Stimulation of dysregulated IFN-β responses by aberrant SARS-CoV-2 small viral RNAs acting as RIG-I agonists

Patients with severe COVID-19 exhibit a cytokine storm characterized by greatly elevated levels of cytokines during worsening disease1-4. Despite this, the interferon (IFN) response is delayed, contributing to disease progression5. Here, we report that SARS-CoV-2 generates excessive amounts of small viral RNAs (svRNAs) encoding exact 5′ ends of positive sense genes in human cells, whereas significantly fewer similar svRNAs are produced by endemic human coronaviruses (OC43 and 229E). SARS-CoV-2 5′ end svRNAs are potent RIG-I agonists associated with IFN-β expression in later stages of infection. The first 60-nt ends bearing duplex structures and 5′-triphosphates are responsible for immune-stimulation. The 5′ end svRNAs were also produced during infection in vivo. The delta variant retains the robust 5’ end svRNA production of the parental strain, whereas omicron no longer produces these erroneous svRNAs. We propose that RIG-I activation by accumulated 5′ end svRNAs overcomes the initial IFN antagonistic ability of viral proteins and drives late over-exuberant IFN production leading to the development of severe COVID-19 and suggest that evolutionary modification of SARS-CoV-2 5’ end svRNA production may correlate with the reduced disease severity likely seen with omicron.