Fig. 2: DAXX is a restriction factor for SARS-CoV-2.

a–c Antiviral activity of ISGs against SARS-CoV-2. A549-ACE2 knocked-out for the indicated genes were generated using a multi-guide approach, leading to pools of KO cells with a high frequency of indels. KO cells were pre-treated with 0 (circles) or 200 (triangles) U/mL of IFNα 24 h prior to infection with SARS-CoV-2 (at an MOI of 0.1). Supernatants were harvested at 72 h p.i. The mean ± SD of three independent experiments, each performed in three biological replicates, is shown. a For the titration of RNA levels, supernatants were heat-inactivated prior to quantification by qRT-PCR. Genome copies/mL were calculated by performing serial dilutions of a synthetic RNA with a known concentration. Statistics: 2-way ANOVA using Dunnett’s test. Significant p values (below 0.05) are indicated on the graph. b For the titration of infectious virus levels by plaque assay, supernatants were serially diluted and used to infect VeroE6 cells. Plaques formed after 3 days of infection were quantified using crystal violet coloration. The limit of detection (LOD) is indicated as a dotted line. Statistics: Dunnett’s test on a linear model, (two-sided). Significant p values (below 0.05) are indicated on the graph. c For each of the indicated KO, the data shown in (a) is represented as fold change in log10 titers (i.e. the log10 titers of the non-treated condition divided by the mean of the triplicate log10 titers IFNα-treated condition, n = 3). Statistics: 2-way ANOVA using Sidak’s test. P values are indicated on the graph (ns: p value > 0.05). d–f Antiviral activity of DAXX against SARS-CoV-2 variants and other viruses. d A549-ACE2 WT or DAXX KO cells were infected at an MOI of 0.1 with the following SARS-CoV-2 strains: Lineage B (original strain); Lineage B.1.1.7. (Alpha variant); Lineage B.1.35.1 (Beta variant); Lineage P1 (Gamma variant). Supernatants were harvested at 72 h p.i. Supernatants were heat-inactivated prior to quantification by qRT-PCR. Genome copies/mL were calculated by performing serial dilutions of a synthetic RNA with a known concentration. The mean ± SD of three independent experiments, with infections carried out in three biological replicates, is shown. Statistics: 2-way ANOVA using Dunnett’s test. Significant p values (below 0.05) are indicated on the graph. e A549-ACE2 WT or DAXX KO cells were infected with Yellow Fever Virus (YFV, Asibi strain, MOI of 0.3) or with Measles Virus (MeV, Schwarz strain expressing GFP, MOI of 0.2). At 24 h p.i., the percentages of cells positive for viral protein E (YFV) or GFP (MeV) was assessed by flow cytometry. The mean ± SD of 3 independent experiments is represented. Statistics: 2-way ANOVA using Sidak’s test. P values are indicated on the graph. f WT or DAXX KO cells were infected at an MOI of 0.1 with SARS-CoV or MERS-CoV. Supernatants were harvested at 72 h p.i. Supernatants were heat inactivated prior to quantification by qRT-PCR. Serial dilutions of a stock of known infectious titer was used as a standard. The mean ± SD of 2 independent experiments, with infections carried out in three biological replicates, is represented. Statistics: 2-way ANOVA using Dunnett’s test. P values are indicated on the graph. Source data are provided as a Source Data file.