Restriction factors are potent, widely expressed, intracellular blocks to viral replication that are an important component of the innate immune response to viral infection. Through evolutionary pressure for both host survival and virus emergence, an evolutionary “arms race” has developed that drives continuous rounds of selection for beneficial mutations in restriction factor genes to avoid viral escape from these factors and virus adaptation to gain the ability to antagonize the restriction factors. The study of the evolution and function of restriction factors allows us to discover the steps that led to the ancient origins of HIV in old world primates to chimpanzees and subsequently to humans. These evolutionary studies also identify “holes” in the human innate immune system as well as important human polymorphisms that affect our antiviral defenses to HIV and other viruses.
We developed a technology for doing high throughput CRISPR/Cas screens for host factors that affect HIV replication. This technique, called HIV-CRISPR, is one where we simultaneously knock out large numbers of genes with libraries of guideRNAs and then trick the virus into revealing which knockouts improve virus replication and which ones decrease virus replication by differential packaging of guideRNAs into budding virions. This screen assays the entire HIV lifecycle and is flexible enough to use different cells and different viral strains. We initially used this technique to define the restriction factors that are induced by interferon to inhibit HIV replication. We are now using it in many other contexts to identify host factors that affect HIV.
Human restriction factors fail to control HIV. We are developing “super restriction factors” that we define as evolution-guided variants of natural antiviral proteins with improved properties such as increased antiviral potency and/or resistance to viral antagonism. The study of super-restrictors helps define mechanisms of how restriction factors fundamentally work and the evolutionary tradeoffs for paths of antiviral resistance not seen in nature.