Eastern equine encephalitis (EEE) and Western equine encephalitis (WEE) are mosquito-borne viral diseases that primarily affect horses east and west of the Mississippi River, as their names imply.  The Centers for Disease Control and Prevention (CDC) last reported cases of EEE and WEE in horses, other animals, and humans in 1997.  Since then, only summaries of human encephalitis cases are reported by CDC.  These numbers likely underestimate the human cases since viral encephalitis is not a reportable disease in all states.
In 2001, the National Veterinary Services Laboratories (NVSL), Ames, Iowa tested 899 diagnostic serum samples for antibodies to EEE and WEE, and performed virus isolation attempts on 224 brain tissue or whole blood samples.  

The majority of samples were of equine origin, with less than 10% of avian origin.  EEE virus isolates obtained by cell culture or mouse inoculation were confirmed by complement fixation assay using Eastern, Western and Venezuelan equine encephalitis virus reference antigens and sera.  All horse brain submissions tested negative for rabies virus antigen.

Of the samples submitted, 95 horses and two birds had laboratory evidence of EEE infection. All EEE virus isolates were obtained from brain tissue samples.  These EEE-positive samples were negative for West Nile virus RNA by nested RT-PCR testing.

Serologic identifications of EEE cases were based on several testing procedures along with reported clinical signs and vaccination history