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Table 2 BKV VP1 subtypes in renal patients detected by MS

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

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     
  1. 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.