Faculty Collaboration Database

Limited Variation in BK Virus T-Cell Epitopes Revealed by Next-Generation Sequencing. J Clin Microbiol 2015 Oct;53(10):3226-33

Date

07/24/2015

Pubmed ID

26202116

Pubmed Central ID

PMC4572525

DOI

10.1128/JCM.01385-15

Scopus ID

2-s2.0-84941978840 (requires institutional sign-in at Scopus site)   18 Citations

Abstract

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.

Author List

Sahoo MK, Tan SK, Chen SF, Kapusinszky B, Concepcion KR, Kjelson L, Mallempati K, Farina HM, Fernández-Viña M, Tyan D, Grimm PC, Anderson MW, Concepcion W, Pinsky BA

MESH terms used to index this publication - Major topics in bold

Adolescent
BK Virus
Child
Child, Preschool
Conserved Sequence
DNA, Viral
Epitopes, T-Lymphocyte
Female
Genetic Variation
Genome, Viral
Humans
Male
Sequence Analysis, DNA
Young Adult