Lorenzo Bulli, Luis Apolonia, Juliane Kutzner, Darja Pollpeter, Caroline Goujon, Nikolas Herold, Sarah-Marie Schwarz, Yannick Giernat, Oliver T. Keppler, Michael H. Malim, Torsten Schaller

Type I interferons (IFNs), including IFNα upregulate an array of interferon-stimulated genes (ISGs) and potently suppress HIV-1 infectivity in CD4(+) T cells, monocyte-derived macrophages (MDMs) and dendritic cells (MDDCs). Recently, we and others identified the ISG myxovirus resistance 2 (MX2) to block HIV-1 nuclear entry. However, additional antiviral blocks exist upstream of nuclear import, but the ISGs that suppress infection e.g. prior to (or during) reverse transcription remain to be defined. Here we show that HIV-1 CA mutants such as N74D or A105T, which both allow escape from inhibition by MX2 and the truncated version of the cleavage and polyadenylation specific factor 6 (CPSF6), as well as the cyclophilin A (CypA)-binding loop mutant P90A, each exhibit increased sensitivity to IFNα-mediated inhibition. Using CRISPR/Cas9 technology, we demonstrate that the IFNα-hypersensitivity of these mutants in THP-1 cells is independent of MX2 or CPSF6. As expected, CypA depletion had no additional effect on the behavior of the P90A mutant, but modestly increased the IFNα-sensitivity of wild type virus. Interestingly, the infectivity of wild type or P90A virus could be rescued from the MX2-independent IFNα-induced blocks in THP-1 cells by treatment with cyclosporine (Cs), or its non-immunosuppressive analogue SDZ-NIM811, indicating that Cs-sensitive host cell cyclophilins other than CypA contribute to the activity of IFNα-induced blocks. We propose that cellular interactions with incoming HIV-1 capsids help shielding the virus from recognition by antiviral effector mechanisms. Thus, the CA protein is a fulcrum for the dynamic interplay between cell-encoded functions that inhibit or promote HIV-1 infection. Human immunodeficiency virus type-1 (HIV-1) is the causative of the acquired immunodeficiency syndrome (AIDS). During acute HIV-1 infection, numerous pro-inflammatory cytokines are produced, including type I interferons (IFNs). IFNs can limit HIV-1 replication by inducing the expression of a set of antiviral genes that inhibit HIV-1 at multiple steps in its life cycle, including the post-entry steps of reverse transcription and nuclear import. This is observed in cultured cell systems, as well as in clinical trials in HIV-1 infected patients. The identities of the cellular antiviral factors, their viral targets and the underpinning mechanisms are largely unknown. We show here that the HIV-1 Capsid protein plays a central role in protecting the virus from IFN-induced inhibitors that block early post-entry steps of infection. We further show that host cell cyclophilins play an important role in regulating these processes, thus highlighting the complex interplay between antiviral effector mechanisms and viral survival.