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Equine Flu or Allergies
Did you realize your horse could have allergies?  It makes sense if you consider the type of environment they live in.  If they are not outside (and in some instances even if they are) they can have an allergic reaction to dust, molds, smoke, and other air borne allergens like burning smudges, bug spray and perfumes or medicinal odors.
The name for this condition is Allergic Respiratory Disease (ARD) and it shows up with flu-like symptoms rather than sinus or nasal difficulties.  The horse's lungs will get inflamed, making them far more susceptible to virus and bacterial infections.  This manifests as a recurring problem your horse never quite gets over.  You'll also likely see coughing, excessive eye discharge and discover they get tired easily.
It seems the most common cause of ARD is several types of mould spores and weeds in hay or straw.  This is a seasonal thing, so you may only see the problem popping up in the spring and the summer.  Problem is, winter and fall feed come from the same source, so what happens is the horse builds up sensitivity over time and their reactions increase.
You can keep them outside in fresh air to try reducing the symptoms.  If however your horse needs to be stalled, store your hay in a different location and make sure the airflow in the barn is good.  Soak your hay before feeding if there is a dust problem.
If your at home solutions aren't helping much, call your Vet and have her take a look at the fluid and cells in the horse's lungs to figure out how severe the allergy is.  There's also a new blood test that can tell the Vet precisely what the horse is allergic to.  Exciting news, because that means customized treatments for each horse.  Other treatments include corticosteroids (cortisone) and bronchodilators. 
Figuring out what the problem is in the first place is half the battle and once you have that under control, your horse is well on his way to making a good recovery. 
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