791 Equine epidemic

In 791, Charlemagne led a campaign to the east in the region of the Avar khaganate to begin the first Avar war. After a brief success, disaster struck as an epidemic spread through and wiped out 90% of Charlemagne's horses. War steeds, travel mounts and pack animals were infected and either died or rendered ineffectual. The fact that Charlemagne did not perform another military campaign for another 2 years (and he is known for having campaigned every year for the rest of his reign/life), brings into evidence how much man relied on the service of horses. In all aspects of medieval life, agriculture, transport, travel and the military, which was an essential part of existence.   

Historians suspect that the cause for the epidemic was Equine Encephalomyelitis virus. This is quite possible for a number of reasons. It is an Alphavirus from the Togaviridae family. It is a vector borne disease transmitted by mosquitoes. The marshy banks of the Danube river would have made a perfect set up for the virus. Mosquitos would have been in elevated numbers after the summer breeding season. The horses would have been totally immuno-naive as then, like now, the disease is not prevalent in Europe; making them absolute sitting ducks. The disease carries a fair mortality rate, even now, as symptomatic treatment and intense nursing is the only form of management. Symptoms range from fever, anorexia, depression to various neurological signs like tremors, ataxia, impaired vision, head pressing, aimless wandering, circling, inability to swallow, weakness, paralysis, convulsions and death. The survivors are likely to subsequently have been rendered ineffectual due to persistent neurological symptoms and/or weakness. Humans can also be affected but mostly children, the elderly or immunocompromised individuals, making it unlikely to infect healthy soldiers.

There is also a theory that the reason for Charlemagne's initial, overwhelming, success was due to the adversary army's horses being affected by the same ailment before the franks arrival. 

The other disease possibility, that I have read about, is that they died of Equine influenza.. This is a very contagious disease, which in my mind fits better with the mortality rate of 90% . It causes a fever, dry cough, loss of appetite and fatigue, weakness. Today, besides being very well controlled by vaccination, it it rarely fatal. This, however would have been very different in 791 without effective medication or knowledge of the nature of disease. 

So, with the lack of more information it is pure speculation as to what caused the disease wiping out nearly the whole horse contingency of a formidable army, thus changing the course of history. 

I would wager that a contagious disease would have been more likely to cause such devastation, however the conditions at the time could certainly account for the ruinous results.

I will continue the reading and research into this fascinating event and update you if more info comes to light.