Researchers from the University of Cambridge and MIT have made a significant discovery regarding the SARS-CoV-2 virus. They have identified a previously unnoticed accessory protein called ORF3c, which plays a crucial role in modulating innate immunity within mitochondria. This finding sheds light on a previously unknown aspect of the virus-host interaction and presents potential targets for therapeutic interventions.
The SARS-CoV-2 virus, a member of the Coronaviridae family, possesses a large RNA genome. It contains various protein-coding open reading frames (ORFs), including ORF1a, ORF1b, and several nested subgenomic mRNAs that encode structural and accessory proteins. While structural proteins are vital for viral replication, accessory proteins help the virus evade the host immune response.
Identifying all the viral proteins encoded by SARS-CoV-2 has been challenging due to the virus’s rapid emergence and the lack of experimental validation for many predicted ORFs. However, through comparative genomics, researchers have uncovered a previously undetected ORF, called ORF3c, which overlaps with ORF3a. This protein had been present during the earlier SARS-CoV-1 outbreak but had not been extensively studied. This study has brought ORF3c to the forefront, revealing its potential significance in viral replication, immune evasion, or transmission.
Understanding the immune response is critical in the context of SARS-CoV-2 infection. The type I interferon (IFN) response, a fundamental aspect of innate immunity, plays a crucial role in limiting viral infections. Host cells produce type I IFNs upon activation of pattern recognition receptors (PRRs), which detect pathogen-associated molecular patterns (PAMPs). This leads to the transcription of type I IFNs and other antiviral genes, initiating a defense mechanism against the virus.
Two central cytoplasmic PRRs responsible for detecting viral RNA and initiating the antiviral response are RIG-I and MDA5. These PRRs interact with mitochondrial antiviral-signaling protein (MAVS) to trigger downstream signaling events. When activated, MAVS forms polymers at the mitochondrial outer membrane, activating transcription factors that stimulate the transcription of type I IFNs and other pro-inflammatory factors.
The researchers have discovered that ORF3c localizes to the mitochondrial outer membrane (MOM), which serves as a critical platform for innate immune signaling. They have found that ORF3c inhibits the production of interferon-beta (IFN-β), thereby evading the host’s antiviral response. ORF3c interacts with MAVS and PGAM5, leading to MAVS cleavage by caspase-3 and a subsequent reduction in IFN-β production. However, it does not impact NF-κB-driven transcripts, indicating specificity in its inhibitory effects on the IFN-β pathway.
Further comparative analysis of SARS-CoV-2 accessory proteins has revealed that ORF3c is the only conserved sarbecoviral protein that directly binds to MAVS within the MOM. Unlike other viral proteins that affect IFN-β signaling, ORF3c operates directly within the mitochondria to suppress the antiviral response.
The discovery of ORF3c as a critical modulator of innate immunity expands our understanding of SARS-CoV-2 infection and provides potential targets for therapeutic interventions. Further investigations into ORF3c and its implications for viral pathogenesis may pave the way for novel strategies to combat COVID-19 and future coronaviral infections. The study findings were published in the peer-reviewed journal iScience.