The study of the hepatitis C virus (HCV) has been hindered by the lack of in vitro model systems. The recent development of HCV subgenomic RNA replicons has permitted the study of viral RNA replication in cell culture; however, the requirements for efficient replication of replicons in this system are poorly understood. Many viral isolates do not function as replicons and most require conserved changes, termed adaptive mutations, to replicate efficiently. In this report, we focus on the HCV nonstructural protein 5A (NS5A), a frequent locus for adaptive mutation. We found the interaction between NS5A and human vesicle-associated membrane protein-associated protein A (hVAP-A), a cellular target N-ethylmaleimide-sensitive factor attachment protein receptor, to be required for efficient RNA replication: NS5A mutations that blocked interaction with hVAP-A strongly reduced HCV RNA replication. Further analyses revealed an inverse correlation between NS5A phosphorylation and hVAP-A interaction. A subset of the previously identified adaptive mutations suppressed NS5A hyperphosphorylation and promoted hVAP-A binding. Our results support a model in which NS5A hyperphosphorylation disrupts interaction with hVAP-A and negatively regulates viral RNA replication, suggesting that replicon-adaptive mutations act by preventing the phosphorylation-dependent dissociation of the RNA replication complex.A pproximately 3% of the worldwide population is infected by the hepatitis C virus (HCV) (1), a positive-strand RNA virus of the family Flaviviridae. Infections frequently become chronic, persisting for the life of the individual, often leading to liver cirrhosis or cancer. The HCV genome is a single-stranded, positivestrand (coding), uncapped RNA Ϸ9,600 nt in length, which encodes a single Ϸ3,000-aa polypeptide, cleaved by cellular and viral proteases into at least 10 mature viral peptides ( Fig. 1 A) (reviewed in refs. 2 and 3). This genome is replicated through a minus-strand RNA intermediate in the cytoplasm of an infected cell.Study of HCV has been hindered by the lack of convenient model systems capable of robust viral replication. The development of HCV subgenomic RNA replicons has enabled study of viral RNA replication in cell culture (4). In this system, hepatocarcinoma Huh7 cells are transfected with a modified HCV RNA encoding the neomycin phosphotransferase gene in place of the structural region of the viral polyprotein (Fig. 1B). Replication of this RNA through the action of the remaining nonstructural (NS) proteins confers G418-resistance to the host cell. The replication potential of particular replicons can be scored as the frequency of G418-resistant colonies derived from each RNA.The determinants for replicon efficiency are poorly understood. Not all HCV isolates make functional subgenomic replicons. Six closely related viral genotypes, classified by sequence homology, comprise the HCV genus (5). Genotype 1, including subtypes 1a and 1b, is the most abundant worldwide (6). Of the six known functional replicons, four...