AAV-mediated delivery of CRISPR/Cas9 targeting conserved overlapping ORFs efficiently suppresses HBV replication in hepatocyte models

Chronic hepatitis B virus (HBV) infection remains a major global health burden due to the persistence of covalently closed circular DNA (cccDNA), which limits current antiviral therapies. We developed an adeno-associated virus (AAV)-delivered CRISPR/Cas9 system targeting conserved regions of the HBV genome. Three guide RNAs (gRNA1–3) targeting overlapping open reading frames of the surface antigen and polymerase genes were evaluated in HepG2.2.15 cells and HBV-infected hepatocyte-like cells (imHCs), with a reverse transcriptase-targeting gRNA and tenofovir alafenamide as controls. All gRNAs significantly reduced intracellular and extracellular HBV DNA levels and moderately decreased HBsAg secretion. Notably, gRNA2 induced a frameshift mutation and demonstrated superior antiviral efficacy, markedly reducing cccDNA levels, viral DNA levels, viral RNA levels, HBcAg expression, and HBsAg secretion with suppression maintained for up to 12 days. These findings highlight AAV-mediated CRISPR/Cas9 as a promising gene-based therapy for chronic HBV infection.