Escape by Shifting: Viral Entry Tropism Shift as an Evolutionary Mechanism of Immune Evasion - PROJECT SUMMARY Viral entry tropism, largely governed by receptor specificity, is a major determinant for virus cellular and tissue tropism, pathogenesis, and host range. Alteration in receptor specificity could be closely related with viral pathogenesis, such as the process of “coreceptor switch” in HIV infection that is associated with faster progression to AIDS, and may contribute to host-jumping, as exemplified by coronavirus and influenza virus. However, the molecular mechanism underlying viral receptor usage alteration is a fundamental gap in knowledge. Recent studies of our group elucidated the evolutionary process of coreceptor switch in natural HIV infection. The findings demonstrate that “driver mutations” responsible for coreceptor switch can confer complete escape to V3 broadly neutralizing antibodies. These observations, together with the fact that the receptor binding regions of many viruses overlap with antigenic epitopes, prompted us to propose a potentially paradigm-shifting concept termed “escape by shifting”. The central hypothesis is that for viruses with entry pathway flexibility, entry pathway alteration can function as an evolutionary mechanism of immune evasion. We coin the term “receptor utilization space” to describe the repertoire of receptors that can be used by a particular virus. Under immune pressure, a virus explores its “receptor utilization space” while exploring the sequence space and fitness landscape. Immune escape mutations and compensatory mutations could both confer novel receptor usage, which functions as a mechanism to maintain viral entry capacity while evading host immune recognition. We aim to test this novel concept by elucidating the biological mechanisms for HIV coreceptor switch. To this end, we will leverage a highly unique opportunity of the RV217 cohort which has longitudinal samples from participants identified in acute infection from East Africa and Thailand. The “escape by shifting” concept will be tested through three specific aims: 1) Determine the moment of coreceptor switch by identifying driver mutations in participants infected by different HIV subtypes. 2) Characterize the function of driver mutations in evading autologous neutralizing antibodies. Participants who did not undergo coreceptor switching will be used as controls to better understand viral and host factors governing coreceptor switch. 3) Elucidate the impact of coreceptor switch on CD4 hemostasis, reservoir landscape, and immune reconstitution on ART. The proposed work is significant for both the HIV field and general virology. It is expected to answer a long-standing question in the HIV field which has direct implications for HIV pathogenesis, therapeutics, and functional cure. While we use HIV as a model, the central hypothesis of the “escape by shifting” concept is generalizable to viruses with flexible entry pathways. Our long-term goal is to understand the molecular mechanisms of viral entry pathway evolution under the immune pressure, which has direct relevance for viral pathogenesis, transmissibility, as well as therapeutic and vaccine design. In summary, this application has the potential to exert long-term impact in general virology.
