The present invention provides compositions and methods that are useful for the treatment of severe acute respiratory syndrome (SARS). More specifically, nucleic acid agents such as siRNA molecules and their analogues that target respiratory infections including SARS coronavirus and their methods of use are described, for clinical treatments of SARS, respiratory viral infections, for prevention and treatment of respiratory infections as needed for bio-defense, for treatment of respiratory diseases, and for discovery of therapeutic targets for respiratory diseases and infections.