Genomic mutations of viral protein 1 and BK virus nephropathy in kidney transplant recipients

Boldorini, Renzo; Allegrini, Sara; Miglio, Umberto; Paganotti, Alessia; Veggiani, Claudia; Mischitelli, Monica; Monga, Guido; Pietropaolo, Valeria

doi:10.1002/jmv.21520

Cited by 31 publications

(23 citation statements)

References 18 publications

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“…In these studies, variants were described, but an association with end-organ disease was not always found. In one study, single base-pair mutations were detected more frequently in samples from patients with BK nephropathy, but amino acid changes were randomly distributed in BK nephropathy patients and controls (28). Other studies have identified amino acid changes in the external loops of VP1, which mediate BKV attachment to target cells but did not find an association with viral load or incidence of BK nephropathy (29,30).…”

Section: Discussionmentioning

confidence: 98%

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing

et al. 2015

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f BK virus (BKV) infection causing end-organ disease remains a formidable challenge to the hematopoietic cell transplant (HCT) and kidney transplant fields. As BKV-specific treatments are limited, immunologic-based therapies may be a promising and novel therapeutic option for transplant recipients with persistent BKV infection. Here, we describe a whole-genome, deep-sequencing methodology and bioinformatics pipeline that identify BKV variants across the genome and at BKV-specific HLA-A2-, HLA-B0702-, and HLA-B08-restricted CD8 T-cell epitopes. BKV whole genomes were amplified using long-range PCR with four inverse primer sets, and fragmentation libraries were sequenced on the Ion Torrent Personal Genome Machine (PGM). An error model and variant-calling algorithm were developed to accurately identify rare variants. A total of 65 samples from 18 pediatric HCT and kidney recipients with quantifiable BKV DNAemia underwent whole-genome sequencing. Limited genetic variation was observed. The median number of amino acid variants identified per sample was 8 (range, 2 to 37; interquartile range, 10), with the majority of variants (77%) detected at a frequency of <5%. When normalized for length, there was no statistical difference in the median number of variants across all genes. Similarly, the predominant virus population within samples harbored T-cell epitopes similar to the reference BKV strain that was matched for the BKV genotype. Despite the conservation of epitopes, low-level variants in T-cell epitopes were detected in 77.7% (14/18) of patients. Understanding epitope variation across the whole genome provides insight into the virus-immune interface and may help guide the development of protocols for novel immunologic-based therapies.

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Section: Discussionmentioning

confidence: 98%

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing

et al. 2015

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“…However, it remains to be determined whether even greater variation in MWPyV can be discovered when broader consensus sequence-based assays are used. Others have speculated that sequence variation in BKPyV and JCPyV plays a role in viral pathogenesis and disease severity (4,44). If MWPyV is ultimately found to be a pathogen, it will be interesting to determine whether there are strain-dependent pathogenic phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Siebrasse

Reyes

Lim

et al. 2012

J Virol

169

152

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We have discovered a novel polyomavirus present in multiple human stool samples. The virus was initially identified by shotgun pyrosequencing of DNA purified from virus-like particles isolated from a stool sample collected from a healthy child from Malawi. We subsequently sequenced the virus' 4,927-bp genome, which has been provisionally named MW polyomavirus (MWPyV). The virus has genomic features characteristic of the family Polyomaviridae but is highly divergent from other members of this family. It is predicted to encode the large T antigen and small T antigen early proteins and the VP1, VP2, and VP3 structural proteins. A real-time PCR assay was designed and used to screen 514 stool samples from children with diarrhea in St. Louis, MO; 12 specimens were positive for MWPyV. Comparison of the whole-genome sequences of the index Malawi case and one St. Louis case demonstrated that the two strains of MWPyV varied by 5.3% at the nucleotide level. The number of polyomaviruses found in the human body continues to grow, raising the question of how many more species have yet to be identified and what roles they play in humans with and without manifest disease.

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“…The main BKV genomic regions depicted as showing sequence divergence are those encoding the VP1 capsid protein and the large T antigen (22,23), while the StAg gene is described as displaying only a few single nucleotide polymorphisms (24). However, despite our assumption that choosing the StAg gene as a PCR target for our in-house PCR would provide a less variable technique for quantification, discrepant BKVL results were observed for some individuals due to mutations at positions G4830A, A4836T, G4876A, and G4877A.…”

Section: Discussionmentioning

confidence: 99%

Toward Standardization of BK Virus Monitoring: Evaluation of the BK Virus R-gene Kit for Quantification of BK Viral Load in Urine, Whole-Blood, and Plasma Specimens

et al. 2014

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Screening of BK virus (BKV) replication is recommended to identify patients at increased risk of BKV-associated diseases. However, the heterogeneity of molecular techniques hinders the establishment of universal guidelines for BKV monitoring. Here we aimed to compare the performance of the CE-marked BK virus R-gene kit (R-gene) to the performance of our in-house assay for quantification of BKV DNA loads (BKVL). A 12-specimen panel from the Quality Control for Molecular Diagnostics (QCMD) organization, 163 urine samples, and 88 paired specimens of plasma and whole blood (WB) from transplant recipients were tested. Both the R-gene and in-house assays showed a good correlation within the QCMD panel (r ‫؍‬ 0.995 and r ‫؍‬ 0.989, respectively). BKVL were highly correlated between assays, although positive biases were observed with the in-house assay in analysis of urine (0.72 ؎ 0.83 log 10 copies/ml), plasma (1.17 ؎ 0.63 log 10 copies/ml), and WB (1.28 ؎ 0.37 log 10 copies/ml). Recalibration with a common calibrator significantly reduced the bias in comparisons between assays. In contrast, BKVL was underestimated with the in-house PCR in eight samples containing BKV genotype II, presenting point mutations at primer-annealing sites. Using the R-gene assay, plasma and WB specimens were found to be equally suitable for quantification of BKVL, as indicated by the high correlation coefficient (r ‫؍‬ 0.965, P < 0.0001). In conclusion, the R-gene assay demonstrated reliable performance and higher accuracy than the in-house assay for quantification of BKVL in urine and blood specimens. Screening of BKV replication by a well-validated commercial kit may enable clinical laboratories to assess viral loads with greater reproducibility and precision.

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Genomic mutations of viral protein 1 and BK virus nephropathy in kidney transplant recipients

Cited by 31 publications

References 18 publications

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing

Identification of MW Polyomavirus, a Novel Polyomavirus in Human Stool

Toward Standardization of BK Virus Monitoring: Evaluation of the BK Virus R-gene Kit for Quantification of BK Viral Load in Urine, Whole-Blood, and Plasma Specimens

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