{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T19:37:22Z","timestamp":1770925042952,"version":"3.50.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,2,2]],"date-time":"2026-02-02T00:00:00Z","timestamp":1769990400000},"content-version":"vor","delay-in-days":32,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2151959"],"award-info":[{"award-number":["DMS-2151959"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["MCB-2029281"],"award-info":[{"award-number":["MCB-2029281"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["CBET-2030750"],"award-info":[{"award-number":["CBET-2030750"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["OT2OD030524"],"award-info":[{"award-number":["OT2OD030524"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01DK133605"],"award-info":[{"award-number":["R01DK133605"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Deletions are prevalent in the genomes of SARS-CoV-2 isolates from COVID-19 patients, but their roles in the severity, transmission, and persistence of disease are poorly understood. Millions of COVID-19 swab samples from patients have been sequenced and made available online, offering an unprecedented opportunity to study such deletions. Multiplex-PCR sequencing (amplicon-seq) has been the most widely used method for sequencing clinical COVID-19 samples. However, through experiments with negative control samples and existing bioinformatics methods, we find that this protocol introduces large numbers of false-positive deletions. These false positives commonly occur in short alignments, at low frequency and depth, and near primer binding sites used for whole-genome amplification. To address this issue, we developed a filtering strategy, validated with positive control samples containing a known deletion. Our strategy accurately detected the known deletion and removed &amp;gt;99% of false positives in Illumina short-read data from ARTIC amplicon sequencing protocols. This method, applied to public COVID-19 swab data, revealed that deletions occurring independently of transcription regulatory sequences were ~20-fold less common than previously reported; however, they remain more frequent in symptomatic patients. Our optimized approach should enhance the reliability of SARS-CoV-2 deletion characterization from surveillance studies. Finally, our approach may guide the development of bioinformatics pipelines for genome sequence analyses of other viruses.<\/jats:p>","DOI":"10.1093\/ve\/veag003","type":"journal-article","created":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T12:37:59Z","timestamp":1769863079000},"source":"Crossref","is-referenced-by-count":0,"title":["Deletion detection in SARS-CoV-2 genomes from COVID-19 patients: elimination of false positives"],"prefix":"10.1093","volume":"12","author":[{"given":"Nan","family":"Jiang","sequence":"first","affiliation":[{"name":"Wisconsin Institute for Discovery, University of Wisconsin-Madison , 330 N. Orchard St, Madison, WI 53715 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Colin N","family":"Dewey","sequence":"additional","affiliation":[{"name":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , 610 Walnut St, Madison, WI 53726 ,","place":["United States"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6146-0594","authenticated-orcid":false,"given":"John","family":"Yin","sequence":"additional","affiliation":[{"name":"Wisconsin Institute for Discovery, University of Wisconsin-Madison , 330 N. 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