A high-resolution landscape of the Epstein-Barr virus humoral repertoire identifies pathogenic modules and biomarkers in nasopharyngeal carcinoma

Epstein-Barr virus (EBV) infection is a primary etiological driver of nasopharyngeal carcinoma (NPC), yet the lack of a high-resolution, disease-specific humoral repertoire has hindered our understanding of viral-host interactions and the development of precision clinical strategies. In this study, we utilized VirScan to systematically profile the virome-wide antibody responses in NPC patients, identifying a complex viral interaction network centered on EBV. To achieve comprehensive coverage and unprecedented resolution, we engineered an EBV-specific phage display library encompassing 42 divergent strains and implemented a quantitative PhIP-seq platform incorporating exogenous internal standards for robust sample normalization. This high-resolution mapping unveiled distinctive viral infection signatures and specific protein modules associated with the risk and clinical progression of NPC. Furthermore, we characterized a repertoire of antibody epitopes across GP350, GP42, gH/gL, and MTP that are associated with protective immunity. Clinically, we validated a peptide derived from TK (TK139-194) as a superior biomarker for NPC screening with an AUC of 0.97. Additionally, a three-peptide signature consisting of RIR1756-811, GP350532-587, and NEC2224-279 demonstrated high predictive accuracy for chemosensitivity (AUC = 0.88). Collectively, our study provides a definitive humoral immune atlas for NPC and establishes a scalable paradigm for investigating infection-associated malignancies and other complex infectious diseases.