I have just finished reading “Viruses, A very Short Introduction” by D.H. Crawford, Oxford University Press, 2011. It has been 30 years since I taught biology classes in high school and thought it would be good to get current.
Many virus are associated with CFS, and there have been no success in finding any specific one responsible. I found this table very interesting because it lists many of the virus associated with CFS — actually, to be clearer. Most of these viruses are in a latent state in the normal population and CFS patients have a far greater percentage in an active state.
|Name||Common Name||Prevalence Percentage|
|HHV-1, HHV-2||Herpes Simplex (Cold Sore)||> 80%|
|HHV-3||Varicella zoster (VZV)||~ 90%|
|HHV-4||Epstein-Barr (EBV)||~ 90%|
|HHV-5||Cytomagalovirus (CMV)||~ 50%|
So the question is: does the virus cause CFS or is the virus activation a result of the CFS, that is a side effect.
The author writes “The trigger for .. activation in an individual carrier are often quite clear and recognizable: decrease immunity due to drugs or illness, fever, increased levels of ultraviolet light (classically precipitated by a skiing trip), or menstruation and stress, but the molecular mechanisms involved are not understood.”
Probiotics and Viruses
We find that some bacteria (probiotics) inhibits viruses. If there are not there, then virus reactivation becomes more likely. A microbiome shift may result in latent viruses becoming active.
“Based on experimental studies, probiotics may exert antiviral effects directly in probiotic-virus interaction or via stimulation of the immune system.” 
” probiotics decreased the presence of picornaviruses after 3 months, which may imply that probiotics play a role against viruses causing common cold.” 
- Antiviral activity of Bifidobacterium adolescentis SPM 0214 against herpes simplex virus type 1.
- In vitro study of the effect of a probiotic bacterium Lactobacillus rhamnosus against herpes simplex virus type 1.
- [Inhibition of herpes simplex virus type 1 reproduction by probiotic bacteria in vitro]. 
- [Effect of probiotic lactic acid bacteria strains on virus infection].