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CRISPR-Cas9 systems can directly target the hepatitis B virus (HBV) major genomic form, covalently closed circular DNA (cccDNA), for decay and demonstrate remarkable anti-HBV activity. Here, we demonstrate that CRISPR-Cas9-mediated inactivation of HBV cccDNA, frequently regarded as the “holy grail” of viral persistence, is not sufficient for curing infection. Instead, HBV replication rapidly rebounds because of de novo formation of HBV cccDNA from its precursor, HBV relaxed circular DNA (rcDNA). However, depleting HBV rcDNA before CRISPR-Cas9 ribonucleoprotein (RNP) delivery prevents viral rebound and promotes resolution of HBV infection. These findings provide the groundwork for developing approaches for a virological cure of HBV infection by a single dose of short-lived CRISPR-Cas9 RNPs. Blocking cccDNA replenishment and re-establishment from rcDNA conversion is critical for completely clearing the virus from infected cells by site-specific nucleases. The latter can be achieved by widely used reverse transcriptase inhibitors.
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A single administration of CRISPR-Cas9 ribonucleoproteins eliminates >98% of the hepatitis B virus (HBV) major genomic form, but HBV rebounds after CRISPR-Cas9 targeting. This rebound is associated with the HBV genomic precursor, relaxed circular DNA. Depleting relaxed circular DNA using the FDA-approved reverse transcriptase inhibitor lamivudine prevents HBV rebound and promotes resolution of infection by CRISPR-Cas9.