Guide to Virology

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The hallways of the SEV Torch are close quarters, and all air and other materials must be recycled to some extent. Due to the extremely claustrophobic nature of the ship, viral pathogens and other infections spread quickly and must be handled promptly to prevent a mass outbreak. In order to ensure that this is done, the Sol Central Government employs specialized personnel, called Virologists, to handle any and all infectious diseases that appear on board the ship.

And to experiment with creating ever more lethal bioweapons of their own design, of course. Because what's the fun in having a locker full of viral samples if at least one of them isn't a super-plague capable of wiping out all life in the galaxy?

General Overview

Virology as a field consists of two separate but related activities: curing viruses and creating viruses.

Bacterial infections sometimes result from improperly-treated or unclean wounds, but these are not your concern. Those are simply an indication that the rest of the department is incompetent, which you should have already known, and they are both easily treated and not infectious. Thus, they are of no interest to you.

No. As a Virologist, you are concerned with viruses. The only patients that should be brought to you are those that the registers as having a viral pathogen in their bloodstream. These are the things that you work with, and nothing else.

Viruses

Viruses are microscopic entities that, left untreated, will rapidly spread throughout an infected patient's body. Mechanically, this means that, if left alone, viruses will progress through four stages, manifesting a new and increasingly powerful symptom at each stage. These can range from simple coughs and itching to exceptionally gruesome and painful death. Your job consists of curing these viruses any time they appear in the crew, securing samples, and altering them to suit your whim.

Various viruses are tied to specific species, which are the only ones that they can infect. Any given virus may be capable of infecting humans, Skrell, monkeys, or any number of other living organisms, or only a handful, or even - in the case of some specially-engineered ones - none at all. Organisms that the virus cannot infect not only won't manifest symptoms but cannot transmit the virus to other people.

Viruses consist of a selection of syndromes, with each syndrome being tied to a stage of that virus' progression, and with more dangerous syndromes tending to manifest during later stages. While the virus is active and unsuppressed, syndromes will apply some (usually unwanted) effects on the patient.

Badness Rating

Syndromes, in the game's code, have a badness rating. This is a rough measure of how dangerous or rare it is, and is a purely OOC consideration; it is included so that an aspiring plague doctor can understand the mechanics behind viral infections, not so that you can go around talking about "badness" in-character. That'll just get you laughed at.

When speaking about a virus as a whole, its badness rating is generally considered to be equal to the highest badness rating possessed by any of its syndromes.

The badness ratings are:

1 - Mild. The most common symptoms. Random sniffles, nothing much to worry about. Common cold medicine is enough to suppress its effects, and it's safe to let it run its course and die.
2 - Common. Worse than a cold, and almost as widespread. Proper cure and antibiotics would be needed here.
3 - Engineered. You will almost never run into these in the wild, as they are most often artificially induced mutations of more common strands. Can be quite dangerous. Most bioweapons you would research/create in your lab would fall into this category.
4 - Exotic. Elusive Rating 4 syndromes are mostly a speculation. Our antibiotics are untested against those, and their effects can be extremely damaging. Finding an antigen for such viruses should be your utmost priority. These generally only exist if the admins are feeling particularly vindictive.

Vector

Viruses also have vectors - the ways they can spread from one person to the next. These, in order from most to least dangerous, are:

Airborne - Carried by the air. This is the most dangerous vector and will cause the virus to spread rapidly to anyone near the infected. Thankfully, the ship's life support systems will scrub out the pathogens when they hit the ventilation systems, but anyone in the same room as the infected is likely to catch the disease as well. In the case of airborne transmission, bodily fluids from the patient can transmit the pathogen in the same way that being in the room with the patient themselves will, so it's important to clean up any mucus or blood.
Contact - Transmitted by physical contact. Being close to the infected, touching them or being touched carries a risk of transmission.
Bloodborne - Only transmitted by direct injection into the bloodstream. This makes it safe to handle in most situations, but if you're trying to make something really virulent, this isn't particularly useful.

Antibiotics

The enemy of all things microscopic. The only antibiotic available on board the Torch, aside from antibodies created in the course of your work, is Spaceacillin. Since you tend to work with the same things that Spaceacillin is used to combat, it's a good idea to familiarize yourself with the details of its usage.

The primary function of Spaceacillin is to handle bacterial infections that have gotten out of control. This is what most Physicians and Medical Technicians will use it for, but as bacterial infections are not your concern, this doesn't matter much to you. What matters for Virology purposes is that Spaceacillin suppresses the symptoms of viral pathogens, but does not actually cure the patient.

As long as Spaceacillin is in your bloodstream, symptoms of any viral infection will be greatly reduced or eliminated, and you will register as not infected on Medical HUDs. This does not, however, mean that you have been cured; the virus is merely dormant. Spaceacillin only has a chance to cure viruses that are still in the very, very early stages of infection, and it is a very rare case indeed that an infection is caught early enough for this to occur.

The other thing to note about Spaceacillin is that, while it is effective at suppressing the symptoms of viral pathogens, relying too heavily upon it will actually damage the patient's immune system, and lower their resistance to further infection.

Spaceacillin has three stages of effectiveness:

Below 10 units: Badness 2 and below syndromes will be suppressed, but virus progression will not halt, and the virus can still progress into stage 3 or otherwise manifest symptoms of Badness 3 and above. This is usually enough to keep any patients from complaining while you synthesize a cure, and is all that you should need against your run-of-the-mill infection.
Between 10 and 15 units: Badness 3 syndromes will be suppressed, and viruses with no syndromes above Badness 2 will be prevented from progressing. At this point, however, it will begin to damage the patient's immune system.
Above 15 units: Badness 4 syndromes will be suppressed, and viruses with no syndromes above Badness 3 will be prevented from progressing. Do note that this is above the overdose threshold for Spaceacillin, and the patient will begin taking toxin damage. In addition, doses this large will cause severe damage to the patient's immune system, which may be irreversible.

Immune System

Humans (and other things that had to deal with viruses and bacteria) have evolved their own internal mechanism to fight it. The state of a patient's immune system affects the chance of patient avoiding infection in the first place, and of fighting off the infection once it sets in. Extremely weak immune systems can cause the patient to become sick from ambient bacteria around (and inside) him, effectively acquiring infections from thin air.

A patient's immune system can be damaged by antibiotics. It will recover to on its own, given time, so long as the Guide to Medicine#Appendix is intact. Lemon juice will help to heal the immune system more quickly.

Protective Gear

While viruses might be your bread and butter, accidentally infecting yourself is usually not the best idea. As such, you are outfitted with a variety of items which, used together, effectively render you immune to any airborne or contact virus. What gear is most important depends on the vector of the disease. Airborne viruses can be avoided by simply keeping yourself on internals or otherwise filtering your air supply, while contact diseases require you to don a protective suit. Until you know what the exact vector is, though, it's generally best to just suit up as completely as you can.

The following items will offer you a level of protection against virus transmission. These protections stack depending on how many of these items you are wearing, ranging from "very little" (if you're just wearing, say, a pair of gloves) to "total immunity" (in full biohazard gear). They are:

Equipment

Of course, you're no magician. You can't work with microscopic organisms using just your bare hands. Fortunately, Virology has a host of handy machines that will help you to work with any viruses you wish, whether to cure or create.

Antibody Scanner

A handy little device that will tell you if any patient scanned with it has any antibodies in their bloodstream.

Pathogenic Isolator

This device can be loaded with syringes full of blood taken from patients and will tell you whether or not there are any viral pathogens present in the sample. If there is, it can isolate the pathogens, producing a virus dish that can be used with the other machines in the laboratory for more detailed work. This is your primary means of creating virus dishes for experimentation.

Pathogenic Incubator

Virus dishes produced by the initially contain only small samples of any given virus. You need larger growths in order to do much work with them. Fortunately, that's what the Incubator is for. Load it with a beaker full of virus food (diluted milk, available from a mounted dispenser on the wall in the laboratory) and a virus dish, then turn it on. This will slowly grow any virus sample to a sufficient size for it to be analyzed, spliced, or whatever you want to do with it. It can also inject pathogens into any chemicals loaded into it, which will allow you to artificially create infected blood samples to infect test subjects with.

Its final function is to irradiate any virus dishes contained within. This will randomly alter a virus' syndromes, allowing you to procure new strains for experimentation.

Disease Analyser

Placing a virus dish into the Disease Analyzer after it has been incubated to sufficient size will cause the machine to create a full reading of the virus' syndromes, vector of infection, species targeted, associated antibodies, and so on for you to easily view. This can be very handy in assessing the danger of an unknown infection. It will also enter the disease into a digital database, allowing it to be detected via Medical HUD or handheld health analyzer.

Isolation Centrifuge

The takes vials filled with blood and, assuming that said blood contains pathogens or antibodies, turns them into a pure virus or pure cure at your discretion. It will automatically detect whether a sample of blood contains either, and can be useful for telling which people are infected. It can then isolate the pathogen, producing a virus dish, or isolate the antibody, producing a vial of antibodies.

Disease Splicer

This device will allow you to examine and manipulate a virus' syndromes in order to create a custom virus of your very own. For more information, see #Splicing, below.

Refrigerated Virus Storage

Exactly what it sounds like. Store your precious viruses in here when you aren't using them for easily-sortable access.

The Curative Process

Fortunately for those who were unlucky enough to contract a viral infection, curative Virology is relatively simple.

Quarantine

If you or a crew member becomes infected by a virus, your first concern should be to isolate them as quickly as possible to prevent the disease from spreading. Ideally, this means getting the patient back to Virology and into a holding cell, but failing that, it's important to get them into an isolated room, shut the door, and keep anyone else from entering. It is also important to clean up any blood or mucus left behind by the patient, as it may spread the virus as well.

Antibodies

Now that your patient is safely hidden away where they can't infect people without your permission, you want to cure them. The basic idea behind that is to get them to start synthesizing antibodies.

Antibodies are produced by living organisms that have started to fight off a virus in their bloodstream. An organism that has produced antibodies is effectively immune to any virus that is weak to those antibodies, which are generally denoted by a short string of letters (say, "KM" or similar) to let you know which viruses they are effective against. Even better, once an organism has synthesized antibodies for itself, you can take a blood sample and use that to create more antibodies, which you can then inject into other people to cure the virus in them, or even to prevent them from catching it in the first place. And you can take blood samples from those people to make even more antibodies.

The issue is that most of the time, a patient's immune system is not powerful enough to create antibodies on its own (space plagues are nasty things), so you have to do that for them. You do that by injecting them with Radium.

Since Radium is radioactive, this is obviously not something that you want to do to your actual patients. It'll cause major toxin damage and quickly lead to organ failure. You get around this by using monkeys, which you can get from the boxes of monkey cubes very handily left on the desk in Virology for this very purpose.

So the process of curing diseases is, really, quite simple. Find an infected patient. Make a monkey (ideally, strap this monkey to a bed in an isolation cell to make the rest of this process easier). Take a blood sample from the infected patient, then inject it into the monkey to infect the monkey. Inject the monkey with Radium. Use the antibody scanner on the monkey every few seconds until it says that the monkey has begun producing antibodies, then take a blood sample (or two or three or four) from the monkey. Put the blood sample(s) into a vial, then put the vial into the isolation centrifuge and isolate the antibodies. Voila: a bottle of virus cure. Inject it into as many people as you like, then throw the (likely dead) monkey into the disposals chute to eject its disease-ridden body into space and clean the isolation cell.

Congratulations! You have now cured a disease.

The important thing to remember is that anyone injected with antibodies becomes a source of those antibodies for the future. You can take a sample of their blood and put it into the isolation centrifuge just like you did with the monkey's to produce more antibodies if you ever run out. For this reason, and because you might have gotten infected yourself in the process of synthesizing a cure, most Virologists will inject themselves with any antibodies they produce.

Note that this process is extremely bare-bones, and will leave you without a virus sample to study and experiment with later. If this is a concern, see #Obtaining a Sample, below.

Experimental Virology

Curing patients is part of your job description, certainly, and it may even be something that you enjoy, but let's be honest - the real reason you're in that lab coat is because you feel the siren call of mad science, and want to have a virus baby of your very own to spread throughout the ship - or, at least, to show off at your next mad science symposium. Actually infecting the entire ship with a custom-built super-virus is heavily frowned upon. Unless it isn't. Or unless you get permission from the Chief Medical Officer and Commanding Officer beforehand.

Obtaining a Sample

The first step to making your own virus is to find a virus to start tinkering with. There are two ways of doing this: grabbing a pre-spawned virus dish from the freezer create in your laboratory, or taking a blood sample from an infected patient that you haven't cured yet and running it through the Pathogenic Isolator to produce a virus dish.

In either case, you'll then need to incubate the virus in the Pathogenic Incubator until it is of sufficient size for you to work with, and ideally also run it through the Disease Analyzer to get an idea of what you're supposed to be handling at the moment. This will also keep the rest of Medical from getting on your case about not giving them the ability to detect viral outbreaks without you, and will cut down on lectures from the CMO.

Once that's all done, you're ready to start the real work.

Deliberate Infections and Backups

Sometimes you just need to infect somebody. Usually, this is because you're doing some splicing work and want to make sure that you'll have some copies of a virus in reserve for future study. Fortunately, the process of deliberately infecting patients, as well as creating backups of your viruses, is actually very simple.

If you have a virus dish and wish to infect a patient, place the dish into the Pathogenic Incubator along with a beaker full of blood. Ideally, this is the patient's (or test monkey's) blood, though anyone's will do in a pinch - just be aware of the possibility of blood rejection, and be ready to deal with it accordingly. The incubator can inject a sample of the virus into the blood, which you can then inject into the patient to infect them.

Once your patient is infected, if you want to create backups of your virus, just take another blood sample and run it through the Pathogenic Isolator. You can repeat this process as many times as you like, to produce as many backup virus dishes as you need.

Splicing

To understand splicing, you must know that every virus has 4 GNA strands, each of which is tied to one of the syndromes that it can manifest. Each syndrome, and thus each strand, is ranked in order of its appearance when symptoms begin to manifest in a patient, and higher-ranked (and thus slower to appear) syndromes are likely to be more powerful than lower-ranked ones. (1) is the lowest, first symptom to manifest, and (4) is the highest, final symptom to manifest.

The Disease Splicer will allow you to examine and manipulate a virus' GNA strands to create a virus with any syndromes that you want.

The splicer has main three functions which allow you to modify viruses and define which GNA strands they contain. The first of these functions is the splicing function, which copies a GNA strand from an inserted virus tray to the disease splicer buffer. This is done by selecting the desired GNA strand under "Reverse Engineering". Doing so will destroy the virus tray in the process, so be sure that you have more samples of the virus on hand if you want to preserve it.

The disease splicer’s second function is to copy whatever strand it has stored in its buffer to a disk. These disks can be re-inserted into the disease splicer later, making their stored GNA strand immediately available for use. Unlike virus trays, disks can be reused without destroying them.

The final function of the disease splicer is to copy over a GNA strand of its loaded virus dish with the corresponding GNA strand that is currently stored in its buffer. This effectively allows you to give a virus any set of symptoms you want, so long as you keep in mind that GNA strands can only be copied over GNA strands of the same ranking; a (1) strand will always overwrite a (1) strand, and so on.

With these functions in mind, the process in order for you to develop your own virus is as follows:

Create lots of virus sample dishes.
If the virus dishes you have already created don't contain the syndromes that you want in your custom virus, irradiate them in the Pathogenic Incubator until they do.
Create backup dishes of your new viruses.
Strip the GNA strands that you want from your virus dishes, saving each one onto a disk.
Load a new virus dish into the Disease Splicer.
Copy over the virus dish's GNA strands with your disks.

Once you have your final product, you can use the Pathogenic Incubator to create a beaker of blood containing the virus. Congratulations! You are now officially a bioweapons manufacturer.

Syndromes

These are some of the syndromes that your viruses might manifest.

Syndromes may appear in any stage of a virus' manifestation equal to or higher than their own stage. For example, a virus could exhibit Coldington's Effect as its third-stage syndrome. Syndromes can not appear in earlier stages than their own rating, however, so Hyperacid Syndrome will never manifest before the third stage of a virus' progression.

Duplicate syndromes do not occur. Any syndromes noted as Badness 4 ("Exotic") are effectively restricted to admin-only usage, and will likely never appear outside of event rounds.

Stage 1 Syndromes

Coldington's Effect: Causes sneezing and mucus. Causes the disease's vector to change to airborne, if it wasn't already.
Flemmington's: Causes mucus to accumulate in the infected's throat.
Saliva Effect: Causes drooling.
Twitcher: Causes twitching.
Headache: Causes headaches.
Itcher: Causes itchiness.
Upset Stomach: Causes stomach upset.
Waiting Syndrome: Harmless, though prevents early detection.

Stage 2 Syndromes

Automated Sleeping Syndrome: Causes drowsiness and sleeping.
Resting Syndrome: Causes the patient to intermittently collapse.
Blackout Syndrome: Causes blindness.
Anima Syndrome: Equivalent to Coldington's Effect.
Appetizer Effect: Causes increased hunger.
Refrigerator Syndrome: Causes shivering.
Hair Loss: Causes hair loss.
Adrenaline Extra: Makes the infected energetic and produce Hyperzine inside his own body.

Stage 3 Syndromes

Hyperacidity: Causes toxin damage.
World Shaking Syndrome: Causes shaky vision.
Telepathy Syndrome: Gives the patient telepathy.
Lazy Mind syndrome: Causes brain damage.
Hard of Hearing Syndrome: Causes slight deafness.
Uncontrolled Laughter Effect: Causes giggling.
Topographical Cretinism: Causes confusion.
DNA Degradation: Causes genetic degradation.
Chemical Synthesis: Generates a random reagent in the infected person.
Nil Syndrome: No effect.

Stage 4

Gibbingtons Syndrome: Causes the infectee to explode, after multiple warnings. Badness 4.
Radian's Syndrome: Causes radiation damage.
Dead Ear Syndrome: Causes deafness.
Two Percent Syndrome: Turns infected into a monkey. Badness 4.
Toxification Syndrome: Causes severe toxin damage.
Reverse Pattern Syndrome: Causes severe genetic degradation.
Shutdown Syndrome: Causes the death of limbs and toxin damage.
Longevity Syndrome: Makes the infected feel old and tired. Causes damage when cured.
Fragile Bones Syndrome: Causes bone fractures.

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