Cattle or sheep farmers will often use metal salt baths, such as zinc sulfate or copper sulfate, to remove prions such as mad cow disease from the hooves of their livestock. Such are also the key ingredients in many viral cold sore treatments.
Iodine salts, such as Lugol's solution or decolorized iodine, preform in similar fashion. These can also be found in most pharmacies too.
It is generally most effective to combine topical application with internal supplementation. The body itself uses zinc ions as the 'business end' of it's pathogen killing proteins, electro-chemicaly denaturing the molecules they attach too. It is important to make sure you are using nutrient forms that can be easily metabolized by the body however. Zinc oxide, for instance, is a stable and unreactive molecule, and hence has low bio-activity (It makes for good natural sunscreen however, and paraben free creams with high concentrations of ZiO can be used for general skin health purposes).
Most 'natural' acid ionic salt forms, such as citrate, malate, fumarate, succinate, or alpha-ketoglutarate, can be easily metabolized. Common forms of zinc which are effective which you may likely find can be zinc citrate, zinc gluconate, or zinc ascorbate. Lithium and Iodine are other micro-nutrients that have effect on immune function that most people tend to be deficient in. I personally also supplement with lithium orotate and kelp form iodine tablets (potassium iodide is another viable source, though of course generally 'food source' nutrient forms are best, since that is what your body has evolved to process).
Anyone who has done research into treatments for sores, warts, cankers, or et cetera, will be likely to have seen this or that herb touted as anti-viral. Not for no reason; in fact, pretty much *any* plant will have anti-viral effects to one degree or another. This is only natural, since vegital species of life have been around a lot longer than animal species, and any family of plants that had not evolved methods of resisting viral attack would have died out long ago.
Which is not to say that some are not more hazardous to certain virii relative to other examples though; garlic or rosemary for instance (extract of which is a commonly used preservative in 'all natural' food products).
There are plenty of things out there that are pretty much fool-proof methods of denaturing any sort of complex replicatory organism in the broad-spectrum, regardless of it's construction. Oxidizers based on chlorine or peroxides (bleaches), for instance. The difficulty of course, is that this also means they effective for un-aliving humaniform organisms too, which largely limits their application to topical surfaces in a limited area. They also do not penetrate very deeply, so it is best used to preemptively catch any dangerous pathogens on the skin, before they can spread under the surface (in which case, more finicky criteria for substances that must both, penetrate into tissue, while not also harming the host, are mandated).
Another thing is that many of the infections that we can find most troubling to treat, such as methicillin resistant staphylococcus, are of course specifically adapted to the conditions you find them in. Namely, places with liberal (and perhaps improper) use of anti-biotics, such as hospitals, or athletic facilities. The pertinent thing is, you don't really find these strains 'out in the wild'. Why? Because the careless use of anti-biotics kills all their competition, meaning hence, that they are adapted more towards the biggest factors of their 'natural environment' (namely, anti-biotics and human immune systems), and less towards competition with other bacteria.
This is pertinent to a personal anecdotal story; there was once a fairly long period where on my wrist there was a sort of rash about the size of a quarter, that looked superficially to be something like psoriasis. It did not really inch or feel painful at all, but it never really went away either, which was mildly disturbing. Some of the treatments described above were methods i utilized, such as dabbing with a copper sulfate solution or decolorized iodine. These were effective in causing open sores to scab over and inducing the overall rash to recede and go into remission, but it still persisted never the less. I went through some stretches of time every now and then with no treatments to see if that was an effect, but no real differences or changes made themselves apparent.
A more permanent solution was something i actually discovered partially by accident almost. The roles one's bodies' 'native flora' play in the processes of life is still being explored (for instance, in most organisms, a great deal of the digestive process is infact performed by symbiotic bacteria in the alimentary canal). The idea of 'probiotic' bactera though, bacteria that are more benign or noninfectious to humans, yet aggressively competitive with other microbial organisms, is becoming better understood wrt to skin health. In accordance with that, i had taken to using the pickling juice of saurkraut or fermented pickles (ie, non-vinegar based [Bubbies was the particular brand]) as a rinse after washing hands to reform a higher performance 'shield' after previously stripping off all microbiota, good or bad. Anecdotally i can say this contributed to a much more protracted feeling of 'cleanliness' that could persist even after a few days from initial application without washing, where before itchiness or 'grody' feeling could become apparent even after a few hours of working outside the house, but that is not really relevant to this story.
Was was interesting i found, was that a few weeks after starting this practice, i suddenly noticed that the perennially persistent rash spot that i had started to wonder if more drastic measures were required, had receded dramatically; redness disappearing and sores exhuming. And unlike any time before, the trend actually continued, until it essentially disappeared completely, with no sign there had ever been anything there besides a patch of fine hairs missing.