{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T20:40:43Z","timestamp":1773866443693,"version":"3.50.1"},"reference-count":50,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2022,1,3]],"date-time":"2022-01-03T00:00:00Z","timestamp":1641168000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"name":"Assistance Publique-H\u00f4pitaux de Paris"},{"DOI":"10.13039\/501100001677","name":"Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001677","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>JC polyomavirus (JCV) mostly causes asymptomatic persistent renal infections but may give rise in immunosuppressed patients to neurotropic variants that replicate in the brain, causing progressive multifocal leukoencephalopathy (PML). Rearrangements in the JCV genome regulator noncoding control region (NCCR) and missense mutations in the viral capsid VP1 gene differentiate neurotropic variants from virus excreted in urine.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>To investigate intrahost emergence of JCV neurotropic populations in PML, we deep sequenced JCV whole genome recovered from cerebrospinal fluid (CSF) and urine samples from 32 human immunodeficiency virus (HIV)\u2013infected and non-HIV-infected PML patients at the single-molecule level.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>JCV strains distributed among 6 of 7 known genotypes. Common patterns of NCCR rearrangements included an initial deletion mostly located in a short 10-nucleotide sequence, followed by duplications\/insertions. Multiple NCCR variants present in individual CSF samples shared at least 1 rearrangement, suggesting they stemmed from a unique viral population. NCCR variants independently acquired single or double PML-specific adaptive VP1 mutations. NCCR variants recovered from urine and CSF displayed opposite deletion or duplication patterns in binding sites for transcription factors.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Long-read deep sequencing shed light on emergence of neurotropic JCV populations in PML.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/infdis\/jiab639","type":"journal-article","created":{"date-parts":[[2021,12,31]],"date-time":"2021-12-31T04:22:50Z","timestamp":1640924570000},"page":"1151-1161","source":"Crossref","is-referenced-by-count":11,"title":["JC Polyomavirus Whole Genome Sequencing at the Single-Molecule Level Reveals Emerging Neurotropic Populations in Progressive Multifocal Leukoencephalopathy"],"prefix":"10.1093","volume":"226","author":[{"given":"Anne Sophie","family":"L\u2019Honneur","sequence":"first","affiliation":[{"name":"Universit\u00e9 de Paris, Institut Cochin, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1016, Unit\u00e9 Mixte de Recherche 8104 , Paris , France"},{"name":"Service de Virologie, H\u00f4pital Cochin, Assistance Publique-H\u00f4pitaux de Paris , Paris , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juliana","family":"Pipoli Da Fonseca","sequence":"additional","affiliation":[{"name":"Plate-forme Technologique Biomics\u2013Centre de Ressources et Recherches Technologiques, Institut Pasteur , Paris , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6286-1138","authenticated-orcid":false,"given":"Thomas","family":"Cokelaer","sequence":"additional","affiliation":[{"name":"Plate-forme Technologique Biomics\u2013Centre de Ressources et Recherches Technologiques, Institut Pasteur , Paris , France"},{"name":"Hub de Bioinformatique et de Biostatistique, D\u00e9partement Biologie Computationnelle, Institut Pasteur , Paris , France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Flore","family":"Rozenberg","sequence":"additional","affiliation":[{"name":"Universit\u00e9 de Paris, Institut Cochin, Institut National de la Sant\u00e9 et de la Recherche M\u00e9dicale U1016, Unit\u00e9 Mixte de Recherche 8104 , Paris , France"},{"name":"Service de Virologie, H\u00f4pital Cochin, Assistance Publique-H\u00f4pitaux de Paris , Paris , France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2022,1,3]]},"reference":[{"key":"2022092817383571800_CIT0001","doi-asserted-by":"crossref","first-page":"e0199171","DOI":"10.1371\/journal.pone.0199171","article-title":"Exploring the role of NCCR variation on JC polyomavirus expression from dual reporter minicircles.","volume":"13","author":"L\u2019Honneur","year":"2018","journal-title":"PLoS 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