title: DNA sequencing of viral capsid protein VP-1 region in patients with BK virus interstitial nephritis.
abstract: BACKGROUND
  Mutations in the viral capsid protein VP-1 region are associated with increased pathogenicity of polyomavirus in experimental systems. This study sought to determine whether analogous viral genetic changes occur in human BK virus (BKV) interstitial nephritis (ISN).
  
  
  METHODS
  PCR was used to amplify a 94-bp nucleotide sequence of the viral capsid protein VP-1 region (positions 1740-1833, Dun numbering) in 49 biopsies obtained from 24 patients with BKV-ISN. DNA sequencing was performed by the dideoxy method.
  
  
  RESULTS
  The VP-1 region was highly polymorphic and 22 "hot spots" of sequence variability were noted. Genotypes I, II, and IV were assigned to 13, 1, and 5 cases, respectively, but 5 cases could not be unambiguously classified due to sequence heterogeneity at sites used to discriminate between genotypes. Even in cases where genotypes could be assigned, only 5 biopsies showed complete sequence identity with published genotype sequences. Sequential biopsies showed temporal changes in one or more nucleotides in all patients with multiple samples. In one patient, the initial biopsy showed viral genotype 1, although subsequent biopsies showed complex genetic patterns, including a biopsy consistent with viral genotype IV.
  
  
  CONCLUSIONS
  Many viral strains associated with BKV-ISN are difficult to classify and possibly distinct from those described in kidney transplant recipients without BKV-ISN. VP-1 sequences undergo continual modification as patients are followed in time. This genetic instability could conceivably have implications for evasion of host immunity and development of resistance to antiviral drugs.
authors.affiliation: Division of Transplantation Pathology, Department of Pathology, Children's Hospital of Pittsburgh, Pittsburgh, PA 15213, USA. RANDHAWAPA@MSX.UPMC.EDU
authors.forename: Parmjeet S
authors.initials: PS
authors.lastname: Randhawa
authors.forename: K
authors.initials: K
authors.lastname: Khaleel-Ur-Rehman
authors.forename: Patricia A
authors.initials: PA
authors.lastname: Swalsky
authors.forename: Abhay
authors.initials: A
authors.lastname: Vats
authors.forename: Velma
authors.initials: V
authors.lastname: Scantlebury
authors.forename: Ron
authors.initials: R
authors.lastname: Shapiro
authors.forename: Sydney
authors.initials: S
authors.lastname: Finkelstein
mesh_terms: D001739:BK Virus / Q000235:genetics*; D001483:Base Sequence; D001706:Biopsy; D002213:Capsid / Q000235:genetics*; D036022:Capsid Proteins; D004279:DNA, Viral / Q000737:chemistry*; D005838:Genotype; D006801:Humans; D009395:Nephritis, Interstitial / Q000821:virology*
chemical_list: D036022:Capsid Proteins; D004279:DNA, Viral