Rabies causes hydrophobia in the encephalitic stage which means when it affects the brain and causes swelling and inflammation of multiple areas of the brain. Hence, it affects the complex areas in the brain needed for swallowing. Initially into the course of the disease, the patient has involuntary contractions of neck muscles when he drinks water. At later stages of disease, the patient starts contracting his muscles even at the thought of water. Rabies virus is a neurotropic virus which means that it travels through nerves because of its preference to attach to acetylcholine receptors in the neurons. That is how the virus spreads from the bite site to the brain(via the nerves).