Bacterial or Viral Infections of the Respiratory Tract. Viral illnesses are the most common cause of upper respiratory symptoms. Symptoms of a viral illness often appear over several hours without prior illness.Common viral illnesses include colds and the flu (influenza). Bacterial respiratory tract infections are less common than viral infections.he most common sites of bacterial infections in the upper respiratory system are the sinuses and throat. Pneumonia is the most common bacterial infection of the lower respiratory system.