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There obviously needs to be a way to ensure a player can't get infected with the infection 5 or 10 times and manage to get out of it each time, while ensuring surviving the first infection is reasonable given low viral load. Changes to how the infection works after the first infection definitely would need careful consideration in terms of balance to represent these ideas while preventing abuse.
The old adage that whatever doesn't kill you makes you stronger couldn't be further from the truth with some illnesses. Acquired immunity isn't even a guaranteed thing, it's a simplification taught because it's easy to grasp and is true for many life-threatening illnesses, but there are people who have caught Chicken Pox more than once due to poor immune systems, and Covid-19 is a prime example of an illness that both mutates and leaves lasting damage.
And just to further back up my point, even though the game design is more than a good enough reason, here's a research paper on this very subject:
https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-021-02228-6
That's also why I suggested that future infections are more random in *both* directions, to represent the times when your specific acquired immunity fought off a similar strain, the natural evolution of the virus as more deadly strains are more likely to survive later into the apocalypse, and the 'scars' on your immune system from previous infections when acquired immunity doesn't match up.
Sure, virus mutation happens, but you are still going to acquire immunity if you survive it, and since there isn't much jumping around between hosts (which happens in our world but would be basically non-existent in an apocalyptic scenario without fresh hosts), the virus you encounter would be very likely to be the same or similar. Even if it mutates, it would have to be drastic for it to be different enough that your acquired resistance is insignificant.
As far as viruses impacting the immune system long-term, there are a few ways to look at this. One, for most diseases (aside from things like hiv), this isn't a trademark of the disease, but a result of many possible mechanisms. A COVID infection generally results in an overactivation of the innate immune system, so seeing the interferon response dampened long term in some cases isn't at all surprising. That's just the body trying to maintain homeostasis. Two, because the virus itself doesn't attack the immune system, it only occurs in a minority of cases.
So yes, adaptive immunity isn't that straightforward, but the exceptions to the rule are outliers and far less likely than gaining resistance from infection.
Except it is only Novel with some illnesses, like Chicken Pox. We catch some illnesses repeatedly, like people catching the same strains of the Flu year after year, and why flu vaccines are yearly, even if the predicted strain is the same. It depends on the illness, and adaptive immunity is NOT near-perfect for every illness.
https://www.cdc.gov/flu/prevent/keyfacts.htm
"Why do I need a flu vaccine every year?
A flu vaccine is needed every year for two reasons. First, a person’s immune protection from vaccination declines over time, so an annual flu vaccine is needed for optimal protection. Second, because flu viruses are constantly changing, the composition of flu vaccines is reviewed annually, and vaccines are updated to protect against the viruses that research indicates will be most common during the upcoming flu season. For the best protection, everyone 6 months and older should get vaccinated annually."
It's combination of protection fading and mutation that leads to the vaccine being annual for this illness.
As already posted above, adaptive immunity varies by illness, of which we have no real-life analog to the zombie virus within Project Zomboid. This is where, as already argued in previous posts, game design becomes an important consideration. Now you do make a good point that the virus probably doesn't travel between hosts, though we also don't know what keeps them "animated". It could be more like a traditional parasite and the virus is needed for the reanimation process, meaning they would continue to reproduce and mutate within that host. Mutation does not need to be drastic to overcome adaptive immunity, and I've already provided the sources as evidence for that twice.
https://www.cdc.gov/flu/prevent/keyfacts.htm
https://bmcmedicine.biomedcentral.com/articles/10.1186/s12916-021-02228-6
You keep saying things are the exception, or that something only happens in a minority of cases. In all of the above cases, you keep citing your own knowledge, and not providing any evidence as backed by other sources. Anyone can claim anything, and common knowledge is not always correct. The Romans added lead to wine to sweeten it, I cocaine was proscribed as a cure all less than 100 years ago, atomic structure taught as electrons orbiting protons is an analogy and not the actual physical process, and I have a crafts book from 1940 of creating stuff out of spare asbestos with your kids when you have some of it laying around. Science marches on, and a lot of what you're citing to back up your arguments are simplifications or outdated information, with no sources to say otherwise.
TLDR version: There are two aspects of long term effects with viruses in real life. One is immunity: your immune system gets better at fighting off a virus after it has experience with that virus. it learns to produce the correct type of white blood cells. This is why we usually only get chicken pox once. HOWEVER. Viruses can leave damage behind, such as Long COVID. Viruses can also remain in the body and resurface later, for example with shingles. Shingles is caused by the chicken pox virus many years after your initial infection.
Therefore, the mod could add the following features:
1. Long Knox: a permanent or very long debuff that is the lingering effects of a Knox virus infection. For the sake of a double pun, maybe call it Hard Knox instead.
2. Increased immunity to Knox virus: bites are now less likely to result in an infection.
These would balance each other out nicely in terms of gameplay, neither making anything too easy nor too hard.