HIV drugs changed AIDs from a fatal illness to a smoldering disease. Like diabetes, HIV is rarely cured. One can never prove if your viral load is zero, that the viruses are totally gone. Once infected it’s possible infect someone else, particularly the case of pregnancy, or to reconvert to clinical disease. This was the subject of a December 22, 2014 New Yorker article by Jerome Groopman, about the hope of curing HIV. That is critical because chronic HIV therapy has a number of bad effects like muscle wasting and susceptibility to diabetes and atherosclerosis. This brings into focus two types of infection, promiscuous ones like colds that attack for a short time and are cured, and infections where host and invader establish a long relationship. An infection that kills a host may be either of the short or long-term type.

Most infections turn chronic by hiding in a body compartment as happens in just the same way with cancer cells. Infection and cancer cells can hide in the nervous system, sequestered from the rest of the body by the blood brain barrier, or in lymph organs. Infectious units come in many forms. Viruses and other sub-cellular agents depend on host cells. So do sub-bacterial organisms like mycoplasmas and rickettsiae. A second type, do it yourselfers like bacteria, fungi, and protozoa, are cells in their own right. Then there are larger multi-celled parasites like worms. The trick is some invaders have mostly extra-cellular existence but the simpler ones exist inside the host cells and are then liberated as individual infectious units.

An infection is not necessarily cured just because it has been cleared from the blood. It hides elsewhere and then enters the blood at intervals, as in bacteremia (sepsis) and viremia (emia=blood). The Herpes family of viruses have probably lived with humans for a long time over our history. This has given invader and host opportunity for mutual adaptation. After an first infections, Herpes viruses remain latent inside cells, especially neurons, for long years, waiting to strike when the immune system which has kept it under control, weakens. Cold sores and shingles are the result. Pathogens have evolved devilish methods of survival as squatters in a hostile environment. They defy immune surveillance and man’s best-planned methods of eradication. The catalogue of mechanisms of survival available to invaders is long. Bacteria are methodical, co-opting the immune system, which is always trying to isolate infections. Sometimes the best immunity can offer is isolate an invader, like confining an opposing army in a war. In so doing, you run a risk of strengthening the enemy which will attack again when surveillance is weak or if looking the other way (when fighting for your life over somethings else.) Some invaders fortify themselves in their dormancy as with spore-formers, like Clostridia. Once gaining access to your body, abscesses and granulomas, formed in your best interest, merely wall off bacteria which survive and can reactivate. Antibiotics often cannot penetrate these privileged hide-outs in high enough concentration to kill invaders. Should the walls be breached for any reason, the bacteria are free to roam again, say after an injury or when you pop a pimple. Staphylococcus is the primary abscess and boil former. Tuberculosis, leprosy, and syphilis, cause granulomas which simply recruit different types of immune cells. The TB or syphilis bacteria survive within immune cells. Skin lesions like pox and exanthems implicate many different bacterial and viral agents, and are also generally infectious between and within vulnerable persons. Parasites encyst and calcify, remaining infectious in latent condition within scar tissue. The best example is Cysticercus in the brain, one stage in the lifecycle of a flatworm Taenia solium. Far better to kill rather than sequester an invader.

You’d be surprised how many privileged environments there are. They give invading organisms and cancer cells too, the run of us, like establishing an outpost. It is easiest to attain killing concentrations of antibiotics, or tumor cells, in the blood compartment by direct injection. Drugs can be absorbed orally, but this depends on absorption through the gut subject to many vicissitudes such as the shape and size of the drug molecule. And your GI tract, no matter how unfriendly it strives to be, is another one of these privileged sites where invaders establish a base camp. There are more foreign cells in our gut than human cells of our own. That is not surprising. The GI tract is like skin, when you consider it, outside our bodies. The GI tract absorbs proteins and complex chemicals by chaperoning them through its walls using specialized cells or proteins that recognize them. Otherwise foreign cells and chemicals are kept at arm’s length in the GI tract which is best thought as inside out version of oneself. The gut differs from the skin in being specialized for absorption of friendly and needed molecules, the skin is designed more to exclude everything,but not entirely. The gut and skin have enormous surface area, lined with all manner of immune cells which jealously block invaders. The GI tract provides additional huge surfaces full of pockets like diverticuli, rugae, crypts, and villi like the sulci of the cerebral cortex is a repository for ideas, that may be absorbed into the conscious self or not, the inner and outer meanderings of the gut and skin are hideouts for other organisms.

Why keep organisms, bacteria, protozoa, fungi close by; why not just blow them away? The answer must be that they serve some purpose within our GI tract and on the surface of the skin, in ways, that are not yet known. In the gut they may help in digestion or even protect in certain ways like competing with pathogens or otherwise provide a whole milieu an ecosystem or environment that further defines us, likes Saturn’s rings. These are not generally just parasites, but symbiotes and commensals performing useful tasks, most of which we have not dreamed of or have the slightest inkling of, on one level, an “other” that further serves to define us an orbiting aura. As mentioned, there are far more of “them” than “us” even on and inside our own bodies over skin and gut.

And we have other compartments, too many to even mention here. Hideouts within our own organs such as liver or spleen, crevices beneath the skin in fat and fascia, places like the vagina or pockets in the gingiva.

The nervous system is our most highly privileged compartment, a sanctus sanctorum with its own cells and spinal fluid, but so is the immune system, with its own lymphoid circulation where foreign cells may hang for long periods. Everyone knows that we have lymph circulation separate from the blood. Lymph is formed and absorbed with its own fluid and immune cells. Should the absorptive system gum up, and you will have lymphedema or elephantiasis, where limbs, breasts and even scrotums blow up to enormous size weeping clear lymph fluid. Macrophages, “big eaters” are ameboid cells that circulate in blood and lymphoid fluid and found practically everywhere over skin and gut. These cells engulf organisms then digest them displaying fragments of invaders on their cell membranes, like decapitating your opponent, then showing off the head, for purposes of inciting a population of other immune cells, especially killing and antibody-forming lymphocytes. One problem is when an invader, such as the tuberculosis bacillus, has figured out a way to become indigestible to macrophages and thus is capable of gaining entrance into our bodies and surviving there, the origin of the granuloma. The fundamental purpose of the immune system with all of its cells, is the recognition of self vs other, and as corollary killing invaders. But immune cells may sometimes be a weak defense, leading the invader to the inner sanctum of the self.