SARS-CoV-2 suppresses IFNβ production mediated by NSP1, 5, 6, 15, ORF6 and ORF7b but does not suppress the effects of added interferon

Type I Interferons (IFN-Is) are a family of cytokines which play a major role in inhibiting viral infection. Resultantly, many viruses have evolved mechanisms in which to evade the IFN-I response. Here we tested the impact of expression of 27 different SARS-CoV-2 genes in relation to their effect on IFN production and activity using three independent experimental methods. We identified six gene products; NSP6, ORF6, ORF7b, NSP1, NSP5 and NSP15, which strongly (>10-fold) blocked MAVS-induced (but not TRIF-induced) IFN beta production. Expression of the first three of these SARS-CoV-2 genes specifically blocked MAVS-induced IFN beta -promoter activity, whereas all six genes induced a collapse in IFN beta mRNA levels, corresponding with suppressed IFN beta protein secretion. Five of these six genes furthermore suppressed MAVS-induced activation of IFN lambda s, however with no effect on IFN alpha or IFN gamma production. In sharp contrast, SARS-CoV-2 infected cells remained extremely sensitive to anti-viral activity exerted by added IFN-Is. None of the SARS-CoV-2 genes were able to block IFN-I signaling, as demonstrated by robust activation of Interferon Stimulated Genes (ISGs) by added interferon. This, despite the reduced levels of STAT1 and phospho-STAT1, was likely caused by broad translation inhibition mediated by NSP1. Finally, we found that a truncated ORF7b variant that has arisen from a mutant SARS-CoV-2 strain harboring a 382-nucleotide deletion associating with mild disease (Delta 382 strain identified in Singapore & Taiwan in 2020) lost its ability to suppress type I and type III IFN production. In summary, our findings support a multi-gene process in which SARS-CoV-2 blocks IFN-production, with ORF7b as a major player, presumably facilitating evasion of host detection during early infection. However, SARS-CoV-2 fails to suppress IFN-I signaling thus providing an opportunity to exploit IFN-Is as potential therapeutic antiviral drugs. Author summary Our immune system provides the first-line of defense to combat viral infection through the localized triggering of Type I Interferons (IFN-Is). This is a family of cytokines which send a localized red alert signal to both infected and adjacent cells, activating hundreds of antiviral genes thus triggering a major arm of innate immunity. So important are IFN-Is, that it is perhaps not surprising that many viruses have evolved mechanisms to block the triggering of IFN-I production and sometimes to additionally block IFN-I signaling. Herein we have demonstrated that SARS-CoV-2, the virus responsible for COVID19, harbors six genes that block the production of IFN beta, a major subtype of IFN-Is. However, even though SARS-CoV-2 infection had the capacity to strongly decrease pSTAT1, a lynchpin molecule required to disseminate IFN-I signaling, enough residual pSTAT1 remained to allow activation of the anti-viral program. Our findings demonstrate that this coronavirus has devoted a significant proportion of its genome to block IFN-I production, presumably in order to help it establish early stage infection. Nevertheless, this virus remains sensitive to the effects of added interferon, providing an opportunity to treat COVID19 patients with IFN-Is therapeutically.

Automated summary

Type I interferons play a crucial role in combating viral infections, yet SARS-CoV-2 virus has evolved to disrupt immune defenses by blocking IFN beta production through six genes. Despite reducing pSTAT1 levels, the virus still activates antiviral programs and remains sensitive to added interferon, presenting a therapeutic opportunity.