ABSTRACT
Background: The continuing spread of SARS-CoV-2 provides opportunities for the virus to evolve. Compared to ancestral strains, the 4 major variants of concern (VOC) exhibit Spike mutations that improve entry and/or diminish antibody neutralization. However, mutations have arisen in other viral genes. Several of these genes may counteract innate immunity mediated by antiviral interferons (IFNs). IFNs show extensive diversity, but only IFNα2 and IFNβ are approved for clinical use. We showed previously that diverse IFNs exhibit variable activities against HIV-1 and trigger distinct transcriptomes. Methods: To assess whether SARS-CoV-2 acquired human IFN resistance over time, isolates representing early lineages A, B, B.1, and VOC lineages B.1.1.7 (alpha), B.1.351 (beta), P.1 (gamma) and B.1.617.2 (delta) were tested for sensitivity to multiple IFNs in an alveolar type II epithelial cell (AT2) line, A549, overexpressing ACE2. Cells were pre-treated with IFNs for 18 h in triplicate, then infected to yield ∼105 copies/reaction. Virus copy numbers were evaluated at 24 h by qPCR. We compared the sensitivity of 5 SARS-CoV-2 isolates to 12 IFNα subtypes, IFNβ, IFNω and 3 IFNa;subtypes at 2 pM, within the dynamic range of preliminary IFN inhibition curves. IC50s for IFNβ and IFNa;1 were compared between lineage B and VOC isolates. Results: Among the 17 IFNs tested, IFNβ, IFNα8, IFNω and IFNα5 most potently inhibited SARS-CoV-2 in A549-ACE2 cells. Inhibition curves with a delta variant isolate showed that IFNα2 and IFNa;1 had >10-fold and >1000-fold higher IC50 than IFNβ, respectively. Interestingly, the antiviral activity patterns of diverse IFNα subtypes against SARS-CoV-2 and HIV-1 were different and did not significantly correlate. Compared to the ancestral lineage B, the alpha, beta, gamma and delta variants exhibited on average 5.2-fold (range: 1.9-8.2) and 6.7-fold (range: 1.3-21) fold higher IC50s for IFNβ and IFNa;1, respectively. The alpha and delta isolates were also more resistant to IFNβ and IFNa;1 than a lineage B.1 isolate in another AT2 cell line, Calu-3. Conclusion: Our findings suggest that diverse IFNs may have evolved to restrict distinct virus families. Emerging SARS-CoV-2 variants are more effective than earlier pandemic viruses at antagonizing antiviral IFN responses. These data have implications for deploying IFNs for early COVID-19 therapy and suggest that innate immunity may be a driving force for SARS-CoV-2 evolution.