{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,27]],"date-time":"2026-02-27T02:47:00Z","timestamp":1772160420985,"version":"3.50.1"},"reference-count":46,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2022,12,12]],"date-time":"2022-12-12T00:00:00Z","timestamp":1670803200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["75D30121C10094"],"award-info":[{"award-number":["75D30121C10094"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Influenza Resp Viruses"],"published-print":{"date-parts":[[2023,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>COVID\u201019 prevalence has remained high throughout the pandemic with intermittent surges, due largely to the emergence of genetic variants, demonstrating the need for more accessible sequencing technologies for strain typing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>A ligation\u2010based typing assay was developed to detect known variants of severe acute respiratory syndrome virus 2 (SARS\u2010CoV\u20102) by identifying the presence of characteristic single\u2010nucleotide polymorphisms (SNPs). General principles for extending the strategy to new variants and alternate diseases with SNPs of interest are described. Of note, this strategy leverages commercially available reagents for assay preparation, as well as standard real\u2010time polymerase chain reaction (PCR) instrumentation for assay performance.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The assay demonstrated a combined sensitivity and specificity of 96.6% and 99.5%, respectively, for the classification of 88 clinical samples of the Alpha, Delta, and Omicron variants relative to the gold standard of viral genome sequencing. It achieved an average limit of detection of 7.4\u00a0\u00d7\u200910\n                      <jats:sup>4<\/jats:sup>\n                      genome copies\/mL in contrived nasopharyngeal samples. The ligation\u2010based strategy performed robustly in the presence of additional polymorphisms in the targeted regions of interest as shown by the sequence alignment of clinical samples.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The assay demonstrates the potential for robust variant typing with performance comparable with next\u2010generation sequencing without the need for the time delays and resources required for sequencing. The reduced resource dependency and generalizability could expand access to variant classification information for pandemic surveillance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1111\/irv.13083","type":"journal-article","created":{"date-parts":[[2022,12,13]],"date-time":"2022-12-13T02:40:36Z","timestamp":1670899236000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Ligation\u2010based assay for variant typing without sequencing: Application to SARS\u2010CoV\u20102 variants of concern"],"prefix":"10.1111","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6912-2052","authenticated-orcid":false,"given":"Dalton J.","family":"Nelson","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering Vanderbilt University  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Meghan H.","family":"Shilts","sequence":"additional","affiliation":[{"name":"Department of Medicine Vanderbilt University Medical Center  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suman B.","family":"Pakala","sequence":"additional","affiliation":[{"name":"Department of Medicine Vanderbilt University Medical Center  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suman R.","family":"Das","sequence":"additional","affiliation":[{"name":"Department of Medicine Vanderbilt University Medical Center  Nashville Tennessee USA"},{"name":"Vanderbilt Institute for Infection, Immunology and Inflammation Vanderbilt University Medical Center  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonathan E.","family":"Schmitz","sequence":"additional","affiliation":[{"name":"Department of Pathology, Microbiology and Immunology Vanderbilt University Medical Center  Nashville Tennessee USA"},{"name":"Vanderbilt Institute for Infection, Immunology and Inflammation Vanderbilt University Medical Center  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frederick R.","family":"Haselton","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering Vanderbilt University  Nashville Tennessee USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2022,12,12]]},"reference":[{"key":"e_1_2_10_2_1","volume-title":"About COVID\u201019"},{"key":"e_1_2_10_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cmi.2021.05.022"},{"key":"e_1_2_10_4_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2020.27124"},{"key":"e_1_2_10_5_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-021-00408-x"},{"key":"e_1_2_10_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03426-1"},{"key":"e_1_2_10_7_1","article-title":"Estimated transmissibility and impact of SARS\u2010CoV\u20102 lineage B.1.1.7 in England","volume":"372","author":"Davies NG","year":"2021","journal-title":"Science (1979)"},{"key":"e_1_2_10_8_1","doi-asserted-by":"publisher","DOI":"10.1146\/annurev\u2010genom\u2010083115\u2010022628"},{"key":"e_1_2_10_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473\u20103099(21)00170\u20105"},{"key":"e_1_2_10_10_1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2021.1612"},{"key":"e_1_2_10_11_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.06.043"},{"key":"e_1_2_10_12_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00859\u201021"},{"key":"e_1_2_10_13_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.00845\u201021"},{"key":"e_1_2_10_14_1","doi-asserted-by":"publisher","DOI":"10.1128\/Spectrum.00315\u201021"},{"key":"e_1_2_10_15_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.01446\u201021"},{"key":"e_1_2_10_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jviromet.2022.114497"},{"key":"e_1_2_10_17_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2021.104903"},{"key":"e_1_2_10_18_1","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.02513\u201021"},{"key":"e_1_2_10_19_1","doi-asserted-by":"publisher","DOI":"10.1016\/J.JMOLDX.2022.02.001"},{"key":"e_1_2_10_20_1","doi-asserted-by":"publisher","DOI":"10.1515\/cclm\u20102021\u20100889"},{"key":"e_1_2_10_21_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcv.2021.104905"},{"key":"e_1_2_10_22_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.3413476"},{"key":"e_1_2_10_23_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth713"},{"key":"e_1_2_10_24_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jmoldx.2015.07.001"},{"key":"e_1_2_10_25_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.36.2.569\u2010572.1998"},{"key":"e_1_2_10_26_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gnf056"},{"key":"e_1_2_10_27_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.ebiom.2019.11.002"},{"key":"e_1_2_10_28_1","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.4.1413\u20101419.2002"},{"key":"e_1_2_10_29_1","doi-asserted-by":"publisher","DOI":"10.1021\/ACS.ANALCHEM.1C05040"},{"key":"e_1_2_10_30_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-020-0770-5"},{"key":"e_1_2_10_31_1","volume-title":"outbreak.info"},{"key":"e_1_2_10_32_1","volume-title":"CoVariants"},{"key":"e_1_2_10_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0261045"},{"key":"e_1_2_10_34_1","article-title":"Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool","volume":"7","author":"O'Toole \u00c1","year":"2021","journal-title":"Virus Evol"},{"key":"e_1_2_10_35_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv898"},{"key":"e_1_2_10_36_1","volume-title":"Substrate specificity and mismatch discrimination in DNA ligases|NEB"},{"key":"e_1_2_10_37_1","volume-title":"Ligase Probe Rxn|NEB"},{"key":"e_1_2_10_38_1","volume-title":"OligoAnalyzer Tool\u2014Primer Analysis|IDT"},{"key":"e_1_2_10_39_1","volume-title":"GISAID\u2014Mission"},{"key":"e_1_2_10_40_1","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-022-15356-7"},{"key":"e_1_2_10_41_1","volume-title":"Overview of Testing for SARS\u2010CoV\u20102 (COVID\u201019)"},{"key":"e_1_2_10_42_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0145962"},{"key":"e_1_2_10_43_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0041253"},{"key":"e_1_2_10_44_1","doi-asserted-by":"publisher","DOI":"10.1097\/QAI.0b013e31817ed7d7"},{"key":"e_1_2_10_45_1","doi-asserted-by":"publisher","DOI":"10.3390\/mi12101204"},{"key":"e_1_2_10_46_1","doi-asserted-by":"publisher","DOI":"10.1063\/1.4788922"},{"key":"e_1_2_10_47_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0130260"}],"container-title":["Influenza and Other Respiratory Viruses"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/irv.13083","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1111\/irv.13083","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1111\/irv.13083","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,19]],"date-time":"2023-08-19T17:24:35Z","timestamp":1692465875000},"score":1,"resource":{"primary":{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/10.1111\/irv.13083"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,12]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2023,1]]}},"alternative-id":["10.1111\/irv.13083"],"URL":"https:\/\/doi.org\/10.1111\/irv.13083","archive":["Portico"],"relation":{"has-review":[{"id-type":"doi","id":"10.1111\/IRV.13083\/v2\/decision1","asserted-by":"object"},{"id-type":"doi","id":"10.1111\/IRV.13083\/v2\/response1","asserted-by":"object"},{"id-type":"doi","id":"10.1111\/IRV.13083\/v1\/decision1","asserted-by":"object"},{"id-type":"doi","id":"10.1111\/IRV.13083\/v1\/review1","asserted-by":"object"},{"id-type":"doi","id":"10.1111\/IRV.13083\/v1\/review2","asserted-by":"object"}]},"ISSN":["1750-2640","1750-2659"],"issn-type":[{"value":"1750-2640","type":"print"},{"value":"1750-2659","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,12,12]]},"assertion":[{"value":"2022-09-28","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-11-25","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2022-12-12","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e13083"}}