Tuning a cellular lipid kinase activity adapts hepatitis C virus to replication in cell culture

Christian Harak, Max Meyrath, Inés Romero-Brey, Christian Schenk, Claire Gondeau, Philipp Schult, Katharina Esser-Nobis, Mohsan Saeed, Petra Neddermann, Paul Schnitzler, Daniel Gotthardt, Sofia Perez-del-Pulgar, Christoph Neumann-Haefelin, Robert Thimme, Philip Meuleman, Florian W. R. Vondran, Raffaele De Francesco, Charles M. Rice, Ralf Bartenschlager, Volker Lohmann

With a single exception, all isolates of hepatitis C virus (HCV) require adaptive mutations to replicate efficiently in cell culture. Here, we show that a major class of adaptive mutations regulates the activity of a cellular lipid kinase, phosphatidylinositol 4-kinase IIIα (PI4KA). HCV needs to stimulate PI4KA to create a permissive phosphatidylinositol 4-phosphate-enriched membrane microenvironment in the liver and in primary human hepatocytes (PHHs). In contrast, in Huh7 hepatoma cells, the virus must acquire loss-of-function mutations that prevent PI4KA overactivation. This adaptive mechanism is necessitated by increased PI4KA levels in Huh7 cells compared with PHHs, and is conserved across HCV genotypes. PI4KA-specific inhibitors promote replication of unadapted viral isolates and allow efficient replication of patient-derived virus in cell culture. In summary, this study has uncovered a long-sought mechanism of HCV cell-culture adaptation and demonstrates how a virus can adapt to changes in a cellular environment associated with tumorigenesis.