The pathogenesis of the EEEV virus is exceedingly challenging to investigate due to its extreme peril and high lethality. The mechanisms of infection and pathogenicity caused by the EEEV virus P protein were investigated in this study using bioinformatics tools for domain searches. The results showed that the EEEV virus P protein has parts that bind cholesterol and very low density lipoprotein, such as SRCR and Lipid-binding serum glycoprotein. ARF7 effector protein C-terminal, BAR, Ephrin RBD, Granulins, MHD1, Sema, TLC, Transient receptor ion channel, Ionotropic glutamate receptor, Voltage-dependent calcium channel alpha-2 are some of the related domains that mess up synaptic guidance and transmission. The protein also includes potassium-ion neuron channel domains, such as the Neurotransmitter-gated ion-channel ligand-binding, Neurotransmitter-gated ion-channel transmembrane domain. The study shows that the EEEV virus P protein attaches to the synaptic membrane through the cholesterol/very low density lipoprotein domain. This creates a depolarization or hyperpolarization potential at the synaptic level by controlling the activity of Ca2+ channels. This results in increased or decreased excitability of postsynaptic nerves, thereby interfering with synaptic guidance. Subsequently, the protein inserts itself as a potassium ion transmembrane nerve channel into the synaptic membrane, and binding to neurotransmitter ligands triggers its potassium ion nerve channel function. This process guides the synaptic membrane to generate vesicles that encapsulate the EEEV virus and internalize them in the synapse.