My guess is Naviaux wasn't referring to muscle biopsy PCR tests, just serology or PCR tests within blood samples. I just looked it up in his article, he was talking about serology not biopsy-
It may be the case that he was referring to blood, but it's rather short-sighted to assume that if the virus not in the blood, then it cannot be elsewhere in the tissues, such as in the brain.
There are examples where infection is localized to specific organs, but is not found in the blood. For example, there is evidence to suggest diabetes is caused by enterovirus infection of the insulin cells of the pancreas. But if you test diabetics for enterovirus infection of the blood, I expect it will be negative. You have to look in their pancreas to detect the infection.
It also seems that the finding of enterovirus in ME/CFS doesn't mean that they are causing symptoms. Enterovirus has been found in healthy controls-
I agree: finding enterovirus in gut or muscle tissues in both ME/CFS patients as well as healthy controls suggests that gut or muscle infection is not the only causal factor, or may not be the causal factor at all. It may be infection elsewhere which is the cause. But the problem is that we cannot get access to really important tissues such as the brain or vagus to test, except in post-mortem cases, which are very rare.
It may be that ME/CFS only occurs when very specific parts of the brain are infected, or for example when the vagus nerve is infected. But testing these cannot be done on living patients.