Coronaviruses (CoVs) are positive-sense RNA viruses that replicate in the interior of double membrane vesicles in the cytoplasm of infected cells (Stertz et al. 2007; Knoops K et al. 2008; V’kovski P et al. 2021). The replication strategy of CoVs can generate double-stranded RNA (dsRNA) intermediates, that may act as pathogen-associated molecular patterns (PAMPs) recognized by cytoplasmic pattern recognition receptor (PRR) such as interferon-induced helicase C domain-containing protein 1 (IFIH1, MDA5). Upon sensing long dsRNA species, IFIH1 binds to the caspase activation and recruitment domain (CARD) of mitochondrial antiviral-signaling protein (MAVS, IPS-1) leading to activation of the type I interferon (IFN)-mediated antiviral response. Knockdown by siRNA/shRNA and CRISPR/Cas9 genetic ablation showed that IFIH1 senses severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) infection in human adenocarcinoma-derived lung epithelial Calu-3 cells (Sampaio NG et al. 2021; Yin X et al. 2021; Rebendenne A et al. 2021; Thorne LG et al. 2021). The IFIH1-MAVS-IRF3 signaling axis was necessary for production of type I and III IFNs, but not pro-inflammatory cytokines, in SARS-CoV-2-infected cells (Sampaio NG et al. 2021; Yin X et al. 2021).

Viruses have developed strategies to evade detection by PRRs. For example, viral RNA replication intermediates derived from SARS-CoV-1 and murine coronavirus mouse hepatitis virus (MHV) were shown to associate with the replicase-transcriptase complex (RTC) bound to double membrane vesicles, which protected viral RNA from host sensors (Stertz et al. 2007; Knoops K et al. 2008; Athmer J et al. 2017). CoV's RTC contains several virus-encoded RNA-processing enzymes, which can also protect the viral RNA from recognition by host RNA sensors. Among these, nonstructural protein 15 (nsp15), a highly conserved nidovirus component with endoribonuclease activity. SARS-CoV-1 nsp15 binds and cleaves viral polyuridine (polyU) RNA sequences degrading dsRNA at the site of viral RNA synthesis (Deng X et al. 2017; Deng X & Baker SC 2018). Similar to SARS-CoV-1 nsp15, SARS-CoV-2 nsp15 showed endoribonuclease activity and hydrolyzed 4, 7, and 20 nucleotide long RNAs (Kim Y et al. 2021). Mutations in the SARS-CoV-2 nsp15 catalytic site resulted in reduced or abrogated RNA cleavage (Frazier MN et al. 2021). Viral nsp15-mediated cleavage of RNA prevented activation of host dsRNA sensors dampening IFN production in mammalian cells during CoV infection (Kindler E et al. 2017; Deng X et al. 2017; Hackbar M et al. 2020). In addition, nsp14 of SARS-CoV-2 possesses guanine-N7-methyltransferase activity that can mimic host 5'-cap structure on the viral RNA (Yan L et al. 2021). Overexpression of SARS-CoV-2 nsp14 inhibits the production of IFN-beta and IFN-stimulated genes (Yuen CK et al. 2020; Xia H et al. 2020; Hsu JCC et al. 2021). CoV's nsp16 further modifies this cap with its 2’-O-methyl-transferase activity, allowing the virus to efficiently evade recognition by IFIH1 (MDA5) and DDX58 (RIG-I) (Chen Y et al. 2011; Menachery VD et al. 2014; Daffis S et al. 2010). SARS-CoV-1 with a mutated nsp16 displays reduced virulence that is dependent on IFIH1 sensing (Menachery VD et al. 2014). Mutated nsp16 also attenuates virulence in MERS-CoV and reduces disease severity in infected mice (Menachery VD et al. 2017). Thus, nsp16 is critical to alter the type I IFN-mediated innate antiviral response upon SARS-CoV-1 and MERS-CoV infections.

Nsp15 derived from SARS‐CoV‐2 shares 88% sequence identity and 95% similarity with its known closest homolog from SARS‐CoV-1 suggesting that both homologs have similar function as potent interferon antagonists (Kim Y et al. 2020, 2021). The amino acid sequence alignment of nsp14 and nsp16 from SARS-CoV-2 and of SARS-CoV-1 showed 95 and 93% of sequence identity respectively (Yoshimoto FK 2020). Structural studies and computational analysis suggest that properties and biological functions of SARS-CoV-2 nsp14 and nsp16 could be very similar to these of SARS-CoV-1 (Rosas-Lemus M et al. 2020; Lin S et al. 2020; Viswanathan T et al. 2020; Krafcikova P et al. 2020; Jiang Y et al. 2020; Wilamowski M et al. 2021).

This Reactome event describes IFIH1-mediated sensing of SARS-CoV-2-derived dsRNA. The event is modulated by virus-encoded nsp14, nsp15 and nsp16. However regulation of host RNA sensors by these SARS-CoV-2 RNA-processing enzymes needs further studies.