Madhavan H N, Bagyalakshmi R, Revathy M, Aarthi P, Malathi J
L and T, Larsen and Toubro Microbiology Research Centre, Kamal Nayan Bajaj Research Centre, Vision Research Foundation, Chennai, Tamil Nadu, India.
Indian J Med Microbiol. 2015 Feb;33 Suppl:37-42. doi: 10.4103/0255-0857.150878.
To optimise a polymerase chain reaction (PCR) based DNA sequencing technique for genotyping polyoma virus in clinical specimens obtained from renal transplant patients.
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.
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.
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.
优化一种基于聚合酶链反应（PCR）的DNA测序技术，用于对肾移植患者临床标本中的多瘤病毒进行基因分型。
本研究纳入了从肾移植患者收集的130份临床标本（106份外周血和24份尿液），通过针对病毒蛋白1（VP1）基因的PCR检测BK病毒（BKV）、JC病毒（JCV）的DNA存在情况。进行基于PCR的DNA测序以确定多瘤病毒的基因型，并进行生物信息学分析以确定氨基酸序列并筛选VP1基因中的突变。
在23份（17.69%）标本中检测到多瘤病毒，其中19份（82.60%）为BKV阳性，3份（13.04%）为JCV阳性，1份同时为BKV和JCV阳性。基于PCR的DNA测序在12份（50%）临床标本中检测到BKV基因型I，8份（33.3%）中检测到基因型IV，4份（16.6%）中检测到JCV。BKV基因型I是印度南部流行的主要基因型（外周血中占64.2%，尿液中占33.33%）。发现了6个新突变——BKV基因型I的第29、30至47位；BKV基因型IV的第11和15位；JCV的第2和30位。
BKV基因型I是印度的主要基因型，并且首次在文献中报道了在BKV和JCV的VP1基因中检测到的新突变。
