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Here, we describe COV-ID, an approach that combines RT-LAMP with deep sequencing to detect SARS-CoV-2 in unprocessed human saliva with a low limit of detection (5\u201310 virions). Based on a multi-dimensional barcoding strategy, COV-ID can be used to test thousands of samples overnight in a single sequencing run with limited labor and laboratory equipment. The sequencing-based readout allows COV-ID to detect multiple amplicons simultaneously, including key controls such as host transcripts and artificial spike-ins, as well as multiple pathogens. Here, we demonstrate this flexibility by simultaneous detection of 4 amplicons in contrived saliva samples: SARS-CoV-2, influenza A, human\n                    <jats:italic>STATHERIN<\/jats:italic>\n                    , and an artificial SARS calibration standard. The approach was validated on clinical saliva samples, where it showed excellent agreement with RT-qPCR. COV-ID can also be performed directly on saliva absorbed on filter paper, simplifying collection logistics and sample handling.\n                  <\/jats:p>","DOI":"10.7554\/elife.69949","type":"journal-article","created":{"date-parts":[[2022,4,25]],"date-time":"2022-04-25T05:15:17Z","timestamp":1650863717000},"update-policy":"https:\/\/doi.org\/10.7554\/elife.69949","source":"Crossref","is-referenced-by-count":9,"title":["A LAMP sequencing approach for high-throughput co-detection of SARS-CoV-2 and influenza virus in human saliva"],"prefix":"10.7554","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4521-0568","authenticated-orcid":true,"given":"Robert","family":"Warneford-Thomson","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00b30xv10","id-type":"ROR","asserted-by":"publisher"}],"name":"Graduate Group in Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine","place":["Philadelphia, United 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