Discovery of Host-Directed Antiviral Therapies

Viruses are obligate parasites, unable to replicate outside of the host to which they are adapted. The adaptation of viruses to their accustomed host cell milieu is exquisite, contacting hundreds or thousands of host proteins in order to hijack host machinery and avoid antiviral defenses. Identifying the key functional interactions between virus and host is a critical step towards interfering with viral replication, as implicated host proteins are attractive and often highly-tractable therapeutic targets. This identification remains challenging, especially as it is best done directly in the primary cells or tissues in which the virus typically replicates. We have built on recent developments using CRISPR-Cas9 ribonucleoproteins that allowed perturbation of genomic sequences in primary human CD4+ T cells to functionally interrogate HIV-human interactions, identifying 86 that significantly alter HIV infection, including 44 not previously reported and 24 that harbor restrictive activity. We sequenced each knockout locus to illuminate the cell-type-specific DNA repair processes in T cells and built an algorithm for enhanced prediction of their CRISPR editing outcomes. We then adapted the CRISPR-Cas9 ribonucleoprotein editing for use in primary human myeloid cells, allowing for interrogation of host factors for many additional pathogens. Finally, faced with a viral pandemic, we identified questions we were well-positioned to answer, first assessing the performance of commercial SARS-CoV-2 antibody assays before returning to host-pathogen interaction mapping. We carried out comparative viral-human protein-protein interaction and viral protein localization analysis for all three pathogenic coronaviruses SARS-CoV-1, MERS-CoV and SARS-CoV-2. Subsequent functional genetic screening identified host factors that functionally impinge on coronavirus proliferation, including Tom70, a mitochondrial chaperone protein that interacts with both SARS-CoV-1 and SARS-CoV-2 Orf9b, an interaction we structurally characterized using cryo-EM. Combining genetically-validated host factors with both COVID-19 patient genetic data and medical billing records identified important molecular mechanisms and potential drug treatments with effectiveness against COVID-19 that merit further molecular and clinical study