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Many respiratory infections share common symptoms, making them difficult to diagnose using only syndromic presentation. Yet, with delays in getting reference laboratory tests and limited availability and poor sensitivity of point-of-care tests, syndromic diagnosis is the most-relied upon method in clinical practice today. Here, we examine the variability in diagnostic identification of respiratory infections during the annual infection cycle in northern New Mexico, by comparing syndromic diagnostics with polymerase chain reaction (PCR) and sequencing-based methods, with the goal of assessing gaps in our current ability to identify respiratory pathogens. Of 97 individuals that presented with symptoms of respiratory infection, only 23 were positive for at least one RNA virus, as confirmed by sequencing. Whereas influenza virus (n = 7) was expected during this infection cycle, we also observed coronavirus (n = 7), respiratory syncytial virus (n = 8), parainfluenza virus (n = 4), and human metapneumovirus (n = 1) in individuals with respiratory infection symptoms. Four patients were coinfected with two viruses. In 21 individuals that tested positive using PCR, RNA sequencing completely matched in only 12 (57%) of these individuals. Few individuals (37.1%) were diagnosed to have an upper respiratory tract infection or viral syndrome by syndromic diagnostics, and the type of virus could only be distinguished in one patient. Thus, current syndromic diagnostic approaches fail to accurately identify respiratory pathogens associated with infection and are not suited to capture emerging threats in an accurate fashion. We conclude there is a critical and urgent need for layered agnostic diagnostics to track known and unknown pathogens at the point of care to control future outbreaks.<\/jats:p>","DOI":"10.1371\/journal.pgph.0000811","type":"journal-article","created":{"date-parts":[[2022,7,20]],"date-time":"2022-07-20T17:28:12Z","timestamp":1658338092000},"page":"e0000811","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgph.corrections_policy","source":"Crossref","is-referenced-by-count":26,"title":["Comparing variability in diagnosis of upper respiratory tract infections in patients using syndromic, next generation sequencing, and PCR-based methods"],"prefix":"10.1371","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1254-4481","authenticated-orcid":true,"given":"Andrew W.","family":"Bartlow","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zachary R.","family":"Stromberg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9949-292X","authenticated-orcid":true,"given":"Cheryl D.","family":"Gleasner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0278-8466","authenticated-orcid":true,"given":"Bin","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2740-1344","authenticated-orcid":true,"given":"Karen W.","family":"Davenport","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shailja","family":"Jakhar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4290-1993","authenticated-orcid":true,"given":"Po-E","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Molly","family":"Vosburg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Madhavi","family":"Garimella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3949-3634","authenticated-orcid":true,"given":"Patrick S. G.","family":"Chain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7012-9921","authenticated-orcid":true,"given":"Tracy H.","family":"Erkkila","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3377-6134","authenticated-orcid":true,"given":"Jeanne M.","family":"Fair","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0931-0545","authenticated-orcid":true,"given":"Harshini","family":"Mukundan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,7,20]]},"reference":[{"key":"pgph.0000811.ref001","doi-asserted-by":"crossref","first-page":"e680","DOI":"10.1016\/S2214-109X(16)30173-5","article-title":"Avoiding catastrophes: seeking synergies among 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A Public Website for the Automated Assessment and Validation of SARS-CoV-2 Diagnostic PCR Assays. Bioinforma Oxf Engl. Oxford University Press; 2020;btaa710.","DOI":"10.1093\/bioinformatics\/btaa710"},{"key":"pgph.0000811.ref053","doi-asserted-by":"crossref","first-page":"2238","DOI":"10.1128\/JCM.02495-14","article-title":"Evaluation of Unbiased Next-Generation Sequencing of RNA (RNA-seq) as a Diagnostic Method in Influenza Virus-Positive Respiratory Samples","volume":"53","author":"N Fischer","year":"2015","journal-title":"J Clin Microbiol"},{"key":"pgph.0000811.ref054","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41576-019-0113-7","article-title":"Clinical metagenomics","volume":"20","author":"CY Chiu","year":"2019","journal-title":"Nat Rev Genet"},{"key":"pgph.0000811.ref055","doi-asserted-by":"crossref","first-page":"5409","DOI":"10.1038\/s41598-019-41830-w","article-title":"Illumina sequencing of clinical samples for virus detection in a public health laboratory","volume":"9","author":"B Huang","year":"2019","journal-title":"Sci Rep"}],"container-title":["PLOS Global Public Health"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0000811","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,7,20]],"date-time":"2022-07-20T17:29:06Z","timestamp":1658338146000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgph.0000811"}},"subtitle":[],"editor":[{"given":"Raquel","family":"Mu\u00f1iz-Salazar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,7,20]]},"references-count":55,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2022,7,20]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgph.0000811","relation":{},"ISSN":["2767-3375"],"issn-type":[{"value":"2767-3375","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,7,20]]}}}