UCSF

Hepatitis C virus (HCV) is a major public health threat, chronically infecting approximately 180 million people worldwide and leading to liver diseases such as cirrhosis and hepatocellular carcinoma. To date, efforts to generate a prophylactic or therapeutic vaccine have been unsuccessful. The failure of vaccine candidates, as well as the rapid emergence of drug-resistant variants, is almost entirely due to the hypervariable nature of HCV. Interestingly, while HCV is highly variable, recombination events between HCV strains are rare. This lack of recombination suggests that immune escape and drug resistance mutations are rarely transferred between strains, providing clear implications for treatment paradigms in patients infected with multiple HCV strains.

When HCV infects a host cell, that cell becomes resistant to further infection by HCV but not other viruses, such as dengue virus. This resistance, termed superinfection exclusion, acts to limit the co-occupancy of cells with multiple viral genomes, and thus prevents recombination. However, the mechanism of this block is poorly understood.

In this thesis I focus on further understanding why these recombination events are so rarely observed, through detailed investigations of the phenomena of superinfection exclusion and intracellular competition between HCV genomes during cell division. To further characterize HCV superinfection exclusion, we created a class of novel reporter HCV strains selected for their ability to infect cells already replicating HCV RNA. Importantly, the evolution of the ability to "superinfect" cells caused these viral strains to become more infectious generally, and led these viruses to expel the HCV RNA already present in the host cells. We further identified key changes in the HCV genome that allowed the virus to overcome the superinfection block.

In addition to our work on superinfection exclusion, we identified a novel means of intracellular competition between HCV genomes co-occupying a host cell that occurs at, or shortly following, mitosis. In the setting of cellular division, we found that when two viral genomes of equivalent fitness are present within a cell, they have an equal opportunity to exclude the other. In a population of dividing cells, the competition between viral genomes proceeds apace, randomly clearing one or the other genome from cells in the span of 9-12 days. In addition to superinfection exclusion, this intracellular competition due to mitosis is likely to further limit HCV's genetic diversity and ability to recombine in vivo.

In sum, this thesis demonstrates that viral competition in HCV infection occurs on many more levels than was previously appreciated. This competition acts to prevent coinfection of host cells and likely explains the lack of natural recombination in HCV biology. Further, these findings shed additional light on basic aspects of HCV replication and hopefully lead in the future to novel therapies for this critical disease.