In patients with MPGN, similar correlations were revealed regarding EBV DNA copy number/μg DNA which was strongly positively associated with TLR9 serum concentration (r = 0.98, p < 0.0001) but negatively with frequencies of mDC BDCA1+CD19-TLR9+ in the peripheral blood (r = −0.98, p < 0.0001) and frequencies of pDC BDCA2+CD123+TLR9+ in the peripheral blood (r = −0.98, p < 0.0001) and additionally negatively correlated with serum complement component C3 (r = −0.83, p < 0.0001). Here, TLR9 is linked to primary membranoproliferative glomerulonephritis.