An improved droplet digital PCR assay reveals the stability of intrahepatic hepatitis B virus cccDNA.

The persistence of covalently closed circular DNA (cccDNA) poses a major obstacle to curing chronic hepatitis B (CHB). Here, we used droplet digital PCR (ddPCR) for cccDNA quantitation. ddPCR measured a less than two-fold difference in the intrahepatic cccDNA content more accurately than conventional real-time PCR (qPCR), (R2=0.9416 and R2=0.8963, respectively) and had also higher sensitivity and specificity than qPCR. The results of ddPCR correlated closely with serum HB core-related antigen and HB surface antigen (HBsAg) in 24 HBV-infected human-liver-chimeric mice (PXB-mice). We demonstrated that the total cccDNA content did not change during liver repopulation, although the cccDNA content per hepatocyte was reduced in PXB-mice after entecavir treatment. In the 6 patients with HBV-related hepatocellular carcinoma, ddPCR detected cccDNA in both tumor and non-tumor tissues. In 13 HBeAg-negative CHB patients with pegylated interferon alpha-2a, cccDNA contents from paired biopsies were more significantly reduced in virological response (VR) than in non-VR at week 48 (p=0.0051). Interestingly, cccDNA levels were the lowest in VR with HBsAg clearance but remained detectable after the treatment. Collectively, ddPCR revealed that cccDNA content is stable during hepatocyte proliferation and persists at quantifiable levels, even after serum HBsAg clearance.