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). 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 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. 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). Further, nonstructural protein 15 (nsp15), a highly conserved nidovirus component with endoribonuclease activity, was reported to remove dsRNA species at the site of viral RNA synthesis thus limiting the exposure of viral dsRNA to host dsRNA sensors in the cytosol (Deng X et al. 2017; Deng X & Baker SC 2018). The endoribonuclease activity of nsp15 derived from SARS-CoV-1 and human coronavirus 229E (HCoV229E) involved a Mn2+-dependent, uridylate-specific cleavage of RNAs (Ivanov KA et al. 2004; Bhardwaj K et al. 2004, 2006, 2008). Middle East respiratory syndrome (MERS)-CoV nsp15 and MHV nsp15 acted in conjunction with the viral RTC (Athmer J et al. 2017; Zhang L et al. 2018). In addition, nsp14 of SARS-CoV-1 possesses guanine-N7-methyltransferase activity that can mimic host 5'-cap structure on the viral RNA (Chen Y et al. 2009). Nsp16 of SARS-CoV 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). Mutating 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 and MERS 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). 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 suggest that properties and biological functions of SARS-CoV-2 nsp14 and nsp16 could be very similar to these of SARS-CoV-1 (Decroly E et al. 2011; Chen Y et al. 2011; Rosas-Lemus M et al. 2020; Lin S et al. 2020; Viswanathan T et al. 2020).

The Reactome event shows IFIH1-mediated sensing of SARS-CoV-1-derived dsRNA. The event is modulated by virus-encoded enzymes nsp14, nsp15 and nsp16 that modify viral RNAs at the site of viral RNA synthesis to protect the viral RNA from recognition by host immune sensors.