{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,17]],"date-time":"2026-09-17T03:37:38Z","timestamp":1789616258350,"version":"build-2803163510"},"reference-count":36,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T00:00:00Z","timestamp":1702944000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/doi.org\/10.1128\/ASMCopyrightv2"},{"start":{"date-parts":[[2023,12,19]],"date-time":"2023-12-19T00:00:00Z","timestamp":1702944000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100013213","name":"ARUP Institute for Clinical and Experimental Pathology","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013213","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2023,12,19]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>Cytomegalovirus (CMV) resistance testing by targeted next-generation sequencing (NGS) allows for the simultaneous analysis of multiple genes. We developed and validated an amplicon-based Ion Torrent NGS assay to detect CMV resistance mutations in UL27, UL54, UL56, and UL97 and compared the results to standard Sanger sequencing. NGS primers were designed to generate 83 overlapping amplicons of four CMV genes (~10 kb encompassing 138 mutation sites). An open-access software plugin was developed to perform read alignment, call variants, and interpret drug resistance. Plasmids were tested to determine NGS error rate and minor variant limit of detection. NGS limit of detection was determined using the CMV WHO International Standard and quantified clinical specimens. Reproducibility was also assessed. After establishing quality control metrics, 185 patient specimens previously tested using Sanger were reanalyzed by NGS. The NGS assay had a low error rate (&lt;0.05%) and high accuracy (95%) for detecting CMV-associated resistance mutations present at \u22655% in contrived mixed populations. Mutation sites were reproducibly sequenced with 40\u00d7 coverage when plasma viral loads were \u22652.6 log IU\/mL. NGS detected the same resistance-associated mutations identified by Sanger in 68\/69 (98.6%) specimens. In 16 specimens, NGS detected 18 resistance mutations that Sanger failed to detect; 14 were low-frequency variants (&lt;20%), and six would have changed the drug resistance interpretation. The NGS assay showed excellent agreement with Sanger and generated high-quality sequence from low viral load specimens. Additionally, the higher resolution and analytic sensitivity of NGS potentially enables earlier detection of antiviral resistance.<\/jats:p>","DOI":"10.1128\/jcm.00829-23","type":"journal-article","created":{"date-parts":[[2023,11,21]],"date-time":"2023-11-21T14:00:16Z","timestamp":1700575216000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":22,"title":["Development and validation of a next-generation sequencing assay with open-access analysis software for detecting resistance-associated mutations in CMV"],"prefix":"10.1128","volume":"61","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-7980-0620","authenticated-orcid":true,"given":"Melanie A.","family":"Mallory","sequence":"first","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weston C.","family":"Hymas","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keith E.","family":"Simmon","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2562-0073","authenticated-orcid":true,"given":"Michael T.","family":"Pyne","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jeffery B.","family":"Stevenson","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adam P.","family":"Barker","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"},{"name":"Department of Pathology, University of Utah , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R.","family":"Hillyard","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"},{"name":"Department of Pathology, University of Utah , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9790-277X","authenticated-orcid":true,"given":"Kimberly E.","family":"Hanson","sequence":"additional","affiliation":[{"name":"ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories , Salt Lake City, Utah, USA"},{"name":"Department of Pathology, University of Utah , Salt Lake City, Utah, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_5_2_2","article-title":"Cytomegalovirus infection in transplant recipients: newly approved additions to our armamentarium","author":"Khawaja F","year":"2022","unstructured":"Khawaja F , Spallone A , Kotton CN , Chemaly RF . 2022. 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