Found this piece in the link below. I have read posts here that when people start the protocol that their cholesterol increases could lysine be the reason
http://www.bodybuildingforyou.com/health-supplements/l-lysine-benefit-side-effects.html
Lysine Supplements
This is one of those amino acids for which a deficiency is very rare, if the diet contains sufficient protein. Signs of a lysine deficiency include fatigue, nausea, dizziness, appetite loss, anxiety, decreased immunity and slow growth. People who have inadequate protein intake, and strict vegetarians (vegans) whose diets lack legumes and don't include a wide variety of foods, may need more lysine and amino acids in general. In that case, a supplement that provides a combination of amino acids would be a better choice than single amino acid supplements. The chances of creating an amino acid imbalance in the body are greater when taking single amino acids, and imbalances can interfere with the absorption of dietary amino acids.
The estimated adult requirement for lysine is 12 milligrams per kilogram of body weight. Again, as with some of the other amino acids, some experts feel that the requirement is set too low. The National Academy of Sciences acknowledges that the state of knowledge concerning amino acid requirements is "unsatisfactory" and expresses the hope that continuing research in the field will yield additional information for consideration. There is no information on the specific amino acid requirements for pregnant or lactating women, and the requirements for older people are considered to be the same as for younger adults.
Lysine Side Effects
Lysine supplements appear to be nontoxic, but they're not without side effects. In general Lysine supplements are considered safe, and there are few reported side effects of Lysine. Some L-lysine side effects include:
lysine can increase cholesterol and triglyceride levels in the blood. People at risk for cardiovascular disease, or who already have elevated cholesterol and triglyceride levels, should definitely talk with their doctors before taking lysine
High doses of lysine (more than 10g/day) can cause nausea, stomach cramps, and diarrhea