Epstein–Barr virus latent gene sequences as geographical markers of viral origin: unique EBNA3 gene signatures identify Japanese viruses as distinct members of the Asian virus family

Abstract

Polymorphisms in Epstein-Barr virus (EBV) latent genes can identify virus strains from different human populations and individual strains within a population. An Asian EBV signature has been defined almost exclusively from Chinese viruses, with little information from other Asian countries. Here we sequenced polymorphic regions of the EBNA1, 2, 3A, 3B, 3C and LMP1 genes of 31 Japanese strains from control donors and EBV-associated T/NK-cell lymphoproliferative disease (T/NK-LPD) patients. Though identical to Chinese strains in their dominant EBNA1 and LMP1 alleles, Japanese viruses were subtly different at other loci. Thus, while Chinese viruses mainly fall into two families with strongly linked 'Wu' or 'Li' alleles at EBNA2 and EBNA3A/B/C, Japanese viruses all have the consensus Wu EBNA2 allele but fall into two families at EBNA3A/B/C. One family has variant Li-like sequences at EBNA3A and 3B and the consensus Li sequence at EBNA3C; the other family has variant Wu-like sequences at EBNA3A, variants of a low frequency Chinese allele 'Sp' at EBNA3B and a consensus Sp sequence at EBNA3C. Thus, EBNA3A/B/C allelotypes clearly distinguish Japanese from Chinese strains. Interestingly, most Japanese viruses also lack those immune-escape mutations in the HLA-A11 epitope-encoding region of EBNA3B that are so characteristic of viruses from the highly A11-positive Chinese population. Control donor-derived and T/NK-LPD-derived strains were similarly distributed across allelotypes and, by using allelic polymorphisms to track virus strains in patients pre-and post-haematopoietic stem-cell transplant, we show that a single strain can induce both T/NK-LPD and B-cell-lymphoproliferative disease in the same patient.

Epstein-Barr virus genetic variants are associated with multiple sclerosis

“…In all cases, the consensus sequence deriving from deep sequencing coincided with the one determined by Sanger sequencing, confirming the cosegregation of newly identified variants with the known EBNA2 alleles. We also found one or more variable positions in all HDs (1-17) and individuals with MS (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17)(18)(19). For all couples of variants lying on the same read (coverage $50), the hypothesis of independent segregation, indicative of random sequencing errors, was rejected through a x 2 test (p , 0.05), thus supporting the coexistence of different genotypes.…”

“…15 Different patterns of EBV genetic variations in different geographic regions could account for inconsistencies, as suggested by the different geographic distributions of EBV-related malignancies. [3][4][5] By investigating a region of EBNA2 that previous studies in MS cohorts did not investigate, we have detected MS-associated EBV genetic variations that are stronger than those previously reported and seem to be independent of the donors' HLA haplotype.…”

“…1 The potential pathogenic role of EBV genetic variants in MS may be in keeping with epidemiologic observations, in particular the geographic gradient of MS and the change in MS risk in migrants, 2 and with the reported association between virus genetic variants and EBV-related malignancies with different geographic distribution. [3][4][5] Also, the discrepancy between the global diffusion of EBV infection and the low prevalence of MS could be at least in part explained by EBV genomic diversity that differently affects MS development.…”

Epstein–Barr Virus: From the Detection of Sequence Polymorphisms to the Recognition of Viral Types

“…Dots indicate amino acid identity. Light gray slashes signify amino acid deletion (Sawada et al 2011). Such a heterogeneity is hardly visible in type 2 viruses.…”

“…In contrast to the EBNA2 1.1b that is common between isolates from China and Japan, the EBNA3 alleles found in Japanese healthy and diseased individuals slightly differ. These sub-alleles are called Wu′ and Li′, Li′′ and differ from their Chinese relatives by one or two point mutations (Sawada et al 2011) (Fig. 6a).…”