During a hepadnavirus infection, viral DNA integrates at a low rate into random sites in the host DNA, producing unique virus-cell junctions detectable by inverse nested PCR (invPCR). These junctions serve as genetic markers of individual hepatocytes, providing a means to detect their subsequent proliferation into clones of two or more hepatocytes. A previous study suggested that the livers of 2.4-year-old woodchucks (Marmota monax) chronically infected with woodchuck hepatitis virus contained at least 100,000 clones of >1,000 hepatocytes (W. S. Mason, A. R. Jilbert, and J. Summers, Proc. Natl. Acad. Sci. USA 102:1139-1144, 2005). However, possible correlations between sites of viral-DNA integration and clonal expansion could not be explored because the woodchuck genome has not yet been sequenced. In order to further investigate this issue, we looked for similar clonal expansion of hepatocytes in the livers of chimpanzees chronically infected with hepatitis B virus (HBV). Liver samples for invPCR were collected from eight chimpanzees chronically infected with HBV for at least 20 years. Fifty clones ranging in size from ϳ35 to 10,000 hepatocytes were detected using invPCR in 32 liver biopsy fragments (ϳ1 mg) containing, in total, ϳ3 ؋ 10 7 liver cells. Based on searching the analogous human genome, integration sites were found on all chromosomes except Y, ϳ30% in known or predicted genes. However, no obvious association between the extent of clonal expansion and the integration site was apparent. This suggests that the integration site per se is not responsible for the outgrowth of large clones of hepatocytes.There are approximately 10 12 hepatocytes in the human liver, virtually all of which can be infected during a hepatitis B virus (HBV) infection. Chronic infection leads to the development of hepatocellular carcinomas (HCC) in ϳ25% of patients, with tumors typically emerging after several decades. The tumors are clonal and usually contain integrated HBV DNA that was acquired at an early step in transformation, prior to tumor outgrowth. The tumors themselves typically do not support virus replication and do not contain covalently closed circular DNA (cccDNA), the virus transcriptional template. The fact that the tumors typically contain integrated HBV DNA suggests that they arise through mutation of mature hepatocytes and not from hepatic stem cells or hepatobiliary progenitor cells (37,44,62). Though contrary reports have appeared (3, 21), hepatocytes are currently the only liver cell type unambiguously established to be susceptible to HBV infection in most individuals.With a few exceptions, the virus integration sites found in HCC samples from different patients have not provided insights into the mechanisms of carcinogenesis (8, 9, 53). Aside from showing a possible preference for transcriptionally active regions (36), the sites of HBV integration have appeared somewhat random in location and, by inference, not directly related to cellular transformation. Thus, it has been hypothesized that hepatocyte trans...