HBV infects quiescent hepatocytes, which are deficient in dNTPs, the critical precursors of HBV replication. Therefore, HBV increases the dNTP pool by inducing R2 expression, a cell cycle gene that is critical for generation of dNTPs. However the question of how HBV induces R2 expression in non-dividing cells remained open. We report here that this process is mediated through the Chk1-E2F1 axis of the cellular DNA damage response. We show that R2 upregulation is E2F1-dependent, and that HBV induces E2F1 accumulation and modification in quiescent HepG2 cells, as well as in primary human hepatocytes. We also found that Chk1, a known E2F1 kinase that functions in response to DNA damage, was upregulated and activated by HBV in both cellular systems. In Chk1-depleted or inhibited cells HBV failed to induce R2 expression. Similar results were obtained by Caffeine treatment, which inhibits ATM/ATR, the upstream kinases of Chk1 in the DNA damage response. Furthermore, we found that HBV attenuates DNA repair, a dNTP consuming process, suggesting that the virus hijacks DNA damage response, in supporting dNTPs synthesis and accumulation. Remarkably, we found that these processes are also mediated by novel HBV non-coding RNA activity. In conclusion, our findings demonstrate that a non-coding HBV RNA induces the Chk1-E2F1 axis of the DNA damage response in ensuring high dNTPs levels in growth-arrested cells.