What Diseases Do Flying Squirrels Carry? Though rabies is strongly associated with wildlife pests, flying squirrels are not known to transmit the virus. In fact, the northern species of the pest doesn't harbor any known diseases that can be passed on to humans. The southern flying squirrel, on the other hand, is a well-established carrier of the bacteria that causes typhus fever. Symptoms include headaches, fever, and vomiting followed by a painful rash across the chest and back. Scientists are still unclear as to how the bacteria is transferred from flying squirrels to humans. Trapping and Removal People are strongly encouraged to keep a healthy distance from flying squirrels to avoid contracting any illnesses. Since they are known to nest in homes and barns, it is crucial that they be removed immediately. Trapping the pests is difficult because they often nest in groups of three to eight. The experts at Critter Control have the knowledge and the tools to humanely and efficiently remove infestations from homes and keep residents safe from flying squirrel diseases.