Immunogenomic landscape of hepatocellular carcinoma with immune cell stroma and EBV-positive tumor-infiltrating lymphocytes.

•EBV positivity in CD20-positive tumor-infiltrating lymphocytes was present in over 70% of HCC-IS.•HCC-IS lacked CTNNB1 mutations and exhibited increased global DNA hypermethylation.•Both PD-1 and PD-L1 in tumor-infiltrating lymphocytes, and PD-L1 in tumor cells were overexpressed in HCC-IS.•HCCs with high EBV positivity, paradoxically, were associated with a poor prognosis.•HCCs with high EBV positivity exhibited increased levels of functionally exhausted CD8 T cells.