Variant-Specific Temporal Transcriptomic Responses of Ex Vivo Dog Lung Explants to SARS-CoV-2 Delta and Omicron Infection

The rapid evolution and emergence of SARS-CoV-2 variants have posed significant public health challenges due to enhanced transmissibility and diverse clinical outcomes. While the effects of these variants in humans have been extensively investigated, their impact on domestic animals remains insufficiently understood. Given the close interaction between humans and dogs, along with documented cases of human-to-animal transmission and the potential role of companion animals as reservoirs for viral evolution, understanding the molecular dynamics of SARS-CoV-2 infection in dogs is of considerable importance. However, in vivo infection studies in non-laboratory animal species are highly resource intensive, time-consuming, require ABSL3 facilities, and involve ethical constraints, limiting their widespread application. In this context, ex vivo culture systems provide a practical and physiologically relevant alternative. Therefore, in the present study, we employed an ex vivo lung explant culture model derived from domestic dogs to investigate host responses to the SARS-CoV-2 Delta and Omicron variants. Comprehensive transcriptomic profiling across multiple time points post-infection revealed significant alterations in genes associated with cell adhesion, structural components, extracellular matrix (ECM) organization and regulation, immune responses, mitochondrial activity, oxidative phosphorylation, and ribosomal function. Both variants induced marked downregulation of ECM-associated and T-cell-related genes, suggesting disruption of tissue integrity and suppression of adaptive immune responses. The Delta variant was characterized by early and sustained suppression of immune-associated signaling pathways, particularly T-cell receptor signaling, whereas the Omicron variant induced stronger activation of genes associated with mitochondrial activity, oxidative phosphorylation, and translational responses. At later stages of infection, especially at 24 h post-infection (hpi), canine lung explants exhibited increased expression of genes related to tissue repair, epithelial maintenance, mitochondrial function, and ribosomal activity, suggesting activation of compensatory responses aimed at maintaining cellular stability under viral stress. Notably, several hub genes were identified, including CD2, CD3D, CD3E, CD27, PTPRC, ZAP70, SYK, and LCP2 in Delta infection, and FLT3LG, MRPL2, MRPL4, MRPS11, MRPS12, RPS13, and RPS5 in Omicron infection, which are involved in critical pathways associated with immune signaling, mitochondrial function, metabolic regulation, and protein synthesis. Furthermore, the observed mitochondrial and ribosomal responses may indicate that therapeutic strategies aimed at supporting mitochondrial function and modulating excessive inflammation could potentially help reduce lung damage during severe infection. Overall, this study provides important insights into the transcriptomic response of dog lung explants following exposure to SARS-CoV-2 Delta and Omicron variants and also highlights the utility of ex vivo canine lung explant cultures as a valuable platform for studying host–pathogen interactions.