{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T20:40:30Z","timestamp":1773866430480,"version":"3.50.1"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"2","license":[{"start":{"date-parts":[[2009,2,6]],"date-time":"2009-02-06T00:00:00Z","timestamp":1233878400000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1000368","type":"journal-article","created":{"date-parts":[[2009,2,7]],"date-time":"2009-02-07T04:16:13Z","timestamp":1233980173000},"page":"e1000368","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":120,"title":["Adaptive Mutations in the JC Virus Protein Capsid Are Associated with Progressive Multifocal Leukoencephalopathy (PML)"],"prefix":"10.1371","volume":"5","author":[{"given":"Shamil R.","family":"Sunyaev","sequence":"first","affiliation":[]},{"given":"Alexey","family":"Lugovskoy","sequence":"additional","affiliation":[]},{"given":"Kenneth","family":"Simon","sequence":"additional","affiliation":[]},{"given":"Leonid","family":"Gorelik","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2009,2,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1007\/0-387-32957-9_2","article-title":"Discovery and epidemiology of the human polyomaviruses BK virus (BKV) and JC virus (JCV).","volume":"577","author":"WA Knowles","year":"2006","journal-title":"Adv Exp Med Biol"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"5","DOI":"10.3109\/13550289509111006","article-title":"Progressive multifocal leukoencephalopathy: the evolution of a disease once considered rare.","volume":"1","author":"JR Berger","year":"1995","journal-title":"J Neurovirol"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1002\/ajh.20492","article-title":"Changes in the natural history of progressive multifocal leukoencephalopathy in HIV-negative lymphoproliferative disorders: impact of novel therapies.","volume":"80","author":"J Garcia-Suarez","year":"2005","journal-title":"Am J Hematol"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"5672","DOI":"10.1128\/JVI.75.12.5672-5676.2001","article-title":"JC virus regulatory region tandem repeats in plasma and central nervous system isolates correlate with poor clinical outcome in patients with progressive multifocal leukoencephalopathy.","volume":"75","author":"LA Pfister","year":"2001","journal-title":"J Virol"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1128\/CMR.5.1.49","article-title":"Pathogenesis and molecular biology of progressive multifocal leukoencephalopathy, the JC virus-induced demyelinating disease of the human brain.","volume":"5","author":"EO Major","year":"1992","journal-title":"Clin Microbiol Rev"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"1730","DOI":"10.1128\/JVI.62.5.1730-1735.1988","article-title":"DNA rearrangements in organ-specific variants of polyomavirus JC strain GS.","volume":"62","author":"G Loeber","year":"1988","journal-title":"J Virol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"306","DOI":"10.1128\/JVI.53.1.306-311.1985","article-title":"Differences in regulatory sequences of naturally occurring JC virus variants.","volume":"53","author":"JD Martin","year":"1985","journal-title":"J Virol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"2035","DOI":"10.1099\/vir.0.80863-0","article-title":"New sequence polymorphisms in the outer loops of the JC polyomavirus major capsid protein (VP1) possibly associated with progressive multifocal leukoencephalopathy.","volume":"86","author":"HY Zheng","year":"2005","journal-title":"J Gen Virol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1016\/j.bbrc.2005.06.012","article-title":"Characterization of the VP1 loop mutations widespread among JC polyomavirus isolates associated with progressive multifocal leukoencephalopathy.","volume":"333","author":"HY Zheng","year":"2005","journal-title":"Biochem Biophys Res Commun"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"2173","DOI":"10.1007\/s007050070047","article-title":"Lack of disease-specific amino acid changes in the viral proteins of JC virus isolates from the brain with progressive multifocal leukoencephalopathy.","volume":"145","author":"A Kato","year":"2000","journal-title":"Arch Virol"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"2800","DOI":"10.1073\/pnas.0711963105","article-title":"Quantitative biochemical rationale for differences in transmissibility of 1918 pandemic influenza A viruses.","volume":"105","author":"A Srinivasan","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nbt1375","article-title":"Glycan topology determines human adaptation of avian H5N1 virus hemagglutinin.","volume":"26","author":"A Chandrasekaran","year":"2008","journal-title":"Nat Biotechnol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"7925","DOI":"10.1128\/JVI.69.12.7925-7931.1995","article-title":"Genetic and structural analysis of a virulence determinant in polyomavirus VP1.","volume":"69","author":"PH Bauer","year":"1995","journal-title":"J Virol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"5826","DOI":"10.1128\/JVI.73.7.5826-5832.1999","article-title":"Discrimination between sialic acid-containing receptors and pseudoreceptors regulates polyomavirus spread in the mouse.","volume":"73","author":"PH Bauer","year":"1999","journal-title":"J Virol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1128\/JVI.65.1.342-349.1991","article-title":"Polyomavirus replication in mice: influences of VP1 type and route of inoculation.","volume":"65","author":"TW Dubensky","year":"1991","journal-title":"J Virol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1128\/JVI.65.1.350-355.1991","article-title":"A single-amino-acid substitution in polyomavirus VP1 correlates with plaque size and hemagglutination behavior.","volume":"65","author":"R Freund","year":"1991","journal-title":"J Virol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1080\/10635150390235520","article-title":"A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.","volume":"52","author":"S Guindon","year":"2003","journal-title":"Syst Biol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1007\/BF02100115","article-title":"Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea.","volume":"29","author":"H Kishino","year":"1989","journal-title":"J Mol Evol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1093\/oxfordjournals.molbev.a025575","article-title":"A Hidden Markov Model approach to variation among sites in rate of evolution.","volume":"13","author":"J Felsenstein","year":"1996","journal-title":"Mol Biol Evol"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1093\/genetics\/126.1.249","article-title":"Detecting isolation by distance using phylogenies of genes.","volume":"126","author":"M Slatkin","year":"1990","journal-title":"Genetics"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1099\/0022-1317-79-10-2491","article-title":"Phylogenetic analysis of 22 complete genomes of the human polyomavirus JC virus.","volume":"79(Pt 10)","author":"DV Jobes","year":"1998","journal-title":"J Gen Virol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1099\/0022-1317-82-5-1221","article-title":"Genotypes of JC virus in East, Central and Southwest Europe.","volume":"82","author":"HT Agostini","year":"2001","journal-title":"J Gen Virol"},{"key":"ref23","first-page":"555","article-title":"PAML: a program package for phylogenetic analysis by maximum likelihood.","volume":"13","author":"Z Yang","year":"1997","journal-title":"Comput Appl Biosci"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1093\/bioinformatics\/btn313","article-title":"Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models.","volume":"24","author":"AF Poon","year":"2008","journal-title":"Bioinformatics"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"5139","DOI":"10.1093\/emboj\/16.16.5139","article-title":"High-resolution structure of a polyomavirus VP1-oligosaccharide complex: implications for assembly and receptor binding.","volume":"16","author":"T Stehle","year":"1997","journal-title":"Embo J"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"25670","DOI":"10.1074\/jbc.M604421200","article-title":"Identification of the sialic acid structures recognized by minute virus of mice and the role of binding affinity in virulence adaptation.","volume":"281","author":"HJ Nam","year":"2006","journal-title":"J Biol Chem"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"1585","DOI":"10.1093\/oxfordjournals.molbev.a003945","article-title":"Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution.","volume":"18","author":"M Anisimova","year":"2001","journal-title":"Mol Biol Evol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1093\/oxfordjournals.molbev.a004152","article-title":"Accuracy and power of bayes prediction of amino acid sites under positive selection.","volume":"19","author":"M Anisimova","year":"2002","journal-title":"Mol Biol Evol"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"4643","DOI":"10.1128\/JVI.72.6.4643-4649.1998","article-title":"Infection of glial cells by the human polyomavirus JC is mediated by an N-linked glycoprotein containing terminal alpha(2-6)-linked sialic acids.","volume":"72","author":"CK Liu","year":"1998","journal-title":"J Virol"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.1016\/S0140-6736(71)91777-6","article-title":"Cultivation of papova-like virus from human brain with progressive multifocal leucoencephalopathy.","volume":"1","author":"BL Padgett","year":"1971","journal-title":"Lancet"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"244","DOI":"10.1080\/13550280490468663","article-title":"Detection of the archetypal regulatory region of JC virus from the tonsil tissue of patients with tonsillitis and tonsilar hypertrophy.","volume":"10","author":"A Kato","year":"2004","journal-title":"J Neurovirol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"9918","DOI":"10.1128\/JVI.72.12.9918-9923.1998","article-title":"Detection of JC virus DNA in human tonsil tissue: evidence for site of initial viral infection.","volume":"72","author":"MC Monaco","year":"1998","journal-title":"J Virol"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1016\/S0002-9440(10)63132-X","article-title":"Differential distribution of the JC virus receptor-type sialic acid in normal human tissues.","volume":"164","author":"S Eash","year":"2004","journal-title":"Am J Pathol"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1099\/0022-1317-82-4-899","article-title":"Progressive multifocal leukoencephalopathy in human immunodeficiency virus type 1-infected patients: absence of correlation between JC virus neurovirulence and polymorphisms in the transcriptional control region and the major capsid protein loci.","volume":"82","author":"M Sala","year":"2001","journal-title":"J Gen Virol"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","article-title":"T-Coffee: A novel method for fast and accurate multiple sequence alignment.","volume":"302","author":"C Notredame","year":"2000","journal-title":"J Mol Biol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"2531","DOI":"10.1093\/bioinformatics\/bti320","article-title":"Datamonkey: rapid detection of selective pressure on individual sites of codon alignments.","volume":"21","author":"SL Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1093\/bioinformatics\/bti079","article-title":"HyPhy: hypothesis testing using phylogenies.","volume":"21","author":"SL Pond","year":"2005","journal-title":"Bioinformatics"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/1743-422X-3-3","article-title":"Comparison of real-time PCR and hemagglutination assay for quantitation of human polyomavirus JC.","volume":"3","author":"ML Chapagain","year":"2006","journal-title":"Virol J"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1093\/infdis\/127.4.467","article-title":"Prevalence of antibodies in human sera against JC virus, an isolate from a case of progressive multifocal leukoencephalopathy.","volume":"127","author":"BL Padgett","year":"1973","journal-title":"J Infect Dis"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"779","DOI":"10.1006\/jmbi.1993.1626","article-title":"Comparative protein modelling by satisfaction of spatial restraints.","volume":"234","author":"A Sali","year":"1993","journal-title":"J Mol Biol"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1002\/jcc.540040211","article-title":"CHARMM: A program for macromolecular energy, minimization, and dynamics calculations.","volume":"4","author":"BR Brooks","year":"1983","journal-title":"Journal of Computational Chemistry"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1000368","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,10,1]],"date-time":"2021-10-01T04:16:48Z","timestamp":1633061808000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1000368"}},"subtitle":[],"editor":[{"given":"Harmit S.","family":"Malik","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2009,2,6]]},"references-count":41,"journal-issue":{"issue":"2","published-online":{"date-parts":[[2009,2,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1000368","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2009,2,6]]}}}