Epstein-Barr virus genetic variants are associated with multiple sclerosis

Abstract

Objective: We analyzed the Epstein-Barr nuclear antigen 2 (EBNA2) gene, which contains the most variable region of the viral genome, in persons with multiple sclerosis (MS) and control subjects to verify whether virus genetic variants are involved in disease development.

Methods: A seminested PCR approach and Sanger sequencing were used to analyze EBNA2 in 53 patients and 38 matched healthy donors (HDs). High-throughput sequencing by Illumina MiSeq was also applied in a subgroup of donors (17 patients and 17 HDs). Patients underwent gadolinium-enhanced MRI and human leucocyte antigen typing.

Results: MS risk significantly correlated with an excess of 1.2 allele (odds ratio [OR] = 5.13; 95% confidence interval [CI] 1.84-14.32; p = 0.016) and underrepresentation of 1.3B allele (OR = 0.23; 95% CI 0.08-0.51; p = 0.0006). We identified new genetic variants, mostly 1.2 allele- and MS-associated (especially amino acid variation at position 245; OR = 9.4; 95% CI 1.19-78.72; p = 0.0123). In all cases, the consensus sequence from deep sequencing confirmed Sanger sequencing (including the cosegregation of newly identified variants with known EBNA2 alleles) and showed that the extent of genotype intraindividual variability was higher than expected: rare EBNA2 variants were detected in all HDs and patients with MS (range 1-17 and 3-19, respectively). EBNA2 variants did not seem to correlate with human leucocyte antigen typing or clinical/MRI features.

Conclusions: Our study unveils a strong association between Epstein-Barr virus genomic variants and MS, reinforcing the idea that Epstein-Barr virus contributes to disease development.

© 2015 American Academy of Neurology.

Figures

Figure 1. Potential of Epstein-Barr virus genetic variants to predict multiple sclerosis status

Receiver operating characteristic curve generated by using a Bayesian Network classifier approach that considers sex and Epstein-Barr virus nuclear antigen 2 (EBNA2) genotypes. Area under the curve = 0.715; area under precision-recall curve = 0.633; F measure = 0.640.

Figure 2. EBNA2 position-specific variant frequency observed in sampled healthy donors and individuals with MS

Upper and lower panels report individual EBNA2 variant frequencies detected in healthy donor and multiple sclerosis (MS) samples, respectively, through the Illumina MiSeq amplicon sequencing (negative values are used for MS variants). Each dot indicates the individual-specific frequency of a variant at a given EBNA2 position, colored according to a heat map. Positions shared among different individuals are displayed by multiple dots in the same position.