There are certainly some negative studies on pubmed. I think the problem may be that nobody really knows what would be a meaningful test for a persistent enterovirus infection. If it finding virus in tissue then the tissue ought to show some sign of being diseased. My memory of the staining of gastric biopsies is that the tissue looked entirely normal. Why would viral RNA in healthy looking stomach tissue have anything to do with PEM or light sensitivity?
I don't think the tissue has to necessarily show sings of being diseased according to conventional standards. I think what should be looked at is how the particular virus could alter intestinal permeability, potentially exposing the intestinal bacteria to host immune system, or letting endotoxins into the blood, etc. maybe even triggering autoimmunity or activating the bloody T-cells or god knows what.
I don't know what that means. I would want to know what a virologist with no commitment to a research theory in ME, and expertise in immunochemistry thought. My suspicion is that it does not mean anything relevant to the symptoms.
And I believe these things wouldn't be checked or considered by most people outside the field. E.g. H. Pylori eradication in otherwise asymptomatic patients seems to produce some iprovement in patients with ITP, and reduce thyroid antibodies in Hashimoto's. Evidence is, of course, weak, but we're just beginning to explore it, so I wouldn't expect anything more at this point.
As far as I am aware the same standards apply to trying to understand ME as any other condition.
For someone not involved in the ME/CFS, the things that I just described may sound like a wild speculation, but I think most people involved would disagree. The differences that most doctors would call insignificant may be very significant in the context of ME. You have to know what to look for.
Personal example, I have some gut symptoms, had both ends scoped, biopsies taken. Results: ileocolitis with active inflammation(mild edema on macro level), some lymphocyte infiltration in small intestine, few eosinophils, etc. So it's not normal, but such findings are never taken seriously, because there's no overt tissue damage, but the damage is irrelevant, imo. What's important is how does it affect the immune system and it certainly does.