Horse Health; The Cough

What you see: Your horse has developed a cough.
What this might mean: In most cases, a cough in an adult horse is a sign of irritation of the windpipe (trachea) due to a mild viral infection, usually the flu (equine influenza) or rhino (equine viral rhinopneumonitis or equine Herpesvirus-1). If treated promptly and properly, the cough should resolve within 3-4 weeks. But coughing also can be a sign of an allergy or a viral and/or bacterial infection in the lungs. The latter two causes can be extremely serious- even fatal.
While you wait:
1) Isolate your horse from other horses in case it's contagious. To prevent spread of possible infectious disease, confine your horse to an open-air paddock or stall with a separate water supply, apart from other horses by at least 20 feet. Wash your hands and disinfect your boots after handling your horse and before handling other horses.
Home treatment:
1) Minimize irritants in his environment. Avoid dusty trails. Replace dusty bedding with clean, less dusty bedding, such as shredded paper. Replace dusty hay with hay of better quality, or dampen it with water just before feeding so dust won't be inhaled.
2) Minimize irritating activities. Tone down your horse's daily exercise program to avoid heavy breathing, which is irritating to his repiratory tract. For example, if he coughs after loping, don't lope. Instead, work at a slower, less strenuous gate that doesn't induce immediate or delayed coughing.
3) Help him stay hydrated. Encourage water intake so discharges in his respiratory tract won't get thick, sticky, and difficult to clear out. Clean his water source daily and add new water sources. Provide free-choice, loose, plain salt. If it's cold outside, offer an extra bucket of water that's been warmed to 120 degree's.
4) Minimize stress. Postpone stressful activities such as vaccinations, breeding, trailer trips, long rides, or competitions, until your horse has been cought-free for at least 3 weeks. Stress during illness has been suggested to increase the risk of secondary infections.
5) Be ready to call for help. If a fever develops, if appetite wanes, if your horse simply fails to improve within 3 days on home treatment, call your veterinarian.

If my horse has a cough, and my vet says it's probably rhino or the flu, should I give a rhino or flu vaccination now?
NO, for 3 reasons. First, if your horse is in the throes of an infection, you shouldn't stress him with a vaccination of any sort. Second, the vaccination is unlikely to do any good at this time- your horse's heightened immune system, which is busy fighting off his current infection, will quickly inactivate it. And third, there's concern among the veterinary research community that vaccinating for rhino in the face of a rhino infection increases the risk that your horse will develop paralytic rhino, a rare, dangerous form of the disease that attacks the nervous system.