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However, RATs based on either nasal swab or saliva samples were used, raising the question as to which type of RAT is most effective at detecting viral infections. Here, we develop a model-driven computational framework to assess different RATs and identify the most suitable test for a specified purpose, such as infection screening or determining the end of isolation, for various viral infections. Using symptomatic COVID-19 cases as a case study, we found that saliva-based RATs reduced transmission risk on average by 6.2% (95% CI: 6.1 \u2013 6.3) compared to nasal-based RATs in the pre-symptomatic period. In addition, by ending isolation of infected individuals who have developed symptoms when consecutive RATs return negative results, the mean risk of transmission was reduced by 5.9% (95% CI: 5.7 \u2013 6.1) using a saliva-based RAT compared to using a nasal-based RAT. These findings suggest that saliva RATs may be a useful option for mitigating SARS-CoV-2 transmission effectively. However, real-world variability in test sensitivity and sample collection should be carefully considered when evaluating the practical use of each RAT type. Our novel approach can be applied to other viruses and types of tests, enabling its use to inform public health policy decisions about which types of RAT to prioritize in future infectious disease epidemics.<\/jats:p>","DOI":"10.1371\/journal.pcbi.1013102","type":"journal-article","created":{"date-parts":[[2026,4,2]],"date-time":"2026-04-02T17:28:22Z","timestamp":1775150902000},"page":"e1013102","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Identifying the optimal rapid antigen test for screening and determining the end of isolation: A modeling study"],"prefix":"10.1371","volume":"22","author":[{"given":"Yong Dam","family":"Jeong","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2504-6860","authenticated-orcid":true,"given":"William S.","family":"Hart","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4719-651X","authenticated-orcid":true,"given":"Masahiro","family":"Ishikane","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kwang Su","family":"Kim","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jong Hyuk","family":"Byun","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Il Hyo","family":"Jung","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Montie T.","family":"Harrison","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kazuyuki","family":"Aihara","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Norio","family":"Ohmagari","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher B.","family":"Brooke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruian","family":"Ke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Robin N.","family":"Thompson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1780-350X","authenticated-orcid":true,"given":"Shingo","family":"Iwami","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2026,4,2]]},"reference":[{"issue":"4","key":"pcbi.1013102.ref001","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1046\/j.1469-0691.2003.00650.x","article-title":"Rapid antigen testing for the surveillance of influenza epidemics","volume":"9","author":"W Wunderli","year":"2003","journal-title":"Clin Microbiol Infect"},{"issue":"33","key":"pcbi.1013102.ref002","doi-asserted-by":"crossref","first-page":"4777","DOI":"10.1016\/j.vaccine.2023.06.082","article-title":"Effectiveness of inactivated influenza and COVID-19 vaccines in hospitalized children in 2022\/23 season in Japan - The first season of co-circulation of influenza and COVID-19","volume":"41","author":"M Shinjoh","year":"2023","journal-title":"Vaccine"},{"key":"pcbi.1013102.ref003","unstructured":"CDC. 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(Basel)"},{"issue":"1","key":"pcbi.1013102.ref055","doi-asserted-by":"crossref","first-page":"406","DOI":"10.1186\/s12916-022-02603-x","article-title":"Head-to-head comparison of the accuracy of saliva and nasal rapid antigen SARS-CoV-2 self-testing: cross-sectional study","volume":"20","author":"E Schuit","year":"2022","journal-title":"BMC Med"},{"issue":"1","key":"pcbi.1013102.ref056","doi-asserted-by":"crossref","first-page":"1533","DOI":"10.1038\/s41467-021-21710-6","article-title":"Infectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China","volume":"12","author":"S Hu","year":"2021","journal-title":"Nat Commun"},{"key":"pcbi.1013102.ref057","article-title":"Inference of the SARS-CoV-2 generation time using UK household data","volume":"11","author":"WS Hart","year":"2022","journal-title":"Elife"},{"issue":"10","key":"pcbi.1013102.ref058","article-title":"Incomplete antiviral treatment may induce longer durations of viral shedding during SARS-CoV-2 infection","volume":"4","author":"KS Kim","year":"2021","journal-title":"Life Sci Alliance"},{"issue":"7824","key":"pcbi.1013102.ref059","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1038\/s41586-020-2324-7","article-title":"Respiratory disease in rhesus macaques inoculated with SARS-CoV-2","volume":"585","author":"VJ Munster","year":"2020","journal-title":"Nature"},{"issue":"7824","key":"pcbi.1013102.ref060","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1038\/s41586-020-2423-5","article-title":"Clinical benefit of remdesivir in rhesus macaques infected with SARS-CoV-2","volume":"585","author":"BN Williamson","year":"2020","journal-title":"Nature"},{"issue":"49","key":"pcbi.1013102.ref061","doi-asserted-by":"crossref","first-page":"2000790","DOI":"10.2807\/1560-7917.ES.2020.25.49.2000790","article-title":"Epidemiological characteristics of COVID-19 cases and estimates of the reproductive numbers 1 month into the epidemic, Italy, 28 January to 31 March 2020","volume":"25","author":"F Riccardo","year":"2020","journal-title":"Euro Surveill"},{"issue":"11","key":"pcbi.1013102.ref062","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0242128","article-title":"Reproductive number of coronavirus: A systematic review and meta-analysis based on global level evidence","volume":"15","author":"MA Billah","year":"2020","journal-title":"PLoS One"},{"issue":"2","key":"pcbi.1013102.ref063","article-title":"The reproductive number of COVID-19 is higher compared to SARS coronavirus","volume":"27","author":"Y Liu","year":"2020","journal-title":"J Travel Med"},{"issue":"2","key":"pcbi.1013102.ref064","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1093\/aje\/kwg103","article-title":"Transmission potential of smallpox: estimates based on detailed data from an outbreak","volume":"158","author":"M Eichner","year":"2003","journal-title":"Am J Epidemiol"},{"issue":"16","key":"pcbi.1013102.ref065","doi-asserted-by":"crossref","first-page":"6146","DOI":"10.1073\/pnas.0307506101","article-title":"Factors that make an infectious disease outbreak controllable","volume":"101","author":"C Fraser","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"5","key":"pcbi.1013102.ref066","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.3201\/eid2605.200198","article-title":"Potential presymptomatic transmission of SARS-CoV-2, Zhejiang Province, China, 2020","volume":"26","author":"ZD Tong","year":"2020","journal-title":"Emerg Infect Dis"},{"issue":"22","key":"pcbi.1013102.ref067","doi-asserted-by":"crossref","first-page":"2081","DOI":"10.1056\/NEJMoa2008457","article-title":"Presymptomatic SARS-CoV-2 Infections and Transmission in a Skilled Nursing Facility","volume":"382","author":"MM Arons","year":"2020","journal-title":"N Engl J Med"},{"key":"pcbi.1013102.ref068","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1111\/irv.12080","article-title":"Routes of influenza transmission","author":"B Killingley","year":"2013","journal-title":"Influenza Other Respir Viruses"},{"key":"pcbi.1013102.ref069","unstructured":"CDC. Transmission of Measles 2020. Available from: https:\/\/www.cdc.gov\/measles\/transmission.html"},{"issue":"6","key":"pcbi.1013102.ref070","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.03923-22","article-title":"Comparison of Nasopharyngeal and Saliva Swab Nucleic Acid Amplification and Rapid Antigen Testing To Detect Omicron SARS-CoV-2 Variant of Concern: a Prospective Clinical Trial (OMICRON)","volume":"10","author":"A Kritikos","year":"2022","journal-title":"Microbiol Spectr"},{"issue":"11","key":"pcbi.1013102.ref071","doi-asserted-by":"crossref","first-page":"1065","DOI":"10.1001\/jama.2021.13967","article-title":"Change in Saliva RT-PCR Sensitivity Over the Course of SARS-CoV-2 Infection","volume":"326","author":"Z Congrave-Wilson","year":"2021","journal-title":"JAMA"},{"key":"pcbi.1013102.ref072","article-title":"Safely return to schools and offices: early and frequent screening with high sensitivity antigen tests effectively identifies COVID-19 patients","author":"YD Jeong","year":"2021","journal-title":"medRxiv"},{"issue":"5","key":"pcbi.1013102.ref073","doi-asserted-by":"crossref","first-page":"892","DOI":"10.1038\/s41591-021-01296-8","article-title":"SARS-CoV-2 infection of the oral cavity and saliva","volume":"27","author":"N Huang","year":"2021","journal-title":"Nat Med"},{"key":"pcbi.1013102.ref074","doi-asserted-by":"crossref","first-page":"104821","DOI":"10.1016\/j.oraloncology.2020.104821","article-title":"Oral saliva and COVID-19","volume":"108","author":"M Baghizadeh Fini","year":"2020","journal-title":"Oral Oncol"},{"issue":"8","key":"pcbi.1013102.ref075","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1012309","article-title":"Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings","volume":"20","author":"I Bouros","year":"2024","journal-title":"PLoS Comput Biol"},{"issue":"11","key":"pcbi.1013102.ref076","doi-asserted-by":"crossref","first-page":"1714","DOI":"10.1038\/s41591-020-1092-0","article-title":"Clustering and superspreading potential of SARS-CoV-2 infections in Hong Kong","volume":"26","author":"DC Adam","year":"2020","journal-title":"Nat Med"},{"key":"pcbi.1013102.ref077","article-title":"Acceptability and Feasibility of Saliva-delivered PCR Coronavirus 2019 Tests for Young Children","volume":"152","author":"RE Lee","year":"2023","journal-title":"Pediatrics"},{"issue":"2","key":"pcbi.1013102.ref078","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1016\/j.bsheal.2024.03.002","article-title":"Superior effectiveness and acceptability of saliva samples for the detection of SARS-CoV-2 in China","volume":"6","author":"H Yao","year":"2024","journal-title":"Biosaf Health"},{"key":"pcbi.1013102.ref079","doi-asserted-by":"crossref","first-page":"67","DOI":"10.12688\/wellcomeopenres.15842.3","article-title":"Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China","volume":"5","author":"Centre for the Mathematical Modelling of Infectious Diseases C-WG","year":"2020","journal-title":"Wellcome Open Res"},{"key":"pcbi.1013102.ref080","author":"YD Jeong","year":"2025","journal-title":"Available from"}],"updated-by":[{"DOI":"10.1371\/journal.pcbi.1013102","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T00:00:00Z","timestamp":1776211200000}}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013102","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T18:11:47Z","timestamp":1776276707000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1013102"}},"subtitle":[],"editor":[{"given":"Jessica M.","family":"Conway","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2026,4,2]]},"references-count":80,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2026,4,2]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1013102","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,2]]}}}