So to my understanding as someone with MS. There are B cells and T cells. Different B cells are trained to recognise certain " patterns" of certain virus proteins like the spike protein of covid. (Like soldiers trained in specific areas) It then recognises that protein and sticks to it alerting surrounding cells to release the flood gates for killer T cells the so called assassins of the immune system.

Now in auto immune disease the immune system mistaken healthy cells/ proteins for bad ones and attacks them. For something like MS that means attacking mylin coating of nerves in the brain or spine. For something like Hashimoto's its the thyroid causing the thyroid to stop producing or produce to much of the thyroid hormones.

So depending on what you have you might have you might be able to just have hormone treatment like thyroxine for Hashimoto's or for ones like MS you may need to suppress certain b cells used to target the wrong parts. Even if the treatment for example Ocrelizumab for MS only targets CD-19 and CD-20 B cells, those B cells are ultimately used to recognise a whole host of virus's there for leaving you at higher risk of infection. Most immuno-suppressants come with a whole host of scary side effects that could happen if your unlucky but like with all medication everything has side effects.

I hope this can help a little. This is also just my understanding so please take with a grain of salt. My family have a while medical textbook worth of auto immune diseases so i try to learn I'm just not always best at conveying what i mean.