SARS-CoV-2 Nsp15 endoribonuclease subverts host defenses to enhance viral fitness in lung cells

ABSTRACT Coronaviruses encode nonstructural protein 15 (Nsp15), a conserved endoribonuclease (EndoU) known to suppress host antiviral responses. It is imperative to understand the role of Nsp15/EndoU during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in its primary target respiratory epithelial cells. Using a recombinant wild-type SARS-CoV-2 (rWT) and a mutant with catalytically inactive EndoU (rH234A), we show that the EndoU activity is dispensable for viral replication in Vero cells but critically facilitates immune suppression and infection in physiologically relevant human lung cells, including human lung-derived epithelial cell lines, primary bronchial air-liquid interface cultures, and alveolar type 2 organoids derived from induced pluripotent stem cells. Compared to rWT, rH234A infection elicited augmented type I and III interferon (IFN) responses and stronger RNase L activation, suggesting that Nsp15 suppresses these antiviral pathways during SARS-CoV-2 infection. Although rH234A infection increased PKR phosphorylation, downstream eIF2α phosphorylation and stress granule formation remained limited, implying incomplete PKR/eIF2α pathway activation. Furthermore, Nsp15 mutants lacking key residues required for hexamerization or double-stranded RNA binding also showed impaired replication and heightened IFN responses, highlighting the importance of these structural features for EndoU function. In vivo , rH234A was attenuated in K18-hACE2 mice, resulting in improved survival, reduced viral loads, and milder lung pathology. Together, these findings demonstrate SARS-CoV-2 Nsp15/EndoU as a key immune antagonist that facilitates lung infection, underscoring its potential as a target for antiviral development. IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects upper and lower airway epithelial cells, and the latter infection can result in severe pneumonia. Understanding how the virus evades host immunity in these primary target cells is critical for developing effective therapies. Nsp15, a conserved coronavirus endoribonuclease (EndoU), is known to suppress antiviral responses, but its precise role in respiratory epithelial cells has remained unclear. This study reveals that while EndoU activity is dispensable for viral replication, it is essential for dampening host defenses in human lung-derived epithelial cell lines, primary bronchial air-liquid interface cultures, and alveolar type 2 organoids. Loss of EndoU activity results in enhanced interferon signaling and RNase L activation, along with partial PKR pathway engagement. Structural integrity, including double-stranded RNA binding and hexamerization, is vital for Nsp15 function. In vivo , an EndoU-deficient virus is attenuated in K18-hACE2 mice. These findings position Nsp15 as a key immune antagonist and a promising target for antiviral intervention.