Genome Diversity of Epstein-Barr Virus from Multiple Tumour Types and Normal Infection. Sanger EBV Sequencing Project

Epstein-Barr virus (EBV) infects most of the worlds population and is causally-associated with several human cancers, but little is known about how EBV genetic variation might influence infection or EBV-associated disease. There is currently no published wild-type EBV genome sequence from a healthy individual and very few genomes from EBV-associated diseases. We have sequenced 71 geographically-distinct EBV strains from cell lines, multiple types of primary tumour, blood samples and the first EBV genome from the saliva of a healthy carrier. We show that the established genome map of EBV accurately represents all strains sequenced, but novel deletions are present in a few isolates. We have increased the number of type 2 EBV genomes sequenced from one to 12 and establish that the type 1/type 2 classification is a major feature of EBV genome variation, defined almost exclusively by variation of EBNA2 and EBNA3 genes, but geographic variation is also present. Single nucleotide polymorphism (SNP) density varies substantially across all known open reading frames and is highest in latency-associated genes. Some T–cell epitopes in EBNA3 genes show extensive variation across strains and we identify codons under positive selection, both important considerations for the development of vaccines and T-cell therapy. We also provide new evidence for recombination between strains, which provides a further mechanism for the generation of diversity. Our results provide the first global view of EBV sequence variation and demonstrate an effective method for sequencing large numbers of genomes to further understand the genetics of EBV infection.