Early Epstein-Barr Virus Genomic Diversity and Convergence toward the B95.8 Genome in Primary Infection

Abstract

Over 90% of the world's population is persistently infected with Epstein-Barr virus. While EBV does not cause disease in most individuals, it is the common cause of acute infectious mononucleosis (AIM) and has been associated with several cancers and autoimmune diseases, highlighting a need for a preventive vaccine. At present, very few primary, circulating EBV genomes have been sequenced directly from infected individuals. While low levels of diversity and low viral evolution rates have been predicted for double-stranded DNA (dsDNA) viruses, recent studies have demonstrated appreciable diversity in common dsDNA pathogens (e.g., cytomegalovirus). Here, we report 40 full-length EBV genome sequences obtained from matched oral wash and B cell fractions from a cohort of 10 AIM patients. Both intra- and interpatient diversity were observed across the length of the entire viral genome. Diversity was most pronounced in viral genes required for establishing latent infection and persistence, with appreciable levels of diversity also detected in structural genes, including envelope glycoproteins. Interestingly, intrapatient diversity declined significantly over time ( < 0.01), and this was particularly evident on comparison of viral genomes sequenced from B cell fractions in early primary infection and convalescence ( < 0.001). B cell-associated viral genomes were observed to converge, becoming nearly identical to the B95.8 reference genome over time (Spearman rank-order correlation test; = -0.5589, = 0.0264). The reduction in diversity was most marked in the EBV latency genes. In summary, our data suggest independent convergence of diverse viral genome sequences toward a reference-like strain within a relatively short period following primary EBV infection. Identification of viral proteins with low variability and high immunogenicity is important for the development of a protective vaccine. Knowledge of genome diversity within circulating viral populations is a key step in this process, as is the expansion of intrahost genomic variation during infection. We report full-length EBV genomes sequenced from the blood and oral wash of 10 individuals early in primary infection and during convalescence. Our data demonstrate considerable diversity within the pool of circulating EBV strains, as well as within individual patients. Overall viral diversity decreased from early to persistent infection, particularly in latently infected B cells, which serve as the viral reservoir. Reduction in B cell-associated viral genome diversity coincided with a convergence toward a reference-like EBV genotype. Greater convergence positively correlated with time after infection, suggesting that the reference-like genome is the result of selection.

Identification and Cloning of a New Western Epstein-Barr Virus Strain That Efficiently Replicates in Primary B Cells

“…Sequencing the BZLF1 open reading frame and miniZp promoter thereof in our complete virus panel revealed that all of them are within the western group and 21/22 viruses are within the B95-8 subgroup and lack the Zp-V3 polymorphism. This fits with previous reports showing that patients with IM carry viruses that are very closely related to B95-8 (36). However, the replicating abilities of these strains widely varied, suggesting that polymorphisms outside of BZLF1 modulate this property.…”

Modified Anoikis Assay That Functionally Segregates Epstein-Barr Virus LMP1 Strains into Two Groups

“…Target enrichment of EBV genomes has enabled the high-throughput sequencing of whole EBV genomes from infected cells and biospecimens to reveal genetic diversity, which is greatest in the latent genes (35). There is early evidence supporting the notion that the diversity of EBV genomes within an infected individual is highest during early infection and steadily decreases during establishment of chronic infection and latency (42). Studies of EBV populations circulating in the peripheral blood and oral lavage fluids of asymptomatic carriers also demonstrate that EBV populations are compartmentalized (22).…”

Genome sequencing analysis identifies high-risk Epstein-Barr virus subtypes for nasopharyngeal carcinoma

“…Previous studies have found that EBV genome usually underwent clonal expansion in NPC tumors or other malignancies 26,27,32 . In the scenario of clonal expansion, EBV genome is stable and intra-host mutation rate is often low, and heterozygous variants as a result of quasi-species evolution within a host are not frequent 12,18,33 . On the contrary, EBV isolates from specimens with multiple infections will have a higher number of heterozygous variants.…”