CpG methylation as a tool to characterize cell-free Epstein-Barr virus DNA

In order to differentiate Epstein-Barr virus (EBV) virion DNA versus viral DNA released from tumor cells, we have taken advantage of the observation that viral episomal genomes of herpesviruses are methylated in latently infected cells whereas un-methylated genomes are synthesized and packaged into virions during the lytic phase. We used paramagnetic beads linked to methylCpG binding protein to separate virion and cell-derived viral DNA. DNA isolated from EBV (Figure 1A) virions failed to bind to the methylCpG binding protein and were detected only in the non-captured (NC) fractions, while DNA isolated from latently infected cell lines were detected predominantly in the bound fractions ( E2000, high salt elute). Unmethylated EBV DNA, presumably virion DNA, was detected in the plasma of 3 AIDS patients without lymphoma, while methylated DNA was detected in the blood of 3 patients with EBV-associated Hodgkin lymphoma (HL) (without HIV infection) (Figure 1B).