Table 2.

JCV VP1 Amino Acid Substitutions in Sequences Derived From Paired Urine, Cerebrospinal Fluid (CSF), and Plasma Samples From PML Patients

	Patient ID	Sample	JCV subtypea	PML-associated substitution	No. of clones with substitution/no. of clones analyzed
1	5067	Urine	1A	none	0/11
	5067	CSF	1A	H122R	27/27
	5067	Plasma	1A	H122R	28/28
2	5167	Urine	2B-v69D,128A	none	0/23
	5167	CSF	2B-v69D,128A	S267Y	PCRb
	5167	Plasma	2B-v69D,128A	S267Y	42/44
3	5166	Urine	1A	none	0/29
	5166	CSF	1A	S269F	14/14
	5166	Plasma	1A	S269Fc	18/21
4	5174	Urine	1B	none	0/19
	5174	CSF	1B	S269F	28/28
	5174	Plasma	1B	S269F	37/38
5	5180	Urine	1A	none	PCR
	5180	CSF	1A	S269F	PCR
	5180	Plasma	1A	S269F	PCR
6	5211	Urine	2B	none	PCR
	5211	CSF	2B	none	PCR
	5211	Plasma	N	NA	NA
7	5087	Urine	1B	none	0/11
	5087	CSF	1B	L55F	19/19
	5087	Plasma	NA	NA	NA
8	5152	Urine	1A	none	0/3
	5152	CSF	1A	H122R; A2V	44/46; 45/46
	5152	Plasma	NA	NA	NA
9	5088	Urine	NA	NA	NA
	5088	CSF	4-v164K	none	0/3
	5088	Plasma	4-v164K	none	0/24
10	5092	Urine	NA	NA	NA
	5092	CSF	1A	L55F	20/20
	5092	Plasma	1A	L55F	PCR
11	5108	Urine	NA	NA	NA
	5108	CSF	4-v128A,345K	L55F	24/24
	5108	Plasma	4-v128A,345K	L55F	30/30
12	5201	Urine	NA	NA	NA
	5201	CSF	1B	K60N	PCR
	5201	Plasma	1B	K60N	PCR
13	5029	Urine	NA	NA	NA
	5029	CSF	2B-v74T,345K	S269F	21/22
	5029	Plasma	2B-v74T,345K	S269F	19/19
14	5060	Urine	NA	NA	NA
	5060	CSF	2B	S269F	23/23
	5060	Plasma	2B	S269F	31/31
15	5121	Urine	NA	NA	NA
	5121	CSF	1B-v117T	S269F	41/41
	5121	Plasma	1B-v117T	S269F	12/12
16	5207	Urine	NA	NA	NA
	5207	CSF	1B	Q271H	PCR
	5207	Plasma	1B	Q271H	PCR
17	5163	Urine	4-v164K	none	0/24
	5163	CSF	NA	NA	NA
	5163	Plasma	4-v164K	L55Fd	32/32

NOTE. JCV indicates JC virus; VP1, viral protein 1; PML, progressive multifocal leukoencephalopathy; PCR, polymerase chain reaction; NA, sequence not available.

^aAccording to [8]. The subgroup, followed by “v” and position, means subgroup variant and polymorphism relative to that subtype.

^bPCR sequence information was obtained directly from a PCR product without cloning.

^cS267F also identified in 3/21 clones.

^dS267P also identified in 2/32 clones.