Type I interferon susceptibility distinguishes SARS-CoV-2 from SARS-CoV
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Abstract
SARS-CoV-2, a novel coronavirus (CoV) that causes COVID-19, has recently emerged causing an ongoing outbreak of viral pneumonia around the world. While distinct from SARS-CoV, both group 2B CoVs share similar genome organization, origins to bat CoVs, and an arsenal of immune antagonists. In this report, we evaluate type-I interferon (IFN-I) sensitivity of SARS-CoV-2 relative to the original SARS-CoV. Our results indicate that while SARS-CoV-2 maintains similar viral replication to SARS-CoV, the novel CoV is much more sensitive to IFN-I. In Vero and in Calu3 cells, SARS-CoV-2 is substantially attenuated in the context of IFN-I pretreatment, while SARS-CoV is not. In line with these findings, SARS-CoV-2 fails to counteract phosphorylation of STAT1 and expression of ISG proteins, while SARS-CoV is able to suppress both. Comparing SARS-CoV-2 and influenza A virus in human airway epithelial cultures (HAEC), we observe the absence of IFN-I stimulation by SARS-CoV-2 alone, but detect failure to counteract STAT1 phosphorylation upon IFN-I pretreatment resulting in near ablation of SARS-CoV-2 infection. Next, we evaluated IFN-I treatment post infection and found SARS-CoV-2 was sensitive even after establishing infection. Finally, we examined homology between SARS-CoV and SARS-CoV-2 in viral proteins shown to be interferon antagonists. The absence of an equivalent open reading frame (ORF) 3b and changes to ORF6 suggest the two key IFN-I antagonists may not maintain equivalent function in SARS-CoV-2. Together, the results identify key differences in susceptibility to IFN-I responses between SARS-CoV and SARS-CoV-2 that may help inform disease progression, treatment options, and animal model development.
Importance
With the ongoing outbreak of COVID-19, differences between SARS-CoV-2 and the original SARS-CoV could be leveraged to inform disease progression and eventual treatment options. In addition, these findings could have key implications for animal model development as well as further research into how SARS-CoV-2 modulates the type I IFN response early during infection.
Article Summary
SARS-CoV-2 has similar replication kinetics to SARS-CoV, but demonstrates significant sensitivity to type I interferon treatment.
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SciScore for 10.1101/2020.03.07.982264: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization No blinding was used in any sample collections, nor were samples randomized. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources The membranes were blocked for 1 h at room temperature with 5% skim milk and then incubated overnight at 4°C with appropriate primary antibody dilution: anti-STAT1 (1:1000, Cell Signaling), anti-pSTAT1 (1:1000, Cell Signaling) or anti-beta actin (1:5000, Invitrogen). anti-STAT1suggested: Noneanti-pSTAT1suggested: (Fluidigm Cat# 3153003A, RRID:AB_2811248)anti-beta actinsuggested: NoneThen, the … SciScore for 10.1101/2020.03.07.982264: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization No blinding was used in any sample collections, nor were samples randomized. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Cell Line Authentication not detected. Table 2: Resources
Antibodies Sentences Resources The membranes were blocked for 1 h at room temperature with 5% skim milk and then incubated overnight at 4°C with appropriate primary antibody dilution: anti-STAT1 (1:1000, Cell Signaling), anti-pSTAT1 (1:1000, Cell Signaling) or anti-beta actin (1:5000, Invitrogen). anti-STAT1suggested: Noneanti-pSTAT1suggested: (Fluidigm Cat# 3153003A, RRID:AB_2811248)anti-beta actinsuggested: NoneThen, the membranes were incubated with the recommended dilution of HRP-conjugated secondary antibody (goat anti-rabbit IgG HRP 1:10000, Invitrogen; goat anti-mouse IgG HRP 1:10000, Invitrogen) at room temperature for 1 h. anti-rabbit IgGsuggested: Noneanti-mouse IgGsuggested: (LSBio (LifeSpan Cat# LS-C149336-10000, RRID:AB_11143677)Following overnight incubation, membranes were probed with the following secondary antibodies in 5% (w/v) non-fat dry milk in TBST for 1 hr at room temperature: anti-rabbit or anti-mouse IgG-HRP conjugated antibody from sheep (both 1:10,000 GE Healthcare). anti-rabbitsuggested: Noneanti-mouse IgG-HRPsuggested: NoneThe following primary antibodies were used: anti-pSTAT1 (Y701) (1:1000 9171L Cell Signaling Technologies), anti-STAT1 D1K9Y (1:1000 14994P Cell Signaling Technologies), anti-IFITM1 (1:1000 PA5-20989 Invitrogen), anti-SARS-CoV/CoV-2 Spike 1A9 (1:1000 GTX632604 GeneTex), and anti-β-Actin (1:1000 ab8227 Abcam). anti-pSTAT1 (Y701)suggested: Noneanti-STAT1 D1K9Ysuggested: (Cell Signaling Technology Cat# 14994, RRID:AB_2737027)anti-IFITM1suggested: (LSBio (LifeSpan Cat# LS-C122003-100, RRID:AB_10799885)anti-SARS-CoV/CoV-2 Spike 1A9suggested: Noneanti-β-Actinsuggested: NoneExperimental Models: Cell Lines Sentences Resources Calu3 2B4 cells were grown in DMEM with 10% defined fetal bovine serum, 1% sodium pyruvate (Gibco), and 1% antibiotic/antimitotic (Gibco). Calu3 2B4suggested: RRID:CVCL_YZ47)Infection and type I IFN pre- and post-treatment: Viral replication studes in Vero E6 and Calu3 2B4 cells were performed as previously described (37, 54). Vero E6suggested: NoneSoftware and Algorithms Sentences Resources Phylogenetic Tree and Sequence Identity Heat Map: Heat maps were constructed from a set of representative group 2B coronaviruses by using alignment data paired with neighbor-joining phylogenetic trees built in Geneious (v.9.1.5). Geneioussuggested: (Geneious, RRID:SCR_010519)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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