Multiple pathways to avoid IFN-β sensitivity of HIV-1 by mutations in capsid.

Type I interferons (IFNs), including alpha IFN (IFN-alpha) and IFN-beta, potently suppress HIV-1 replication by upregulating IFN-stimulated genes (ISGs). The viral capsid protein (CA) partly determines the sensitivity of HIV-1 to IFNs. However, it remains to be determined whether CA-related functions, including utilization of known host factors, reverse transcription, and uncoating, affect the sensitivity of HIV-1 to IFN-mediated restriction. Recently, we identified an HIV-1 CA variant that is unusually sensitive to IFNs. This variant, called the RGDA/Q112D virus, contains multiple mutations in CA: H87R, A88G, P90D, P93A, and 4112D. To investigate how an IFN-hypersensitive virus can evolve to overcome IFN-beta-mediated blocks targeting the viral capsid, we adapted the RGDA/Q112D virus in IFN-beta-treated cells. We successfully isolated IFN-beta-resistant viruses which contained either a single Q4R substitution or the double amino acid change G94D/G116R. These two IFN-beta resistance mutations variably changed the sensitivity of CA binding to human myxovirus resistance B (MxB), cleavage and polyadenylation specificity factor 6 (CPSF6), and cyclophilin A (CypA), indicating that the observed loss of sensitivity was not due to interactions with these known host CA-interacting factors. In contrast, the two mutations apparently functioned through distinct mechanisms. The Q4R mutation dramatically accelerated the kinetics of reverse transcription and initiation of uncoating of the RGDA/Q112D virus in the presence or absence of IFN-beta, whereas the G94D/G116R mutations affected reverse transcription only in the presence of IFN-beta, most consistent with a mechanism of the disruption of binding to an unknown IFN-beta-regulated host factor. These results suggest that HIV-1 can exploit multiple, known host factor-independent pathways to avoid IFN-beta-mediated restriction by altering capsid sequences and subsequent biological properties. IMPORTANCE HIV-1 infection causes robust innate immune activation in virus-infected patients. This immune activation is characterized by elevated levels of type I interferons (IFNs), which can block HIV-1 replication. Recent studies suggest that the viral capsid protein (CA) is a determinant for the sensitivity of HIV-1 to IFN-mediated restriction. Specifically, it was reported that the loss of CA interactions with CPSF6 or CypA leads to higher IFN sensitivity. However, the molecular mechanism of CA adaptation to IFN sensitivity is largely unknown. Here, we experimentally evolved an IFN-beta-hypersensitive CA mutant which showed decreased binding to CPSF6 and CypA in IFN-beta-treated cells. The CA mutations that emerged from this adaptation indeed conferred IFN-beta resistance. Our genetic assays suggest a limited contribution of known host factors to IFN-beta resistance. Strikingly, one of these mutations accelerated the kinetics of reverse transcription and uncoating. Our findings suggest that HIV-1 selected multiple, known host factor-independent pathways to avoid IFN-beta-mediated restriction.