Early endonuclease-mediated evasion of RNA sensing ensures efficient coronavirus replication

Abstract

Coronaviruses are of veterinary and medical importance and include highly pathogenic zoonotic viruses, such as SARS-CoV and MERS-CoV. They are known to efficiently evade early innate immune responses, manifesting in almost negligible expression of type-I interferons (IFN-I). This evasion strategy suggests an evolutionary conserved viral function that has evolved to prevent RNA-based sensing of infection in vertebrate hosts. Here we show that the coronavirus endonuclease (EndoU) activity is key to prevent early induction of double-stranded RNA (dsRNA) host cell responses. Replication of EndoU-deficient coronaviruses is greatly attenuated in vivo and severely restricted in primary cells even during the early phase of the infection. In macrophages we found immediate induction of IFN-I expression and RNase L-mediated breakdown of ribosomal RNA. Accordingly, EndoU-deficient viruses can retain replication only in cells that are deficient in IFN-I expression or sensing, and in cells lacking both RNase L and PKR. Collectively our results demonstrate that the coronavirus EndoU efficiently prevents simultaneous activation of host cell dsRNA sensors, such as Mda5, OAS and PKR. The localization of the EndoU activity at the site of viral RNA synthesis–within the replicase complex—suggests that coronaviruses have evolved a viral RNA decay pathway to evade early innate and intrinsic antiviral host cell responses.

Propagation of respiratory viruses in human airway epithelia reveals persistent virus-specific signatures

“…The ability of coronaviruses to remain undetected by innate immune sensors has been unraveled recently. 40 Interestingly, for most viruses that affected cilia beating and MCC, a limited number of cells was infected, and the ciliated cell layer was preserved. This observation suggests a paracrine effect, propagated disorganization of cilia beating, or both.…”

Porcine deltacoronavirus nsp15 antagonizes interferon-β production independently of its endoribonuclease activity

“…Although all tested endoribonuclease of nidoviruses have been demonstrated to antagonize IFN production, it is still inconclusive whether this function fully depends on its endoribonuclease activity. Several studies showed that overexpression of WT nsp15 s of CoV or nsp11 s of arterivirus significantly suppressed IFN production, while the mutants lacking endoribonuclease activity lost this capacity (Kindler et al, 2017;Shi et al, 2011;Sun et al, 2016). These evidences appear to indicate that the endoribonuclease activity is essential for nsp15/ nsp11-mediated inhibition of IFN production.…”

“…However, it is appears that different mechanisms are utilized by the endoribonucleases from different nidoviruses. For example, the nsp15 s of MHV and HCoV-229E prevent the activation of IFN response by mediating the evasion of host recognition of viral dsRNA (Deng et al, 2017;Kindler et al, 2017); PRRSV nsp11, the orthologue of CoV nsp15, antagonizes type I IFN production by suppressing both MAVS and RIG-I expression . SARS-CoV nsp15 antagonizes type I IFN production by inhibiting MAVS-induced apoptosis (Lei et al, 2009), however, MERS-CoV nsp15 does not utilize this strategy although it also inhibits type I IFN production with a yet-to-be identified mechanism.…”

MERS coronavirus outbreak: Implications for emerging viral infections

“…In common with other coronaviruses, the MERS-CoV nsp3 PLpro removes ubiquitin (Ub) (deubiquitination; DUB), and interferon-stimulated gene 15 (ISG15) (deISGylation) from host cell proteins, which in turn blocks production of IFN-β and hence reduces type-1 interferon responses in cell line studies (Báez-Santos et al, 2014;Daczkowski et al, 2017). MERS-CoV nsp15, which contains an endonuclease (EndoU) activity, has also been recently shown in primary cell lines and in macrophages to reduce early innate immune responses by inhibition of MDA-5, PKR and OAS responses and IFN activation (Kindler et al, 2017). Nsp16, a viral 2'O-methyltransferase (2'O-MTase), has also been recently implicated in viral pathogenesis and type I-IFN inhibition in both primary human airway cell cultures and in vivo mouse models (Menachery et al, 2017a).…”