Human Polyomavirus JC monitoring and noncoding control region analysis in dynamic cohorts of individuals affected by immune-mediated diseases under treatment with biologics: an observational study

Table 5 NCCR analysis in samples collected from Crohn’s Disease and Multiple Sclerosis patients

A. Crohn’s Disease patients
Samples	N° JCPyV positive samples	N° archetype* (%) (IIS)^†	*37 T→G and 217 G→A (IIS)*** ^†	N° rearranged NCCR sequences (%)
Samples	N° JCPyV positive samples	N° archetype* (%) (IIS)^†	*37 T→G and 217 G→A (IIS)*** ^†	*37 T→G , 217 G→A and boxD deletion (IIR)*** ^†	*Mad1-like sequence (IR)* ^†
Urine	34	34 (100%)	0	0	0
Plasma	28	20 (71%)	8 (29%)	0	0
Ileum	21	10 (47%)	7 (33%)	4 (20%)	0
Colon-rectum	16	8 (50%)	5 (32%)	1 (6%)	2 (12%)
Total (%)	99	72 (72%)	20 (21%)	5 (5%)	2 (2%)
B. Multiple Sclerosis patients
Samples	N° JCPyV positive samples	*N° archetype (%) (IIS)** ^†	N° rearranged NCCR sequences (%)
Samples	N° JCPyV positive samples	*N° archetype (%) (IIS)** ^†	*duplication of a 98bp unit and 66bp insert (boxD)(IIR)* ^†
Urine	13	13 (100%)	0
Plasma	7	7 (100%)	0
PBMC	3	1 (33%)	2 (67%)
Total (%)	23	21 (91%)	2 (9%)

* JCPyV archetype CY[38] with random occurrence of few point mutations and constant G to A transition at position nucleotide number 217 in the boxF.
** T to G transversion at position nucleotide number 37 in the box A within Spi-B binding site, and G to A transition at position nucleotide number 217 in the boxF considering the nucleotide numbering based on non-pathogenic JCPyV archetype CY[38].
† Jensen and Major (2001) NCCR forms classification is also reported[35].

ISSN: 1743-422X