Terminal Repeat Analysis of EBV Genomes

Epstein-Barr virus (EBV) was the first human virus associated directly with human malignancies. During EBV infection of various host cells the double-stranded linear EBV DNA carried by the virions undergoes circularization. Since there are variable numbers of terminal repetitions (TRs) at the ends of the linear EBV genome, the resulting circular episomes enclose a variable number of TRs. Thus, in cells carrying viral episomes, the sizes of the terminal restriction enzyme fragments of EBV is affected by the number of TRs (Raab-Traub and Flynn Cell 47:883-889, 1986). Southern blot analysis revealed that in monoclonal proliferations, arising from a single cell, there was only a single band representing the joined EBV termini, whereas multiple terminal restriction enzyme fragments that differ in size were characteristic for oligoclonal or polyclonal proliferations. Using suitable probes, one can distinguish the episomal form from the linear EBV genomes that are formed during lytic EBV replication or during integration into the host genome. TR analysis is a useful tool for the determination of EBV clonality in different clinical samples and in cell lines carrying EBV genomes. A single terminal restriction enzyme fragment may indicate EBV infection at an early phase of clonal cell proliferation, whereas polyclonal EBV genomes may derive from multiple infections of proliferating cells.