The accessory protein ORF3a hijacks the CLCC1 chloride channel to disrupt ER homeostasis in betacoronavirus pathogenesis.

Beta-coronavirus infection disrupts endoplasmic reticulum (ER) homeostasis; however, the mechanisms by which viral proteins manipulate ER-resident factors remain unclear. Here, we report that the SARS-CoV-2 accessory protein ORF3a binds to the ER chloride channel CLCC1, thereby impairing ER ion homeostasis, activating the unfolded protein response, and inducing endomembrane remodeling. Using newly developed ratiometric reporters, we showed that this interaction exacerbated the basal levels of ER-phagy and nucleophagy. Importantly, CLCC1 counteracted ORF3a by sequestering it within the ER, attenuating its toxicity and suppressing viral replication, which established CLCC1 as a host restriction factor. We further elucidated a spatiotemporal mechanism: during early infection, ORF3a accumulates in the ER, co-assembles with CLCC1 into puncta, and disrupts ER homeostasis; at the later stage, ORF3a overload enables its escape from CLCC1-mediated ER retention and subsequent translocation to lysosomes, facilitating viral egress. This ER-centric function is conserved across diverse beta-coronaviruses, including SARS-CoV-1 and bat- or pangolin-derived strains, revealing a unified pathogenic strategy. Furthermore, in mouse brains, the ORF3a-CLCC1 axis recapitulates key neuropathological features, including ER stress, autophagic dysfunction, neuronal death, and neuroinflammation, providing a mechanistic link to COVID-19-associated neurological symptoms. Our findings identify CLCC1 as an essential host defense protein and establish a conceptual framework to guide future research on antiviral responses at the organelle level and related disease mechanisms.