{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,23]],"date-time":"2025-10-23T04:44:47Z","timestamp":1761194687379,"version":"build-2065373602"},"reference-count":51,"publisher":"MDPI AG","issue":"20","license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Virginia G. Piper foundation","award":["CTR053916"],"award-info":[{"award-number":["CTR053916"]}]},{"DOI":"10.13039\/100000030","name":"U.S. Centers for Disease Control and Prevention","doi-asserted-by":"crossref","award":["CDC BAA 75D30121C11084"],"award-info":[{"award-number":["CDC BAA 75D30121C11084"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Tohono O\u2019odham Nation","award":["2020-01 ASU"],"award-info":[{"award-number":["2020-01 ASU"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Diagnostics"],"abstract":"<jats:p>Background\/Objectives: Monitoring community health and tracking SARS-CoV-2 evolution were critical priorities throughout the COVID-19 pandemic. However, widespread shortages of personal protective equipment, the necessity for social distancing, and the redeployment of healthcare personnel to clinical duties presented significant barriers to traditional sample collection. Methods: In this study, we evaluated the feasibility of using self-collected saliva specimens for the qualitative detection of SARS-CoV-2 infection. Following confirmation of reliable viral detection in saliva, we established a large-scale surveillance program in Arizona, USA, to enable clinical diagnosis and genomic sequencing from self-collected samples. Between April 2020 and December 2023, we tested approximately 1.4 million saliva samples using RT-PCR, identifying 94,330 SARS-CoV-2 infections. Whole genome sequencing was performed on 69,595 samples, yielding 54,040 high-quality consensus genomes. Results: This surveillance approach enabled real-time monitoring of general infection trends that matched regional case counts. We monitored multiple wave-like introductions of viral lineages over the course of the pandemic. We identified three periods of S gene target failure on a commercial assay and assessed its ability to make fast, genotyping assignment during the pandemic (PPV = 0.98, 95% CI = 0.97\u20130.99; NPV = 0.94, 95% CI = 0.94\u20130.96). The co-location of clinical testing and sequencing capabilities within the same facility resulted in low turnaround time from the sample collection to the generation of sequencing data (median = 12 days, IQR: 9.0\u201319.75). Conclusions: Our findings support the use of self-collected saliva as a scalable, cost-effective, and practical strategy for infectious disease surveillance in future pandemics.<\/jats:p>","DOI":"10.3390\/diagnostics15202663","type":"journal-article","created":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T15:36:31Z","timestamp":1761060991000},"page":"2663","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Large-Scale Saliva-Based Clinical Surveillance Enables Real Time SARS-CoV-2 Outbreak Detection and Genomic Tracking (Arizona, 2020\u20132023)"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0649-3611","authenticated-orcid":false,"given":"Steven C.","family":"Holland","sequence":"first","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"name":"ABCTL Diagnostic Testing and Sequencing Teams","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ian","family":"Shoemaker","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Theresa","family":"Rosov","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carolyn C.","family":"Compton","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua","family":"LaBaer","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Efrem S.","family":"Lim","sequence":"additional","affiliation":[{"name":"Communicable Diseases Agency, Singapore 307684, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7368-7742","authenticated-orcid":false,"given":"Vel","family":"Murugan","sequence":"additional","affiliation":[{"name":"Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA"},{"name":"College of Health Solutions, Arizona State University, Phoenix, AZ 85004, USA"},{"name":"Health Observatory, Arizona State University, Phoenix, AZ 85004, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2025,10,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"265","DOI":"10.1038\/s41586-020-2008-3","article-title":"A new coronavirus associated with human respiratory disease in China","volume":"579","author":"Wu","year":"2020","journal-title":"Nature"},{"key":"ref_2","unstructured":"World Health Organization (2025, October 01). WHO Director-General\u2019s Statement on IHR Emergency Committee on Novel Coronavirus (2019-nCoV). 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