Afflicting almost 200 million worldwide, hepatitis C virus (HCV) mounts a chronic infection of liver hepatocytes that causes substantial morbidity and mortality. An understanding of host-virus interactions will drive the development of therapeutics, but research is restrained by available experimental tools. Due to the cost and unreliability of existing humanized mouse and primate in vivo models, HCV research is almost exclusively performed using in vitro platforms which suffer from three major limitations. First, challenges in primary hepatocyte culture and the general non-permissiveness of liver cell lines have necessitated the use of a uniquely permissive hepatoma line derived from a single donor, questioning the generalizability of findings to the broader population. Second, this cell line deviates appreciably from native liver in functions central to HCV infection, including innate immune signaling, polarization, and proliferation. Third, infection is typically studied using bulk assays with suboptimal specificity, sensitivity, and content. Here, we describe three technologies for overcoming these limitations in the study of host-virus interactions. We demonstrate their utility in exploring innate immune signaling, a clinically significant component of HCV pathogenesis. Section I describes an in vitro platform for investigating inter-host variations in the natural history of infection and treatment response. We show that directed differentiation of induced pluripotent stem cells (iPSCs) yields patient-specific liver tissue that is permissive to HCV and responds to infection with a robust innate immune response, opening the door to "personalizing" the study and treatment of infection. In Section II, we demonstrate that tissue-engineered, micropatterned co-cultures (MPCCs) of primary hepatocytes and supportive stroma are permissive to HCV, enabling investigations in a more natural host. We then show that innate immune signaling curtails infection in this model, and that its inhibition enhances infection 2-3 orders of magnitude. Lastly, we use MPCCs to uncover a novel liver immunoregulatory mechanism whereby innate immune surveillance is depressed, permitting efficient replication of hepatotropic pathogens. Finally, Section III details a high-content imaging assay that enables visualization and enumeration of single viral genomes in individual cells. We demonstrate that single-cell, multiplexed quantification of viral genomes and host gene transcripts can be used to dissect host-virus interactions, yielding an unexpected positive correlation between stage of infection and response to an innate immune cytokine. The solutions described here will enable the pursuit of previously intractable research questions for HCV and other viruses, accelerating progress towards the development of antivirals and vaccines. Further, the insights gained regarding the interplay between HCV and innate immunity have important clinical ramifications, including a novel therapeutic strategy.