title: Optimisation and analysis of polymerase chain reaction based DNA sequencing for genotyping polyoma virus in renal transplant patients: a report from South India.
abstract: OBJECTIVE
  To optimise a polymerase chain reaction (PCR) based DNA sequencing technique for genotyping polyoma virus in clinical specimens obtained from renal transplant patients.
  
  
  METHODS
  A hundred and thirty (106 peripheral blood and 24 urine) clinical specimens collected from renal transplant patients were included in the study for detecting the presence of  DNA of BK virus (BKV), JC virus (JCV) by PCR targeting the viral protein 1 (VP1) gene. PCR based DNA sequencing was performed to determine the genotypes of polyoma virus and subjected to bioinformatics analysis to determine the amino acid sequences and screen for mutations in the VP1 gene.
  
  
  RESULTS
  Polyoma virus was detected in 23 (17.69%) specimens of which 19 (82.60%) were positive for BK virus, 3 (13.04%) for JC virus and 1 for both BK and JC virus. PCR based DNA sequencing detected BK virus genotype I in 12 (50%), genotype IV in 8 (33.3%) and JC virus in 4 (16.6%) clinical specimens. BKV genotype I was the predominant genotype (64.2% in peripheral blood and 33.33% in urine) prevalent in south India. Six novel mutations were found--at position 29, 30 to 47 of BKV genotype I; at position 11 and 15 of BKV genotype IV and at position 2 and 30 of JCV.
  
  
  CONCLUSIONS
  BKV genotype I is the prominent genotype in India and novel mutations detected in the VP1 gene of BKV and JCV are being reported for the first time in literature.
authors: L and T, Larsen and Toubro Microbiology Research Centre, Kamal Nayan Bajaj Research Centre, Vision Research Foundation, Chennai, Tamil Nadu, India.
authors: H N
authors: HN
authors: Madhavan
authors: R
authors: R
authors: Bagyalakshmi
authors: M
authors: M
authors: Revathy
authors: P
authors: P
authors: Aarthi
authors: J
authors: J
authors: Malathi
mesh_terms: D000595:Amino Acid Sequence; D001739:BK Virus / Q000235:genetics; D036022:Capsid Proteins / Q000737:chemistry / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods / Q000592:standards; D006801:Humans; D007194:India; D007577:JC Virus / Q000235:genetics; D016030:Kidney Transplantation / Q000009:adverse effects*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D011120:Polyomavirus / Q000145:classification* / Q000235:genetics*; D027601:Polyomavirus Infections / Q000175:diagnosis* / Q000821:virology*; D060888:Real-Time Polymerase Chain Reaction; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D036022:Capsid Proteins; C062481:VP1 protein, polyomavirus