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Ganciclovir and valganciclovir (GCV\/VGCV) improve long-term audiologic and neurodevelopmental outcomes for patients with cCMV infection; however, antiviral drug resistance has been documented in some cases. Long-read sequencing can be used for the detection of drug resistance mutations. The objective of this study was to develop full-length analysis of <jats:italic>UL97<\/jats:italic> and <jats:italic>UL54<\/jats:italic>, target genes with mutations that confer GCV\/VGCV resistance using long-read sequencing, and investigate drug resistance mutation in patients with cCMV infection.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Drug resistance mutation analysis was retrospectively performed in 11 patients with cCMV infection treated with GCV\/VGCV. <jats:italic>UL97<\/jats:italic> and <jats:italic>UL54<\/jats:italic> genes were amplified using blood DNA. The amplicons were sequenced using a long-read sequencer and aligned with the reference gene. Single nucleotide variants were detected and replaced with the reference sequence. The replaced sequence was submitted to a mutation resistance analyzer, which is an open platform for drug resistance mutations.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Two drug resistance mutations (<jats:italic>UL54<\/jats:italic> V823A and <jats:italic>UL97<\/jats:italic> A594V) were found in one patient. Both mutations emerged after 6\u2009months of therapy, where viral load increased. Mutation rates subsided after cessation of GCV\/VGCV treatment.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>Antiviral drug resistance can emerge in patients with cCMV receiving long-term therapy. Full-length analysis of <jats:italic>UL97<\/jats:italic> and <jats:italic>UL54<\/jats:italic> via long-read sequencing enabled the rapid and comprehensive detection of drug resistance mutations.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12879-022-07537-6","type":"journal-article","created":{"date-parts":[[2022,6,22]],"date-time":"2022-06-22T13:03:10Z","timestamp":1655902990000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":14,"title":["Detection of antiviral drug resistance in patients with congenital cytomegalovirus infection using long-read sequencing: a retrospective observational study"],"prefix":"10.1186","volume":"22","author":[{"given":"Yuka","family":"Torii","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazuhiro","family":"Horiba","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jun-ichi","family":"Kawada","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kazunori","family":"Haruta","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makoto","family":"Yamaguchi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takako","family":"Suzuki","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hideko","family":"Uryu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naoyuki","family":"Kashiwa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Keiji","family":"Goishi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tomoo","family":"Ogi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yoshinori","family":"Ito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2022,6,22]]},"reference":[{"key":"7537_CR1","doi-asserted-by":"publisher","first-page":"196","DOI":"10.1016\/j.jpeds.2018.04.043","volume":"200","author":"KB Fowler","year":"2018","unstructured":"Fowler KB, Ross SA, Shimamura M, Ahmed A, Palmer AL, Michaels MG, Bernstein DI, S\u00e1nchez PJ, Feja KN, Stewart A et al: Racial and ethnic differences in the prevalence of congenital cytomegalovirus infection. 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Written informed consent was obtained from a parent or legal guardian for participants.  This study was carried out in compliance with the Declaration of Helsinki guidelines.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"568"}}