A major area of interest has been the discovery and characterization of proteins that comprise intrinsic cellular antiviral defenses. The lab revealed that non-human primate cells possess an activity that targets incoming lentiviral capsids whose antiviral activity varied in a species-dependent manner. The protein responsible for this activity was later identified by others as TRIM5, and the lab performed key studies mapping determinants of its specificity and providing key insights into the TRIM5 mechanism of action.

The group discovered a protein that traps a remarkably set diverse enveloped virus particles on the surface of cells, that they termed ‘Tetherin’. The lab showed how Tetherin inserts itself into the lipid envelope of virions to cause their entrapment, in a way that explains why the overall protein structure, and not the primary sequence, of Tetherin is important for activity. The lab showed how Tetherin evolved from a protein of unrelated function, that the HIV-1 accessory protein Vpu antagonized the action of Tetherin, and that simian immunodeficiency viruses (SIVs) lacking a Vpu protein often employ another viral accessory protein, Nef, as a Tetherin antagonist. The specificity of these viral antagonists is governed by host species-dependent Tetherin sequence variation. The team have also discovered a number of additional host proteins, including CNP, AhR, IDO1, TRIM56 and TRIM69, that either induce or have direct antiviral activity against HIV-1 or other viruses.

The lab found that RNA molecules that have too many CpG dinucleotides are recognized as non-self by cell intrinsic mechanisms and depleted from the cytoplasm. The recognition of CpG rich RNA’s as non-self was enabled by the progressive purging of CpG dinucleotides from the genomes of tetrapods that occurred over hundreds of millions of years. The lab identified zinc-finger antiviral protein (ZAP) as the protein responsible for the recognition of CpG rich foreign RNA, and showed that ZAP binds directly to CpG containing RNA to trigger its cytoplasmic depletion. With collaborators, the lab showed the structural basis for ZAP’s ability to discriminate of CpG-rich RNA, revealing that ZAP has a dinucleotide binding pocket that can accommodate a CpG, but no other dinucleotide. The team has also found that designing viral genomes with optimal numbers, context and spacing of CpG dinucleotides generates rationally and conditionally attenuated viruses that can work well as vaccines in model systems. Currently the lab is working to define the molecular details of how viral RNA is depleted following its recognition by ZAP.

Among the proteins discovered by the lab to exhibit antiviral  activity is the interferon induced protein Mx2, which prevents capsid-dependent entry of HIV-1 preintegration complexes into the nucleus, The lab showed that Mx2 antiviral activity was dependent on nucleoporins - through a detailed examination of HIV-1 nuclear entry, the group showed that there are likely multiple independent paths by which HIV-1 can access the nucleus and that Mx2 inhibits subset of nuclear entry pathways that are preferentially exploited by HIV-1. Building on this work, the lab is developing new methods to track virus particles and subviral structures following viral entry and during nuclear import.

The lab continues to pursue the identification of host proteins with antiviral activity against HIV-1 and other viruses, and works to understand mechanistically how they inhibit viral replication. This work has recently extended into respiratory viruses in general and coronavirus in particular.