PhIP-Seq reveals geography- and disease-associated human herpesvirus antibody repertoires and distinct EBV response modules

Epstein-Barr virus (EBV) has been implicated in immune-mediated inflammatory diseases, but herpesvirus-directed humoral responses across populations and disease states remain incompletely defined. We profiled antibodies to all nine human herpesviruses by PhIP-Seq in 908 serum samples from 848 individuals in Madagascar and Germany. Cohorts showed distinct reactivity patterns, including cross-virus associations between homologous alphaherpesvirus envelope glycoproteins. German cohorts recognized a broader range of latent and lytic EBV proteins than Malagasy controls, with increased reactivity in primary sclerosing cholangitis. Proteome-wide profiling detected reactivity to 60 of 79 EBV proteins; 29 contained at least one peptide recognized in >5% of participants. Co-occurrence analyses identified an EBNA2–EBNA3A/B/C module and BFRF3–EBNA1 and BZLF1–BMRF1 pairs in German cohorts. Peptide ELISA showed individual-level concordance with PhIP-Seq for EBNA1. These findings reveal geography- and disease-associated herpesvirus antibody repertoires incompletely captured by single-antigen serology.