Originally Posted by kiwi33

Mat, this is very complicated.

Immune deficiency comes in various forms. One is Common Variable Immunodeficiency (CVID), which ElaineD mentioned in another thread. Although it is labelled as "Common" it is very rare, affecting about 1:25000 - 1:50000 people. It shows up as abnormally low levels of antibodies which means that people with it susceptible to infections and other health problems. It seems that mutations in a number of genes may be important in it but this is not clear.

Another form of immune deficiency is Severe Combined ImmunoDeficiency (SCID) which is also very rare, affecting about 1:50000 people. It has various causes and sometimes a bone marrow transplant can be effective for it.

HIV infection can also cause immune deficiency because HIV kills helper T cells, which are needed for the production of effector B and T cells, which are needed (in different ways) for dealing with infections. In Western countries HIV infection is seen as a chronic rather than an acute problem because of the availability of anti-retroviral drugs which stop HIV from replicating.

In general autoimmune diseases are a bit different. The immune system can recognise foreign proteins (antigens) made by pathogens (viruses, bacteria, etc). When this happens both T and B cells get activated and, in different ways, work together to destroy the pathogen. Usually the immune system ignores proteins made by normal body cells - in immunological jargon it is "tolerant" to them.

Sometimes this goes wrong. A protein antigen made a pathogen might, in a chemical sense, "look like" a protein made by normal body cells. When this happens the immune system damages the normal body cells which make that protein, "thinking" that those normal body cells are pathogens - this is an autoimmune disease.

I hope that this is not too long and makes sense.