Two main strains of Epstein-Barr virus (type 1 and type 2) can be defined largely based on the sequence of their EBV nuclear antigen 2 (EBNA2) gene. Type 1 EBV is more efficient in transforming B-cells than type 2, but the mechanism underlying this difference in transformation efficiency is unclear. Evidence indicates that type 2 EBNA2 may activate some cellular genes less efficiently than type 1 EBNA2. In this report, we summarized on the hypothesis that whether the differences between type 1 and type 2 EBNA2 in activating cellular genes correlates with their ability to bind a host cell tumour suppressor and transcription repressor protein, BS69. Previous studies identified two PXLXP peptide motifs in conserved regions of type 1 EBNA2, which bind BS69. These motifs are also present in the sequence of type 2 EBNA2. A single amino acid mutation (S442D) increases the transformation efficiency of type 2 EBNA2, indicating that this amino acid is the defining factor in the difference in the transformation efficiency of type 1 and type 2 EBV. This residue is present near the second BS69 binding site with BS69. In conclusion, we hypothesize that it is the stronger association between BS69 and type 2 EBNA2 that could contribute in the reduction of type 2 EBV transformation efficiency.