bioRxivBioinformaticsPreprint
SARS-CoV-2 ORF9c Is a Membrane-Associated Protein that Suppresses Antiviral Responses in Cells
Ana Dominguez Andres, Yongmei FengiD, Alexandre Rosa CamposiD, Jun YiniD, Chih-Cheng Yang, Brian P. JamesiD, Rabi MuradiD, Hyungsoo KimiD, Aniruddha J. DeshpandeiD, David Ezra GordoniD, Nevan J. KroganiD, Raffaella PippaiD, Ze’ev A. RonaiiD
Abstract
Disrupted antiviral immune responses are associated with severe COVID-19, the disease caused by SAR-CoV-2. Here, we show that the 73-amino-acid protein encoded by ORF9c of the viral genome contains a putative transmembrane domain, interacts with membrane proteins in multiple cellular compartments, and impairs antiviral processes in a lung epithelial cell line. Proteomic, interactome, and transcriptomic analyses, combined with bioinformatic analysis, revealed that expression of only this highly unstable small viral protein impaired interferon signaling, antigen presentation, and complement signaling, while inducing IL-6 signaling. Furthermore, we showed that interfering with ORF9c degradation by either proteasome inhibition or inhibition of the ATPase VCP blunted the effects of ORF9c. Our study indicated that ORF9c enables immune evasion and coordinates cellular changes essential for the SARS-CoV-2 life cycle. One-sentence summarySARS-CoV-2 ORF9c is the first human coronavirus protein localized to membrane, suppressing antiviral response, resembling full viral infection.
Abstract summary
Claude Opus 5.5 · xhigh effort · 2 Nov 2026 · from the abstract
The 73-amino-acid SARS-CoV-2 membrane-associated protein ORF9c suppresses interferon, antigen presentation, and complement pathways while inducing IL-6 signaling in lung epithelial cells, an effect blunted by proteasome or VCP inhibition.
Severe COVID-19 is linked to disrupted host antiviral immune responses during SARS-CoV-2 infection. Expressing the 73-amino-acid viral protein ORF9c alone in lung epithelial cells reveals a membrane-associated mechanism that suppresses host antiviral signaling while inducing IL-6 pathways.
Key results
ShownExpressing the unstable 73-amino-acid SARS-CoV-2 ORF9c protein alone in a lung epithelial cell line targets membrane proteins across multiple compartments, suppresses antiviral and immune pathways, and induces IL-6 signaling.
Proteomic, interactome, transcriptomic, and bioinformatic analyses of cells expressing the 73-amino-acid ORF9c protein showed impaired interferon, antigen presentation, and complement signaling alongside induced IL-6 signaling. · Abstract
ShownBlocking the degradation of ORF9c attenuates its downstream cellular and immunomodulatory effects.
Inhibiting either the proteasome or the ATPase VCP blunted the effects of ORF9c expression (quantitative effect sizes not reported in the abstract). · Abstract
Methods, data and reproducibility
The authors expressed the 73-amino-acid SARS-CoV-2 ORF9c protein in a lung epithelial cell line, characterized its host effects using proteomic, interactome, transcriptomic, and bioinformatic analyses, and tested the impact of blocking ORF9c degradation via proteasome or ATPase VCP inhibition.
- Proteomic, interactome, and transcriptomic profiles of a lung epithelial cell line expressing the 73-amino-acid SARS-CoV-2 ORF9c protein · SARS-CoV-2 (expressed in an unnamed lung epithelial cell line)
Limitations (2)
- Experiments described in the abstract rely on overexpressing isolated ORF9c in a single lung epithelial cell line rather than live SARS-CoV-2 viral infection. · noted in this summary
- The abstract does not report the identity of the lung epithelial cell line, sample sizes, statistical metrics, or data accessions. · noted in this summary
Read this if you investigate SARS-CoV-2 accessory proteins or host immune evasion mechanisms and want to understand how membrane-associated ORF9c alters interferon and IL-6 signaling.
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