Detection of BK virus in urine from renal transplant subjects by mass spectrometry

Table 2 BKV VP1 subtypes in renal patients detected by MS

Patient	decoy cells	qPCR titer	dominant subtype	Sequence coverage VP1	aa	unique Peptides detected from dominant infection	co-infection subtype	Sequence coverage VP1	aa	unique Peptides detected from co-infection
3	> 10	negative	Ic	21%	40–64	K.TGVDAITEVECFLNPEMGDPDENLR.G
					173–195	K.YPEGTITPKNPTAQSQVMNTDHK.A
5	>10	3.1×10⁵	Ib-1	74%	171–181	R.TKYPDGTITPK.N	IV	40%	94–135	R.IPLPNLNEDLTCGNLLMWEAVTVKTEVIGITSMLNLHAGSQK.V
7	>100	4.1×10³	Ib-2	60%	40–64	K.TGLDAITEVECFLNPEMGDPDENLR.G	Ib-1	51%	171–181	R.TKYPDGTITPK.N
8	>10	2.0×10⁴	IV	55%	40–64	K.TGVDAITEVECFLNPEMGDPDNDLR.G	Ic	37%	334–349	R.VFDGTEKLPGDPDMIR.Y
9	>100	1.4×10³	Ib-2	22%	40–69	K.TGLDAITEVECFLNPEMGDPDENLRGFSLK.L
10	<5–10	not done	Ib-2,Ic	20%	70–84	K.LSAENDFSSDSPERK.M
11	>10	negative	Ia,Ib-1	46%	40–64	K.TGVDAITEVECFLNPEMGDPDENLR.G	IV	29%	94–135	R.IPLPNLNEDLTCGNLLMWEAVTVKTEVIGITSMLNLHAGSQK.V
					221–256	R.YFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCK.A
13	>100	2.2×10⁴	Ib-2	72%	40–64	K.TGLDAITEVECFLNPEMGDPDENLR.G	IV	53%	350–360	R.YIDRQGQLQTK.M
14	negative	negative	Ib-2	35%	40–64	K.TGLDAITEVECFLNPEMGDPDENLR.G
15	>10	2.4×10⁴	IV	64%	40–64	K.TGVDAITEVECFLNPEMGDPDNDLR.G	Ic	42%	334–349	R.VFDGTEKLPGDPDMIR.Y
16	>10	not done	Ia, Ib-1	56%	201–215	K.NNAYPVECWVPDPSR.N	IV	23%	94–135	R.IPLPNLNEDLTCGNLLMWEAVTVKTEVIGITSMLNLHAGSQK.V
17	<5	5×10¹		not detected		not detected
18	>10	1.9×10⁴	Ia, Ib-1,Ic	19%	40–69	K.TGVDAITEVECFLNPEMGDPDENLRGFSLK.L
19	>10	negative	Ia, Ib-1	64%	40–64	K.TGVDAITEVECFLNPEMGDPDENLR.G	IV	44%	40–64	K.TGVDAITEVECFLNPEMGDPDNDLR.G
					221–256	R.YFGTFTGGENVPPVLHVTNTATTVLLDEQGVGPLCK.A

For those subjects in whom peptides from VP1 were detected the number of decoy cells, the viral load in serum samples, the dominant viral subtype identified, and percent sequence coverage of VP1 protein are listed. Serum samples were collected within 2 weeks of the urine sample (except for patient 9 where the interval was 4 months). The peptides identified that defined the dominant viral subtype (based on greater BKV VP1 protein sequence coverage) are shown. In some cases the presence of two peptides gave evidence for a precise subtype specification. Further, peptides demonstrating the presence of co-infection with a different viral subtype are also shown where co-infection was observed. Residues highlighted in bold differ between the subtype groups Ia,Ib-1, Ic or Ib-2 or IV.

ISSN: 1559-0275