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Epstein-Barr virus (EBV) infection is a significant factor in the pathogenesis of nasopharyngeal carcinoma, especially in the undifferentiated carcinoma of nasopharyngeal type (UCNT, World Health Organization type III), which is the dominant histopathological type in high-risk areas. The major EBV oncogene is latent membrane protein 1 (LMP1). LMP1 gene shows variability with different tumorigenic and immunogenic potentials. EBV nuclear antigen 1 (EBNA1) regulates progression of EBV-related tumors; however, the influence of EBNA1 sequence variability on tumor pathogenesis is controversial. The aims of this study were to characterize polymorphisms of EBV genes in non-endemic nasopharyngeal carcinoma biopsies and to investigate potential sequence patterns that correlate with the clinical presentation of nasopharyngeal carcinoma. In total, 116 tumor biopsies of undifferentiated carcinoma of nasopharyngeal type (UCNT), collected from 2008 to 2014, were evaluated in this study. The genes  EBNA2 ,  LMP1 , and  EBNA1  were amplified using nested-PCR.  EBNA2  genotyping was performed by visualization of PCR products using gel electrophoresis. Investigation of  LMP1  and  EBNA1  included sequence, phylogenetic, and statistical analyses. The presence of EBV DNA was significantly distributed between TNM stages.  LMP1  variability showed six variants, with the detection of the first China1 and North Carolina variants in European nasopharyngeal carcinoma biopsies. Newly discovered variants Srb1 and Srb2 were UCNT-specific  LMP1  polymorphisms. The B95-8 and North Carolina variants are possible predictors for favorable TNM stages. In contrast, deletions in  LMP1  are possible risk factors for the most disfavorable TNM stage, independent of  EBNA2  or  EBNA1  variability. A newly discovered  EBNA1  subvariant, P-thr-sv-5, could be a potential diagnostic marker, as it represented a UCNT-specific  EBNA1  subvariant. A particular combination of  EBNA2 ,  LMP1 , and  EBNA1  polymorphisms,  type 1/Med/P-thr  was identified as a possible risk factor for TNM stage IVB or progression to the N3 stage.

Characterization of the Variability of Epstein-Barr Virus Genes in Nasopharyngeal Biopsies: Potential Predictors for Carcinoma Progression