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Most Common
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This is a disease caused by herpes virus subtypes EHV-1 and EHV-4. The first symptoms are coughing, nasal discharge and problems breathing. Mares catching equine herpes usually develop inflammation of the uterus. If they are already pregnant, they will abort the fetus. This is a potentially lethal to the adults because it will sometimes cause such problems with coordination that the horse has to be euthanized.
Another Herpes
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Caused by the herpes virus subtype EHV- 3, this horse reproduction disease is called coital exanthema. The Merck Veterinary Manual speculates that this type of equine herpes happens around the world. Coital exanthema causes pus or liquid filled bumps on the horse's gentailia and sometimes down the hind legs. These eventually break open to become painful sores. Mares will also exude a lot of unusual discharge from their vulvas. Not only will a stallion be reluctant to mate, but his sperm count will go down.
Rare
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Contagious equine metritis is a rare disease that could damage a mare's reproductive tract and cause her to become infertile. It is caused by an organism called Taylorella equigenitalis. The mare's vulva oozes a gray discharge one to two days after being bred. Usually the mare will be too ill to conceive from that mating and through her season. The USDA notes that thoroughbreds are more susceptible to this disease.
Parasite
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According to "The Complete Equine Veterinary Manual" (Tony Pavord, MRCVS, et al; 2004) a parasitic protazoa, Typanasama equiperdum, that can live in a horse's blood is responsible for causing the disease dourine. This parasite is transmitted through mating. This causes swelling, discharge, blisters and ulcers on the mare's or stallion's genitals. They often have problems urinating and can develop and coordination problems if left untreated.
Fun Fact
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An equine herpes virus called rhinopneumonitis decimated the rare Lippizan (Lippizanner) breed in 1983. More than 30 horses died--five adults and 25 foals in Austria, the nation that breeds the most Lippizans. This is still a rare breed with only a few thousand living worldwide.
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Horse Reproduction Diseases
Because a mare's gestation is 11 months long, losing one foal to a horse reproductive disease is a significant loss of income for a horse breeder. The most foals a mare can have in her life is 20. But losing a widely sought after stallion is an even bigger blow to the horse breeder because stallions can sire far more foals in his reproductive lifetime. But many reproductive diseases can be prevented through inoculation.