An upper respiratory tract infection or “cold” in a horse, like in a human, can be caused by many different viruses or bacterial infections—adenovirus, herpesvirus (Type 1, 2, 4, 5), influenza virus, rhinitis A or B virus, Strep equi (“Strangles”)—or even a combination of these agents. Horses can be vaccinated against some respiratory pathogens, namely herpesvirus Type 1 and 4, Influenza, and Strangles, but many other viruses especially are not included in the routine vaccinations (much as humans can be vaccinated against influenza but not the common cold). Additionally, each horse’s immune system will respond differently to a given vaccine, and a small percentage of horses will be “non-responders.” These horses do not mount an adequate immune response following even properly administered vaccinations. If your horse develops an upper respiratory infection even when they have received their yearly vaccinations, they could be infected by one of these other viruses (adenovirus, other herpesvirus types, rhinitis virus), or their immune system simply did not respond to the vaccine as well as some other horses.
Vaccination FAQ - My horse is vaccinated—why did it still get a cold?