Infections are caused by other organisms, known as parasites. The group comprises viruses, bacteria, yeasts, fungi and other organisms that are also referred to "parasites" in a more narrow sense. Parasites are the main drivers of evolution and they are directly responsible for sexual reproduction. Without parasites there would be no genders.
The body responds to parasites using a large array of defensive mechanisms that are not well understood. The terminology used reflects our lack of understanding and to say it is confusing is an understatement. A term that is frequently used is the immune system. But the immune system proper is only a small part of it and its role in fighting infection is limited.
I am convinced that many, if not all, so-called use or overuse injuries are also caused by infections or the response to infections. That includes the Achilles tendonitis example I discussed yesterday.
We already know that stiff neck syndrome and other muscle stiffness can be caused by viruses. Flu syndromes include muscle, esp. lower back muscle pain. But it is unlikely that Achilles tendonitis is caused by a viral infection.
A more likely scenario runs as follows. From time to time the tendon gets injured from exercise. We know that scenario well and often after hard exercise, muscles, tendons and ligaments can be painful and sore. The condition happens more frequently, but not exclusively, when there are underlying mechanical issues. There is probably also an underlying genetic component (strength of protein for example).
In nearly all cases, such soreness goes away in a few days. Rarely it does not. I suspect that that is because the injury is aggravated by an immune system cross-reaction to an infectious particle. The infection may have happened weeks or months before the injury and it may or may not have been clinically apparent. It could have been a simple cold or flu.
In such cases we see tendonitis with obvious inflammation. Once again, most of these cases will heal by themselves, although now it will take several weeks to several months. They heal because the tendon gets repaired and the immune response is essentially self-terminating.
A very small number of those will not heal but get worse. The condition may become chronic with acute exacerbations. In most cases it will still be limited to the tendon or tissue of origin. But in a few individuals, it may expand its scope and blossom into a full-blown auto-immune disease like lupus, RA, etc. Fibromyalgia as an entity also resides here. It seems likely that a genetic predisposition is needed for such expansions (be they in time or in scope, or both).
That sums up my hypothesis. It neatly explains why many overuse injuries appear out of the blue. It explains the bilateral, symmetric cases. Those invariably point to a systemic cause.
It also explains why the lesions go away pretty much regardless of treatment, which is nothing more than symptomatic in any case. Mechanical correction, although frequently applied is probably of no use in 99% of cases. If it is useful at all, it is probably limited to those cases with gross deformity and the reason it helps is because it reduces (but does eliminate) the likelihood of primary injuries.