Persistent immune response to the persistent pathogen could be causing continuous production and systemic circulation of things like TNF-alpha, IL-1, etc. that have the ability to modify PDH function (
source) and thus cause hypometabolism in cells distant from the viral reservoir. These immune messengers are what would be present in the serum causing the dysfunction(s).
Ron Davis wrote the following in August when Bob Naviaux's metabolomics study results were released.
"Another important finding from this study is that the metabolomic response observed in ME/CFS is opposite to the pattern seen in acute infection and metabolic syndrome. This result supports the controversial idea that while infection is often the initiating event for ME/CFS, it does not contribute to the ongoing illness. What is important to note is that in the absence of evidence of an active infection, it is plausible that the long-term antimicrobial treatments often used for ME/CFS patients are doing more harm than good."
I'm under the impression that the infection-driven hypothesis as the cause of the disease seems to have been abandoned or at least considered much less likely given recent research findings,
Bob Naviaux stated in September...
"In most of the cases of ME/CFS that I have seen where IgG antibody titers have been measured before, during, and after antiviral therapy, the antibody titers remain high after treatment, even though the patient may report symptomatic improvement.
I believe the symptomatic improvement after antiviral treatment may have more to do with the metabolic effects of antivirals in ME/CFS than their action on viral replication."