Western equine encephalitis (WEE) is a virus that can be transmitted to humans and horses by mosquitoes. Mosquitoes can transmit several strains of the encephalitis virus, but WEE is the most prevalent type in California. Culex tarsalis, is the mosquito considered to be the primary vector of this disease. It is found in all California counties, and likes to breed in relatively clean, standing water sources such as wetlands, rice fields, cemetery urns, and backyard sources. Aedes melanimon, which breeds in wetlands and flooded pastures, has also been found to be a vector of the disease.

Historically, both the San Joaquin and Sacramento valleys have been the regions where most WEE has occurred. Encephalitis viruses are believed to be brought into the Central Valley by migrating wild birds, which are the natural reservoirs for the disease. When an uninfected mosquito bites an infected bird, the virus is transferred to the mosquito. The insect can subsequently transmit the virus to horses and humans through its bites. Encephalitis cannot be transmitted directly from person to person, or from birds to people.