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2. EBV (Epstein Barr Virus). Approximately 95% of adults have EBV - also called HHV-4 - and it is best known as the virus behind mononucleosis. Of course, everyone gets over mono in a matter of week or months, but EBV can do much more long term damage. For example, it has long been known as a contributor to lymphomas and possibly throat/mouth cancers as well.  EBV can also lead to debilitating fatigue and thus any increase or activation of EBV may first lead to a state of quasi-chronic fatigue followed by one of various types of cancers.
3. HHV-6 (Human Herpes Virus 6). This not-as-well-known herpes virus is known to negatively affect neurological tissues. It has been implicated as one of the root causes of Mulitple Sclerosis.  Therefore, increasing Arginine levels may possibly lead to increased risk for certain autoimmune disorders as well.
4. Herpes Zoster (Shingles). The herpes virus behind childhood chicken pox can surface later in life as shingles, where it infects and attacks the nerves. Shingles can be very painful and irritating and can lead to bright red patches and swelling on the face and body. In some cases, it can cause joint pain, hearing loss, drooping facial muscles and many other nasty symptoms.
So it becomes clear that, whatever we do, we do not want to cause an outbreak of any of the above viruses. Futhermore, it is quite likely that most men will have two or more these herpes viruses and so more than one outbreak could occur.
Are there any reasonable solutions? Well, I asked Naturopathic Doctor and Christopher Pick from the U.K. to give us some insights. Below are some questions are answers that I received from him. (You can read Chris' profile in this link or visit his web site at Erectile Dysfunction Help Information.)
Q. I'm wondering if Citrulline, which seems much more powerful than Arginine, can cause even more problems for men with latent viruses? What's your take on this?
A. It is estimated that around 95% of the US population over the age of 35 are infected with EBV. As you will know Herpes, EBV, shingles, chickenpox & lyme disease are all related. The immune system under normal conditions can keep these problems under control and in most cases it ONLY JUST manages this. Any type of additional immune stress such as hard exercise, general stress, lack of sleep, sun exposure, etc will overwhelm the immune system and an outbreak occurs.
A. Now, we know that arginine fuels the herpes virus and must deduce that it will also fuel similar viruses by the same mechanism. We also know that citrulline is a precursor to arginine. So, more citrulline equals more arginine equals more fuel for herpes type viruses. In the instance of certain dormant infections citrulline must be loosely considered as an immune system stressor.
You mentioned Lysine as a solution? Do you think a man can simply take a few grams of Lysine per day to counteract the effects of the Citrulline on any herpes viruses? In other words, can you get the best of both worlds by taking both Citrulline and Lysine?
A. Lysine is a solution for some. But as it antagonises arginine the down side may be a total or partial reduction in any vasodilation properties that were exhibited. This will vary considerably from person to person. Basically supplementing any amino in large quantities (over that found in foods) can up-regulate or down-regulate the metabolic pathway utilisation. Of course, this can create negative or positive effects.
I know that the Citrulline is a big help to some guys in the erectile department. Is there any chance that they can "take 2 grams of Citrulline per day and 3 grams of Lysine per day for safety"? What would you advise?
A. The bottom line. Taking 2 grams of Citrulline and 3 grams of lysine may work for some and not for others. It would need individual experimentation. This is probably not the best route. Considering the infection rate it would be better to seek other alternatives for increasing nitric oxide for vasodilation requirements. For those who are willing to experiment, it may well be worthwhile.
It has always been a problem for me when I try to advise on supplementation & the metabolic pathway interactions. People do not want to hear it &rightfully so if it is not their interest. They just know from advertising that this cures that or this effect can be had……etc. Further, the majority of manufactures & sellers of supplements have no knowledge of interactions. They can follow the research of an effect of a single ingredient on a particular issue & sell it on. Rarely does the research on a single substance follow the metabolic pathways to see what else may occur – the expense would be astronomical.
Q. So right now there is no way good way to keep the EBV/HPV/HSV's in check other than the body's own immune system plus, in some people, extra L-Lysine?
A. Correct again. The drug Aciclovir is effective for cutting down on break outs. Some people have been on it for years. But whether it is Citrulline or Aciclovir, there are checks a balances.
So what's a fella to do? Well, there are several options:
1. Avoid Citrulline and Arginine Supplementation. Erectile function may still be restored through an Erectile Strength Diet, exercise and a few choice supplements. This requires patience and experimentation of course.
2. Supplemental L-Lysine. A man could take some a gram of Citrulline in the a.m. upon waking, Lysine at lunch and another gram of Citrulline in the early evening, since that is the prime love-making time. In addition, one could try to get Arginine from food instead, which will also provide some Lysine for protection. For example, the meats, such as chicken and beef, provide an approximate 1:1 ratio of Lysine to Arginine. However, many plant foods actually provide more Arginine than Lysine. Oats, for example, have about twice as much Arginine as Lysine and peanut butter over 3 times. 
3. Citrulline Only. Of course, one can also just take Citrulline. Short term studies, at least to date, have shown no side effects from Citrulline usage (at levels in the 0.5-3 grams/day range). This is a certainly a promising sign, but if there are long term risks that come to light through activation of the Arginine pathway, these would not have come to light in the these studies. And keep in mind that usage of Citrulline as an erectile supplement is quite new.
Which of these safest? I cannot answer that for you, of course, for many reasons, but one of which is that every man's situation is different. Do you have any of the above viruses? Have you had symptoms that seem to tie into of the herpes viruses? Unfortunately, you must do any your own self-assessment, research and discuss things (with hopefully knowledgeable) physicians that can give you good advice along the way.
2) Am J Pathol, 1986 Jan, 122(1):62–70, "Virus-induced atherosclerosis. Herpesvirus infection alters aortic cholesterol metabolism and accumulation"
3) Eur Heart J, 1993 Dec, 14(Suppl)K:12-6, "Infection and inflammation as risk factors for myocardial infarction"
4) Nature, 1970, 228:1056-8, "Epstein-Barr virus in Burkitt's lymphoma and nasopharyngeal carcinoma. [ii] EBV DNA in biopsies of Burkitt tumours and anaplastic carcinomas of the nasopharynx"
5) J Clin Virol, 2006 Dec, 37 Suppl 1:S24-6, "Clinical parameters and HHV-6 active replication in relapsing-remitting multiple sclerosis patients"
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