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FINAL UPDATE: Thank you for your amazing points and answers, everyone! I mixed up all your ideas and posted the final answer as a community wiki.

So, I'm developing a bacterial infection where the bacterium is slightly magical. This is how the infection develops. Question below. I know it's a bit of a pain, but please REREAD this list before you comment or answer. I will update it to modify my question and info as questions are asked and comments are made. I'll try to highlight my edits to make them more visible. Thank you.

Bacteria enter through open wound and begin secreting digestive toxin. The body reacts by activating macrophages to absorb the bacteria and producing antibodies to bind to the antigens on the surface of the peptidoglycan cell wall/surface to mark them for destruction by phagocytosis. The bacterium responds by using its first magical defense: magically warping its antigens (surface receptor proteins) and by continuing to divide and secrete digestive toxin. The body responds by adapting to the new antigen and by raising a fever to denature the toxin. The bacteria (all at the same time, magically) switch their antigen over and over again as antibodies are produced.

They can only do this for ten different antigens, though. So once the tides turn in the body's favor, the bacteria switch their antigens one last time and then hide, either near the skin surface or in the reproductive system (to protect themselves from the fever so they can still secrete toxins.)

The toxin causes nausea and headaches at first. The body continues with a higher fever to denature the toxin. Then the bacteria, having multiplied, attach to the insides of blood vessels and manufacture huge quantities of toxin, absorbing sugar from the blood. The body releases a new batch of antibodies. The bacteria can't switch their antigens. Instead, they vanish their non-essential surface proteins entirely. Then they release restriction enzymes (DNA-cutting enzymes.) They release these in lipid vesicles, but they do something genius: they put one of each of the previous ten antigens on the surface of the enzyme package and then release the whole things into lymph vessels, which means the whole immune system and all immune cells will be at risk. Any of the antibodies that are in the blood mark the package for destruction via phagocytosis. But the package fuses with the cell membranes and then slowly (the restriction enzymes) mangle the cell's DNA, killing it over time. Because, though, it's a lipid membrane, it also fuses with B cells and helper T cells. The B cells cannot divide, since their DNA is mangled up. And the T cells die, unable to activate the B cells and macrophages.

The immune system is wrecked now, and the bacteria happily multiply and secrete their toxin, which causes splitting headaches, fever, dizziness, and vomiting. The bacteria start flooding blood vessels with the toxin, reducing the effectiveness of the kidneys (causing dark, dark urine.) Then the bacteria release antigens that bind twice: once to red blood cell receptors, and once that are like the bacterial surface antigens.The immune system begins an auto-immune response, destroying red blood cells, since the killer T cells were left intact. The neurotoxin and loss of oxygen kill the brain. This bacterium can essentially "vanish" from the immune system's senses and quickly kill off the body's defense.

MY QUESTION: This is all caused by magical mutation and some enzymes. My question is: how would a (1) a vaccine and (2) a cure develop for such a bacterium? Take into account elemental magic (fire, water, earth, air) and nature magic (influencing magical organisms takes huge power, but nature magic includes muscle, skin, and blood cell regeneration, analysis of magical organisms, and toxin/poison resistance).

Approximately 4% of the population can access elemental magic and 1% can access nature magic. Include both types into the vaccine and cure, using medium-light power per dose. The vaccine and cure should be

  1. non-conventional (antibiotics should only be one component)
  2. easy and inexpensive to manufacture (including the amount of magic required)
  3. 90% effective
  4. fast.

Assume geneticists have analyzed the protein-coding genes that code for

  1. the restriction enzyme
  2. the toxin
  3. the 10 different antigens.

Update: These are the magic systems

Elemental: The usual manipulation of fire (also usable for any type of temperature manipulation) water (ice, water, water vapor) earth (also binding and a little bone/muscle regeneration type of healing) air (wind and latent air.) Also combos: water+fire makes lightning, water+earth=tissue regeneration, water+air+earth=blood magic (focusing mainly on control) (oxygen, iron, plasma) and different crafts. Using a single element is easy, using two is harder, three is difficult, four is very, very complex. Most mages specialize in 2 elements.

Nature: Essentialy witches. Good grasp of how poisons work, tissue regeneration-style healing magic. A little influence over living organisms; more influence (with more snags) over magical ones. Magical ones are more in tune with these nature witches, however, they are more aware and much more able to resist. This includes everything from primates to germs. Nature witches, however, are good at finding out exactly what magical organisms do (not how. But this is how the disease researchers found out about this bacterium anyway. A good witch might be able to not only look at the amino acid sequence for a toxin but also how it's built.)--

There are limitations here: use your common sense. With a low number like this, using "handwavium" is unreasonable; the magic should take a minor supporting role in the vaccine. And short-term vaccines for bacteria are possible, using surface antibody/antigen solutions. The problem here is the bacteria instantaneously change and/or vanish their antigens, making them immune to normal antibodies, and have an attack system that blocks the immune system, much like HIV/AIDS would. It's okay if an antibiotic is used, but it should only make up a part of the cure/vaccine.

This is a bacterial infection, not a viral one. The bacteria can reproduce on their own, they secrete toxins, have double-stranded DNA, they respond to their environment, they evolve naturally. They are composed of cells and have regular metabolisms. They are simply unique in their defense against the immune system.The issue is that after the ten switches, the bacteria vanish their antigens completely. I was hoping for a vaccine that would stop this process somehow. I have no idea how a cure would work.

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    $\begingroup$ You don't develop a vaccine - you develop ten of them. Then the bacterium is killed on sight, whatever antigens it decides to show. Or you develop a magic vaccine, that feeds on the host's mana and turns some of its T-cells into magical responders, or produce magic antibodies that short-circuit magical organisms, making them self-combust. However, you clearly have a well-developed magic system there -- and it's not easy to come up with an answer in accordance with it, without knowing its details. $\endgroup$ – LSerni Apr 18 '18 at 21:46
  • $\begingroup$ Also note that peptidoglycan itself ("antigens on the surface of the peptidoglycan cell wall/surface") will immediately activate the innate immune system - no need for specific antibodies in the first place $\endgroup$ – Nicolai Apr 19 '18 at 9:35
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    $\begingroup$ A little tip: to make a soft linebreak in markdown you need to put two spaces at the end of a line before hitting Enter once. To get a paragraph you need to hit Enter twice. There is a little bar at the top of the box where you type your posts that can help you with markdown and you can see the results below the box. $\endgroup$ – Secespitus Apr 19 '18 at 12:19
  • $\begingroup$ Thank you, @Secespitus. Didn't know that; I was struggling to get paragraphs the entire time. $\endgroup$ – FoxElemental Apr 19 '18 at 12:20
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    $\begingroup$ "The body reacts by beginning to absorb the bacterium" I'm not sure that's how the immune system works. $\endgroup$ – RonJohn Apr 19 '18 at 15:48
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So you mention that the bacteria use your worlds version of magic to alter their surface antigens, which seems to be the primary factor making this bacteria more dangerous than the diseases we have in our world. I'm not immediately clear if their shape-changing abilities fall under one of the classifications of magic you mention (does it have a specific elemental affinity, for example?). However, the most obvious cure would be some magic that could freeze their shape, preventing their chameleon ability to fool the immune system. I don't see any "ice" style magics, but surely there are counters and counters to counters in the military applications of magic, so there should be something similar in the medical side.

Alternatively, I note that you said the bacteria ALL change their surface antigens at once, implying some sort of communication. A chemical, biological, or magical interruption of that communication could give the immune system a huge boost in catching up to the disease.

Since you said that the bacteria can only change its antigens 10 times, that seems to imply that it has a fairly set collection of disguises that don't vary from patient to patient, which should allow a vaccine to be prepared that innoculates the immune system to each of the 10 antigen profiles. While that would be time-consuming and quite annoying, it shouldn't be technically difficult. A researcher should just keep some active in a petri dish watching with microscope/colored-chemical-tags/magic and then kill the bacteria with radiation or chemicals when each new stage of antigen presents themselves, and then use those cells as a basis. A world with magical manipulation of blood and similar factors should find the process of developing a vaccine much simpler than our world.

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I like the detail and science behind the question, but the premise has a few scientific inconsistencies that you need to work out.

First, antigenic variation is something almost all infectious organisms engage in to fool our immune system. You don't need to invoke magic here. Check out this article for examples of real-world, magic-less antigenic variation.

It's also important to fully understand exactly what constitutes an antigen. Any protein on the surface of the bacteria can be treated as an antigen by the body. The bacteria doesn't get to choose what the immune system is going to attack with antibodies. Any protein that is visible to the immune system and is unique to the bacteria is fair game. This means that a bacteria can't simply turn off every antigen. If the bacteria had no surface proteins at all then it would have no way of interacting with the rest of the body. It wouldn't be able to take in nutrients, or adhere to somewhere in the body, or even maintain homeostasis. Perhaps this is somewhere you might use magic to permit a protein-less membrane to function.

Your scheme of using vesicles filled with restriction enzymes also has a couple issues. The first is that antibodies don't just mark antigens, they also adhere to and inactive them by occluding surface proteins. Any proteins that the vesicle is going to use to try to use to fuse to immune cells is likely to be recognized and occluded by an antibody. This is perhaps somewhere antigenic variation or magic might come in handy. Your choice of restriction enzymes as a toxic payload is a strange one. Restriction enzymes would have to get past the nuclear membrane in order to kill the cell. Why not instead use a more traditional bacterial toxin such as a pore-forming toxin? These are already designed to kill immune cells. When the vesicle membrane merges with the cell membrane it will kill the cell quickly and easily. There are many other exotoxins designed to kill cells.

I know the above isn't an answer to your question but I hope you find it helpful regardless.

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They don't need to do anything special.

there are already viruses and bacterium that behave like this changing their antigens as they spread nothing magical is needed. Ten varieties is nothing to the immune system, bacteria have dozens of different antibodies on their surface.

also introducing DNA cutting enzymes will have little effect since eukaryotic cells have a double protection against this, the DNA is hidden behind other barriers. worse those lipids can only get added to the membrane with the right signal molecule which is itself an antigen. On top of that by constantly switching strategies the bacteria will actually have very little impact on the cells it is targeting is simply will not reach most of them, if the bacteria is at the stage it can release large quantities of a a substance into the blood stream the fight is already mostly over, and that is the the first step in their "abilities".

If you insist on including magic if bacteria can use magic, multicellular life will have a magical component to their immune system as well, so you are back to handwavium.

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  • $\begingroup$ The "handwavium" here is the passive diffusion of the restriction enzyme. And please note the highlighted sections in the question: "After the antigens change the final time, they vanish completely." In addition, the correct "lock and key" is the antigens that the bacterium already put on the "death" package. And they are able to become so widespread because they vanish all antigens and then hide to reproduce. $\endgroup$ – FoxElemental Apr 19 '18 at 13:45
  • $\begingroup$ except you already stated they only do this ten times, most bacteria come in with dozens of varieties, antibodies are already present in the bloodstream. plus your bacteria is doing a lot of things, toxins and attachments will alll require targetable antigens, your bacteria's strategy is only effective if they are introduced in large numbers into the body which basically means they have to be spread artificially. Also they cannot have no antigens and survive naked cell membranes will be destroyed in the body. $\endgroup$ – John Apr 19 '18 at 13:52
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There's the obvious answer: every living organism in nature has some other organism that prey on it.
Find it.
Work out how it targets your bacterium.
Replicate the mechanism, or, if it seems relatively benign to humans, deploy it as a cure. Antibiotics started as mould secretions that attacked bacterial colonies.

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Thank you for your feedback, everyone. I decided to combine all of this into a canonical answer as a community post to be fair.

Karl Justice said:

"I note that you said the bacteria ALL change their surface antigens at once, implying some sort of communication. A chemical, biological, or magical interruption of that communication could give the immune system a huge boost in catching up to the disease."

Good point. I'll use a chemical/magical interruption in their communication.

Mike Nichols said:

"[By disappearing its receptors] It wouldn't be able to take in nutrients, or adhere to somewhere in the body, or even maintain homeostasis. Perhaps this is somewhere you might use magic to permit a protein-less membrane to function."

Hmm. I'll give the bacterium that superpower, then take it away in the cure I develop. Good idea.

Mike Nichols said:

"Any proteins that the vesicle is going to use to try to use to fuse to immune cells is likely to be recognized and occluded by an antibody. This is perhaps somewhere antigenic variation or magic might come in handy. Your choice of restriction enzymes as a toxic payload is a strange one.[It wouldn't work]"

Thanks for alerting me. The solution? Simple. Switch the antigens continuously as the vesicle travels. And I'll magic the restriction enzymes to work quickly--my point in using them is to stop the dying cells from dividing.

TL;DR and the conclusion:

THE SUPERCURE: A x5 punch. It uses three separate cures (enhanced with magic), an antibiotic, and an antidote. The antibiotic is just penicillin (or something similar). The antidote (designed by the witches and geneticists) is the perfect shape to lock+block the toxin, effectively stopping it from killing any cells. Over time, the toxin and the toxin inhibitor unfold, and are filtered and excreted through the kidneys. The first cure is a communication inhibitor; best given early on in the infection. It makes each individual bacterium scramble its antigens differently. It also forces all of the surface receptors to rematerialize. This is an advantage because larger amounts of the bacteria are wiped out because they cannot know whether the immune system is targeting them or not. Also, macrophages and antibodies can bind to the bacterium. The second cure is a type of magic-enhanced antibody. It's a really simple water/earth magic. What it does is the antibody binds not to the disease antigens but to the active transport and facilitated transport surface proteins (which have rematerialized due to the first treatment). Now, the bacterium is slightly resistant to penicillin, but its cell walls/cell membrane are still stretched thin from the penicillin inhibiting production of peptidoglycan. Now that the magical antibodies have attached to the mineral-diffusion receptors, they pump minerals using earth magic into the bacterium. Using water magic, they keep the surrounding water out . . . until they detach. Water suddenly rushes into the cell to balance the gradient. The cell membranes are already stretched too thin, and the bacterium lyses (bursts.) The third cure minimizes the damage by stopping the double-antigen cell-mediated autoimmune response and by saturating immune cells to block the restriction enzymes. You're cured!

THE 2-PART VACCINE: The first thing that is done is the ten antibodies, plus the communication inhibitor/protein rematerializor, are combined. This allows the antibodies to fuse to the bacterium's surface. This constitutes the short-term vaccine, since it allows the body to immediately launch an immune response, but is only effective for as long as the antibodies stay in the bloodstream/interstitial fluid/lymph vessels. The long-term part of vaccine utilizes the ten different antigens. This is difficult, since the memory cells cannot work against the magical switching of the bacterium; however, it keeps symptoms high and actual bacterial counts low enough for the body to either (1) eventually fight the disease out or (2) buy time to take the supercure.

TL;DR the TL;DR:

Sorry about that. I was trying to reason through everything. The cure is 100% effective and the vaccine is partially effective in all cases, so it buys time to get the cure.

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  • $\begingroup$ I wasn't sure how to develop the vaccine, so I kept it at a minimum (adhering to standard vaccines) and focused on the more important cure instead. $\endgroup$ – FoxElemental Apr 22 '18 at 12:53
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You don't develop anything.

You cast Bacterium removium and the patient is cured. When you introduce magic into story as a disease the cure will be always magic (or death but that is magic onto itself). No matter how much science you will have at the end you wrap it in hand waving.

Also vaccines are for viruses not bacteria. Bacteria's are fought with antibiotic that target the bacteria itself not the cause or symptom. Strong antibiotic can destroy every bacteria you have in your body without the need to name it or mark. Ingestions bacteria? You swallow pill. Skin/body bacteria? You take a dip in antibiotic. You're cured, see you next month.

NEXT!

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  • $\begingroup$ There are limitations here: using "handwavium" is unreasonable; the magic should take a minor supporting role in the vaccine. And short-term vaccines for bacteria are possible, using surface antibody/antigen solutions. The problem here is the bacteria instantaneously change and/or vanish their antigens, making them immune to normal antibodies, and block the immune system, much like HIV/AIDS would. It's okay if an antibiotic is used, but it should only make up a part of the cure/vaccine. $\endgroup$ – FoxElemental Apr 19 '18 at 13:00
  • $\begingroup$ So it's a virus not bacteria. HIV is a virus. Virus is not classified as living organism. Viruses can be "deactivated" by ph, solvents, heat (or lack of it). Again, use magic. $\endgroup$ – SZCZERZO KŁY Apr 19 '18 at 13:09
  • $\begingroup$ "Much" like HIV/AIDS. These bacteria are living: they reproduce by themselves, maintain homeostasis, respond to their environment, etc. And one of the rules of the magic system is using magic to directly influence a magical organism takes too much power : Hence, sadly, no miracle Bacterium removium cure. $\endgroup$ – FoxElemental Apr 19 '18 at 13:26

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