Lyme disease is a very serious, debilitating illness. Every hiker should educate himself regarding the disease and take whatever precautions he feels necessary. At the least, be able to recognize the symptoms so you can seek treatment if infected. It is NOT an unlikely occurrence for a thru-hiker, and ticks are very prevalent and quite small. Unfortunately, many will contract the disease and some will not be treated and will suffer permanent damage.
http://www.ninds.nih.gov/disorders/lyme/lyme.htm
Seven to 10 days following an infected tick's bite, the first stage of Lyme disease begins with flu-like symptoms such as fever, chills, swollen lymph nodes, headaches, fatigue, muscle aches, and joint pain. Neurological complications most often occur in the second stage of Lyme disease, with numbness, pain, weakness, Bell's palsy (paralysis of the facial muscles), visual disturbances, and meningitis symptoms such as fever, stiff neck, and severe headache. Other problems, which may not appear until weeks, months, or years after a tick bite, include decreased concentration, irritability, memory and sleep disorders, and nerve damage in the arms and legs.