The effect of TBEV infection (TBE1) and TBEV+Bb/Ap co-infection (TBE+LD1) as well as therapy (TBE2 and TBE+LD2) on the effectiveness of the NFkB transcription factor, visible in the expression of subunits NFkB (p65 (A) and p52 (B)) assessed in granulocytes and product its activity—TNFα (C) measured in plasma of patients and compared with healthy subjects (control). The mean values for TBE patients (before–TBE1 and after treatment–TBE2, n = 40), patients with TBE+LD (before–TBE+LD1 and after treatment–TBE+LD2, n = 6) and control subjects (n = 20) with SD are shown as follows: x—differences vs. control group, p < 0.05; a—differences vs. TBE1 group, p < 0.05.