Hepatitis A virus (HAV) is an hepatotropic human picornavirus that is associated only with acute infection. Its pathogenesis is not well understood because there are few studies in animal models using modern methodologies. We characterized HAV infections in three chimpanzees, quantifying viral RNA by quantitative RT-PCR and examining critical aspects of the innate immune response including intrahepatic IFN-stimulated gene expression. We compared these infection profiles with similar studies of chimpanzees infected with hepatitis C virus (HCV), an hepatotropic flavivirus that frequently causes persistent infection. Surprisingly, HAV-infected animals exhibited very limited induction of type I IFN-stimulated genes in the liver compared with chimpanzees with acute resolving HCV infection, despite similar levels of viremia and 100-fold greater quantities of viral RNA in the liver. Minimal IFN-stimulated gene 15 and IFIT1 responses peaked 1-2 wk after HAV challenge and then subsided despite continuing high hepatic viral RNA. An acute inflammatory response at 3-4 wk correlated with the appearance of virus-specific antibodies and apoptosis and proliferation of hepatocytes. Despite this, HAV RNA persisted in the liver for months, remaining present long after clearance from serum and feces and revealing dramatic differences in the kinetics of clearance in the three compartments. Viral RNA was detected in the liver for significantly longer (35 to >48 wk) than HCV RNA in animals with acute resolving HCV infection (10-20 wk). Collectively, these findings indicate that HAV is far stealthier than HCV early in the course of acute resolving infection. HAV infections represent a distinctly different paradigm in virus-host interactions within the liver.innate immunity | viral persistence | immune evasion H epatitis A virus (HAV) is a small, hepatotropic positivestrand RNA virus. Although it is classified among the Picornaviridae, it differs in several important respects from most other human picornaviral pathogens in having a very slow and nonlytic replication cycle (reviewed in ref. 1). Several primatederived cell lines are permissive for infection by HAV, and in the absence of extensive adaptation of the virus to cell culture, these infections are typically noncytopathic. Despite this, HAV causes only acute disease in humans and has never been documented to establish long-term persistent infection within the liver (1-3). However, relatively little is known about the pathogenesis of HAV infections and how the virus is cleared from the liver as there has been little impetus for research on hepatitis A since the development of effective inactivated vaccines almost 2 decades ago.The absence of long-term persistent HAV infection is well documented by disappearance of the virus from isolated human populations over time (4, 5) and differs dramatically from the outcome of hepatitis C virus (HCV) infections, which persist for life in the majority of persons (6). HCV is the cause of considerable human morbidity and mortality. Like HAV, it...