While innate immune pathways were evident in the gt1‐infected liver biopsies (e.g. activation of IRF by cytosolic pattern recognition receptors and interferon signalling), pathways relating to adaptive immune responses were more apparent in the gt3‐infected liver biopsies (e.g. altered T‐ and B‐cell signalling in rheumatoid arthritis, calcium‐induced T‐lymphocyte apoptosis, iCOS‐iCOSL signalling in T‐helper cells, B‐cell development and CD28 signalling in T‐helper cells). Here, ICOS is linked to rheumatoid arthritis.