal swab specimens for detection of respiratory viruses by multiplex reverse transcription-PCR","volume":"55","author":"Kim","year":"2016","journal-title":"J Clin Microbiol"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"3492","DOI":"10.1128\/JCM.00957-17","article-title":"Multiplex reverse transcription-PCR for simultaneous surveillance of influenza A and B viruses","volume":"55","author":"Zhou","year":"2017","journal-title":"J Clin Microbiol"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"e0033621","DOI":"10.1128\/Spectrum.00336-21","article-title":"Use of saliva swab for detection of influenza virus in patients admitted to an emergency department","volume":"9","author":"Galar","year":"2021","journal-title":"Microbiol Spectr"},{"key":"ref32","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1016\/J.CCA.2015.12.006","article-title":"Evaluation of saliva as diagnostic materials for influenza virus infection by PCR-based assays","volume":"453","author":"Sueki","year":"2016","journal-title":"Clin Chim Acta"},{"key":"ref33","doi-asserted-by":"publisher","first-page":"3480","DOI":"10.1038\/s41598-022-07152-0","article-title":"Clinical validation of a multiplex PCR-based detection assay using saliva or nasopharyngeal samples for SARS-CoV-2, influenza A and B","volume":"12","author":"Sahajpal","year":"2022","journal-title":"Sci Rep"},{"key":"ref34","doi-asserted-by":"publisher","DOI":"10.1371\/currents.outbreaks.0371243baa7f3810ba1279e30b96d3b6","article-title":"Surveillance of acute respiratory infections using community-submitted symptoms and specimens for molecular diagnostic testing","volume":"7","author":"Goff","year":"2015","journal-title":"PLoS Curr Outbreaks"},{"key":"ref35","doi-asserted-by":"publisher","first-page":"e2146805","DOI":"10.1001\/jamanetworkopen.2021.46805","article-title":"SARS-CoV-2 variant tracking and mitigation during in-person learning at a midwestern university in the 2020-2021 school year","volume":"5","author":"Avendano","year":"2022","journal-title":"JAMA Netw Open"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1186\/S12889-021-11525-X","article-title":"The impact of phased university reopenings on mitigating the spread of COVID-19: a modeling study","volume":"21","author":"Rennert","year":"2021","journal-title":"BMC Public Health"},{"key":"ref37","doi-asserted-by":"publisher","first-page":"e0251296","DOI":"10.1371\/journal.pone.0251296","article-title":"Launching a saliva-based SARS-CoV-2 surveillance testing program on a university campus","volume":"16","author":"Ehrenberg","year":"2021","journal-title":"PLoS One"},{"key":"ref38","doi-asserted-by":"publisher","first-page":"3207","DOI":"10.1038\/s41467-022-30833-3","article-title":"Mitigation of SARS-CoV-2 transmission at a large public university","volume":"13","author":"Ranoa","year":"2022","journal-title":"Nat Commun"},{"key":"ref39","doi-asserted-by":"publisher","first-page":"e0108921","DOI":"10.1128\/Spectrum.01089-21","article-title":"Routine, cost-effective SARS-CoV-2 surveillance testing using pooled saliva limits viral spread on a residential college campus","volume":"9","author":"Vander Schaaf","year":"2021","journal-title":"Microbiol Spectr"},{"key":"ref40","doi-asserted-by":"publisher","first-page":"e0263114","DOI":"10.1371\/journal.pone.0263114","article-title":"Pooling saliva samples as an excellent option to increase the surveillance for SARS-CoV-2 when re-opening community settings","volume":"17","author":"Moreno-Contreras","year":"2022","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1506","DOI":"10.1002\/jmv.26460","article-title":"Saliva sample pooling for the detection of SARS-CoV-2","volume":"93","author":"Pasomsub","year":"2021","journal-title":"J Med Virol"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/j.cll.2022.02.006","article-title":"Strategies for scaling up SARS-CoV-2 molecular testing capacity","volume":"42","author":"Das","year":"2022","journal-title":"Clin Lab Med"},{"key":"ref43","doi-asserted-by":"publisher","first-page":"e63395","DOI":"10.3791\/63395","article-title":"Efficient SARS-CoV-2 quantitative reverse transcriptase PCR saliva diagnostic strategy utilizing open-source pipetting robots","volume":"180","author":"Ham","year":"2022","journal-title":"J Vis Exp"},{"key":"ref44","doi-asserted-by":"publisher","first-page":"1821","DOI":"10.3201\/EID2707.210462","article-title":"Multiplex real-time reverse transcription PCR for influenza A virus, influenza B virus, and severe acute respiratory syndrome coronavirus 2 - volume 27, number 7\u2014July 2021 - emerging infectious diseases journal - CDC","volume":"27","author":"Shu","year":"2021","journal-title":"Emerg Infect Dis"},{"key":"ref45","doi-asserted-by":"publisher","first-page":"e0079722","DOI":"10.1128\/spectrum.00797-22","article-title":"Identifying SARS-CoV-2 variants of concern through saliva-based RT-qPCR by targeting recurrent mutation sites","volume":"10","author":"Ham","year":"2022","journal-title":"Microbiol Spectr"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"45","DOI":"10.4103\/0301-4738.37595","article-title":"Understanding and using sensitivity, specificity and predictive values","volume":"56","author":"Parikh","year":"2008","journal-title":"Indian J Ophthalmol"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"2","DOI":"10.1177\/104063871102300102","article-title":"Selection of a cutoff value for real-time polymerase chain reaction results to fit a diagnostic purpose: analytical and epidemiologic approaches","volume":"23","author":"Caraguel","year":"2011","journal-title":"J Vet Diagn"},{"key":"ref48","doi-asserted-by":"publisher","first-page":"e0267750","DOI":"10.1371\/journal.pone.0267750","article-title":"SARS-CoV-2 variants of concern alpha and delta show increased viral load in saliva","volume":"17","author":"King","year":"2022","journal-title":"PLoS One"},{"key":"ref49","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2021\/5313832","article-title":"Viral coinfection among COVID-19 patient groups: an update systematic review and meta-analysis","volume":"2021","author":"Malekifar","year":"2021","journal-title":"Biomed Res Int"},{"key":"ref50","doi-asserted-by":"publisher","first-page":"102262","DOI":"10.1016\/J.TMAID.2022.102262","article-title":"COVID-19 and influenza coinfection: the rise of \u00d4micron and H3N2 in Brazil \u2013 2022","volume":"46","author":"Fujita","year":"2022","journal-title":"Travel Med Infect Dis"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"2657","DOI":"10.1002\/JMV.26125","article-title":"Influenza and COVID-19 coinfection: report of six cases and review of the literature","volume":"92","author":"Ozaras","year":"2020","journal-title":"J Med Virol"},{"key":"ref52","doi-asserted-by":"publisher","first-page":"2870","DOI":"10.1002\/JMV.26163","article-title":"The epidemiology and clinical characteristics of co-infection of SARS-CoV-2 and influenza viruses in patients during COVID-19 outbreak","volume":"92","author":"Yue","year":"2020","journal-title":"J Med Virol"},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1745","DOI":"10.3390\/v14081745","article-title":"Extinction of the influenza B Yamagata line during the COVID pandemic-implications for vaccine composition","volume":"14","author":"Vajo","year":"2022","journal-title":"Viruses"},{"key":"ref54","doi-asserted-by":"publisher","first-page":"5411","DOI":"10.2147\/IDR.S373748","article-title":"Performance evaluation of TaqMan SARS-CoV-2, Flu A\/B, RSV RT-PCR multiplex assay for the detection of respiratory viruses","volume":"15","author":"Neopane","year":"2022","journal-title":"Infect Drug Resist"},{"key":"ref55","doi-asserted-by":"publisher","first-page":"1146","DOI":"10.3201\/eid2704.204199","article-title":"Stability of SARS-CoV-2 RNA in nonsupplemented saliva","volume":"27","author":"Ott","year":"2021","journal-title":"Emerg Infect Dis"},{"key":"ref56","doi-asserted-by":"publisher","first-page":"YE01","DOI":"10.7860\/JCDR\/2016\/18129.8744","article-title":"Requirements for minimum sample size for sensitivity and specificity analysis","volume":"10","author":"Bujang","year":"2016","journal-title":"J Clin Diagn Res"}],"container-title":["Frontiers in Public Health"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2023.1168551\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,9,1]],"date-time":"2023-09-01T08:27:30Z","timestamp":1693556850000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpubh.2023.1168551\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,9,1]]},"references-count":56,"alternative-id":["10.3389\/fpubh.2023.1168551"],"URL":"https:\/\/doi.org\/10.3389\/fpubh.2023.1168551","relation":{},"ISSN":["2296-2565"],"issn-type":[{"value":"2296-2565","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,9,1]]},"article-number":"1168551"}}