DNA sequence heterogeneity within the Epstein-Barr virus family of repeats in the latent origin of replication

To detect the presence of variability in the tandemly repeated sequences of the Epstein-Barr virus latent origin of replication, we analyzed the length of the family of repeats in 14 lymphoblastoid and Burkitt's lymphoma cell lines by PCR amplification. The gel electrophoresis analysis of the PCR products revealed a broad banding pattern, characteristic of each line, consisting of several fragments, sometimes smeared, of variable length. This finding was interpreted as a result of the hairpin-like structures generated by the palindrome within the family of repeats, able to originate artefacts. Since the banding pattern was different only in strictly non-correlated cell lines, we supposed that the sequence of the repeat units was polymorphic. We therefore sequenced the family of repeats in three healthy bone marrow derived lymphoblastoid cell lines carrying an endogenous EBV as well as in a B95-8 infected cell line as control. The sequence analysis revealed that each line is different both in the number and in the sequence of repeats. At the 3' end of the family of repeats the B95-8 virus was found to have a 252 bp region missing in the GenBank standard sequence. This one is probably a partial sequence since it was shorter than the control specimens obtained from different sources of B95-8 DNA analyzed by Southern blot hybridization. The length analysis of the family of repeats can be used to characterize EBV strains by PCR.