A SARS-CoV-2 enzyme activates one antiviral defense while disabling another

A recent study from the Overall Lab in Cell Reports shows that effective antiviral defense relies on the coordinated activity of interferon-stimulated genes (ISGs), which are turned on by interferon, a key immune signal. Among these are the four 2´–5´-oligoadenylate synthetases, or OAS proteins; when OAS binds viral double-stranded RNA (dsRNA), it produces 2´–5´ oligoadenylates (2-5A), which cause RNase L to dimerize—meaning two RNase L molecules pair up and become active. Once activated, RNase L cuts both viral and host RNAs, thereby inhibiting global protein synthesis and promoting apoptosis to limit viral replication.

The OAS1 p46 isoform displays a membrane anchor at its C terminus, the tail end of the protein, which helps position p46 to detect viral dsRNA at membrane-bound viral replication sites inside the cell. Interestingly, p46 is inherited from Neanderthals and was positively selected, meaning it provided a benefit that made it more common over time. It is found at frequencies of about 80–90% in African populations, 50–65% in Europeans, and 10–25% in East Asians, suggesting it plays an important role in antiviral defense and may help explain differences in susceptibility to SARS-CoV-2 among populations.

Bell et al. report that the SARS-CoV-2 3C like main protease, also called 3CL^pro or M^pro, removes the C terminus of OAS1 p46. This disrupts p46’s ability to sense viral dsRNA near membrane-associated replication sites and weakens early activation of the OAS1–RNase L pathway during SARS-CoV-2 infection.

Their study also found a paradoxical role for 3CL^pro in the OAS–RNase L pathway. Although 3CL^pro blocks antiviral signaling by removing the prenylated anchor of the OAS1 p46 isoform, it also directly activates RNase L by cutting it at a highly conserved site, ⁴⁰⁶SCLQ⁴⁰⁹↓S. This cleavage removes the inhibitory N-terminal 2-5A-binding domain of RNase L and produces a catalytically active C-terminal proteoform, meaning a functional protein form, that restricts viral replication even without the usual OAS-2-5A signaling pathway.

As 3CL^pro builds up inside infected cells, RNase L cleavage increasingly compensates for the earlier loss of upstream signaling, creating a response that unfolds in stages over time. In this way, the virus’s antagonism of OAS1 is linked to a non-canonical, or alternative, activation of RNase L.

The fact that the ⁴⁰⁶SCLQ⁴⁰⁹↓S motif is broadly retained across species suggests that it is an evolutionarily conserved antiviral regulatory feature that acts like a 'molecular tripwire' against immune evasion. Its position allows RNase L to be activated by proteolytic cleavage when the normal OAS-2-5A pathway is bypassed by viruses that make 3CL or 3C proteases.

By targeting both OAS1 and RNase L, 3CL^pro reveals an important constraint on viral immune evasion: the protease activity that the virus needs to process its own proteins and replicate also creates a host defense the virus cannot completely avoid. This appears to be one of the first antiviral host defenses shown to be activated by a viral protease, which usually serves to disable host immunity. It also raises the possibility that additional protective host proteins and pathways may be activated in similar ways.

Source Publication: Bell PA, Baid K, Pan C, Grin PM, de Jesus VCR, Kappelhoff R, Pablos I, Butler GS, Shrivastava S, Ansari A, Banerjee A, Overall CM. Non-canonical proteolytic activation of RNase L by SARS-CoV-2 3CLpro offsets inactivation of OAS1 p46 antiviral signaling. Cell Rep. 2026;45(4):117257. doi:10.1016/j.celrep.2026.117257.