SARS-CoV-2 PLpro Hijacks a Conserved Stress Signaling Network to Drive Organ-Specific Loss of Epithelial Homeostasis

Severe SARS-CoV-2 infection manifests as a systemic disorder characterized by catastrophic loss of epithelial homeostasis and dysregulated host inflammation. However, which specific viral factors initiate this tissue damage in intact, living organisms remains unresolved. Using a comprehensive in vivo screen of all 25 SARS-CoV-2 nonstructural proteins (NSPs) and accessory factors (ORFs) in the Drosophila wing imaginal epithelium, here we have identified NSP5 (Main protease, Mpro) and NSP3--specifically its papain-like protease (PLpro) domain--as individual triggers of tissue injury. Focusing further on PLpro, we demonstrate that its expression initiates a self-amplifying host cell stress signaling circuit driven by metabolic overdrive, oxidative stress, and hyperactivation of Akt, JNK, and JAK-STAT signaling. However, this pathogenic loop is fragile; genetic suppression of any of the hyperactivated signaling nodes collapses this network, thereby restoring epithelial homeostasis. This organ-intrinsic, PLpro-induced epithelial vulnerability is also seen in the adult midgut and larval respiratory system. Notably, in the larval respiratory system, PLpro drives compartment-specific pathologies: it induces fibrosis-like remodeling in terminally differentiated squamous tracheal tubes, while catastrophically depleting the progenitor-competent tracheoblasts and air sac precursors (ASP). Both these defects are reversed by the genetic knockdown of PLpro-induced JAK-STAT signaling. Finally, we show that PLpro expression in mammalian MDCK epithelia similarly triggers junctional remodeling and inflammatory stress signaling. Our findings position PLpro as a central driver of COVID-19 pathogenesis through a self-amplifying epithelial stress circuit that compromises epithelial homeostasis across organs and species.