title: Sequencing and analysis of JC virus DNA from natalizumab-treated PML patients.
abstract: BACKGROUND
  Progressive multifocal leukoencephalopathy (PML) in natalizumab-treated MS patients is linked to JC virus (JCV) infection. JCV sequence variation and rearrangements influence viral pathogenicity and tropism. To better understand PML development, we analyzed viral DNA sequences in blood, CSF and/or urine of natalizumab-treated PML patients.
  
  
  METHODS
  Using biofluid samples from 17 natalizumab-treated PML patients, we sequenced multiple isolates of the JCV noncoding control region (NCCR), VP1 capsid coding region, and the entire 5 kb viral genome.
  
  
  RESULTS
  Analysis of JCV from multiple biofluids revealed that individuals were infected with a single genotype. Across our patient cohort, multiple PML-associated NCCR rearrangements and VP1 mutations were present in CSF and blood, but absent from urine-derived virus. NCCR rearrangements occurred in CSF of 100% of our cohort. VP1 mutations were observed in blood or CSF in 81% of patients. Sequencing of complete JCV genomes demonstrated that NCCR rearrangements could occur without VP1 mutations, but VP1 mutations were not observed without NCCR rearrangement.
  
  
  CONCLUSIONS
  These data confirm that JCV in natalizumab-PML patients is similar to that observed in other PML patient groups, multiple genotypes are associated with PML, individual patients appear to be infected with a single genotype, and PML-associated mutations arise in patients during PML development.
authors.affiliation: Biogen Idec Inc., Cambridge, MA 02142, USA. carl.reid@biogenidec.com
authors.forename: Carl E
authors.initials: CE
authors.lastname: Reid
authors.forename: Huo
authors.initials: H
authors.lastname: Li
authors.forename: Gargi
authors.initials: G
authors.lastname: Sur
authors.forename: Paul
authors.initials: P
authors.lastname: Carmillo
authors.forename: Steven
authors.initials: S
authors.lastname: Bushnell
authors.forename: Rich
authors.initials: R
authors.lastname: Tizard
authors.forename: Michele
authors.initials: M
authors.lastname: McAuliffe
authors.forename: Christopher
authors.initials: C
authors.lastname: Tonkin
authors.forename: Kenneth
authors.initials: K
authors.lastname: Simon
authors.forename: Susan
authors.initials: S
authors.lastname: Goelz
authors.forename: Paola
authors.initials: P
authors.lastname: Cinque
authors.forename: Leonid
authors.initials: L
authors.lastname: Gorelik
authors.forename: John P
authors.initials: JP
authors.lastname: Carulli
mesh_terms: D019943:Amino Acid Substitution / Q000235:genetics; D000911:Antibodies, Monoclonal / Q000008:administration & dosage*; D061067:Antibodies, Monoclonal, Humanized; D001769:Blood / Q000821:virology*; D036022:Capsid Proteins / Q000235:genetics; D004279:DNA, Viral / Q000737:chemistry / Q000235:genetics; D006801:Humans; D007155:Immunologic Factors / Q000008:administration & dosage*; D007577:JC Virus / Q000235:genetics* / Q000302:isolation & purification*; D007968:Leukoencephalopathy, Progressive Multifocal / Q000188:drug therapy* / Q000821:virology*; D020125:Mutation, Missense; D000069442:Natalizumab; D017422:Sequence Analysis, DNA
chemical_list: D000911:Antibodies, Monoclonal; D061067:Antibodies, Monoclonal, Humanized; D036022:Capsid Proteins; D004279:DNA, Viral; D007155:Immunologic Factors; D000069442:Natalizumab; C062481:VP1 protein, polyomavirus