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

Abstract

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.

BK Polyomavirus: Clinical Aspects, Immune Regulation, and Emerging Therapies

“…Using this highly innovative approach, Cioni et al successfully expanded the list of BKV T cell epitopes to at least 39, among which 21 epitopes were further confirmed by HLA peptide streptamer staining (105). Sahoo et al assessed genetic variability in sections of the BKV genome coding for T cell epitopes, demonstrating very limited variability (less than 5%) in a cohort of 65 samples (106). Cioni and colleagues demonstrated that some of the epitopes they identified shared strong homology with JC polyomavirus (JCV) (105).…”

BK polyomavirus genotypes in renal transplant recipients in the United States: A meta‐analysis

“…After exclusion of 231 articles based on title and abstract for clearly not fulfilling inclusion criteria due to type of article, study design, population or outcome of interest, and 47 articles excluded due to being duplicates, 71 articles were left for full‐length review. Subsequently, 63 articles were additionally excluded (25 articles did not report the outcome of interest; 17 were not observational studies; and 21 articles were excluded because they were from countries outside the United States and/or consisted of a pediatric population). Thus, eight observational studies with a total of 193 samples (urine, blood, and kidney tissues) from 188 BKV‐infected KTX adult recipients in the United States were enrolled.…”

BK nephropathy in the native kidneys of patients with organ transplants: Clinical spectrum of BK infection

“…This factor is involved in a complex regulatory pathway that can affect the course of BKV infection[ 375 ]. The genetic variation of BKV strains is limited[ 425 ]. In HLA-A*0201 individuals, cytotoxic T-cell lymphocyte (CTL) responses are elicited towards two of the VP1 epitopes, VP1(p44) and VP1(p108)[ 347 ].…”