Molecular Methods for Detecting Epstein-Barr Virus (Part II): Structural Analysis of Epstein-Barr Virus DNA as a Marker of Clonality

The Southern blot technique can be used to determine the clonality of Epstein-Barr virus (EBV) infected cells (1 ,2 ). This clonality assay capitalizes on measurable polymorphisms in EBV genomic structure, namely, the variable number of tandem repeats lying at either end of the linear viral genome. Thus, the size of genome varies from virion to virion depending on the number of terminal repeat sequences. When a particular virion infects a cell, its linear genome circularizes by fusing the terminal repeats to form an episome containing from 1–20 tandem repeat sequences. If an infected cell undergoes malignant transformation, the viral DNA replicates along with cell DNA during mitosis, and the same terminal repeat structure is inherited by all tumor cell progeny. Therefore, Southern blot analysis of the EBV terminal restriction fragment serves as a marker of cellular clonality.