Comparative analysis of phase-specific plasma Epstein–Barr virus DNA signatures in Malaysian nasopharyngeal carcinoma

Nasopharyngeal carcinoma (NPC) is an Epstein–Barr virus (EBV)-associated malignancy and a biologically distinct inflammation-associated subtype of head and neck cancer (HNC). This study investigated whether gene-specific circulating EBV DNA signatures reflect phase-dependent viral activity and clinically relevant tumour characteristics in NPC. Plasma EBV DNA targeting EBNA1 (latent infection), BARF1 (immune-modulatory activity), and BALF5 (lytic replication) was quantified by quantitative polymerase chain reaction in NPC patients and healthy controls. BARF1 achieved the highest accuracy of AUC at 0.92 (95%CI: 0.85–0.99) with p < 0.0001, which significantly outperforming EBNA1 and BALF5 in in detecting EBV-associated NPC in plasma. BARF1 also demonstrated the strongest diagnostic performance, outperforming conventional VCA-IgA serology and the other EBV biomarkers and was considered significantly associated with metastatic features and pro-inflammatory lifestyle exposures. These findings suggest that circulating EBV DNA composition reflects phase-specific viral dynamics rather than uniform viral burden and provides mechanistic insight into tumour-associated virus–host interactions. These findings demonstrate that gene-specific plasma EBV DNA profiling provides additional diagnostic information beyond conventional serological testing and identifies BARF1 as a promising minimally invasive biomarker for NPC detection and patient stratification. Further validation in larger independent cohorts is warranted.