Overview of JC virus NCCR rearrangements (i.e. deletions and insertions) identified by Sanger sequencing and 454 sequencing.

Comparison of the consensus NCCR as determined by Sanger sequencing (n = 61) revealed four distinct groups of samples: 1) archetype sequences with no DNA rearrangements compared to the reference NCCR (CY isolate), 2) samples harboring polymorphic deletions, 3) samples carrying polymorphic insertions and 4) sample harboring both a deletion and an insertion. 454 sequencing was further applied (n = 54) to identify JCV quasispecies. Healthy subject (HS) samples in which quasispecies were identified, the nature of the minority sequences contributing to the quasispecies and the percentage of viral NCCR sequences harboring the minority sequences are indicated. The sequence blocks (a to f) affected by the NCCR rearrangements are indicated between brackets. Of note, HS11 carries a 1 bp deletion at position 165 that in ∼1.5% of the viral population is part of a more extensive deletion. The numbering scheme is based on [12].