The enterovirus theory of ME/CFS dates back to the 1970s. It was mainly in the UK were all the early research took place. A list of all the enterovirus ME/CFS studies is found here
The early British studies took muscle biopsy tissue samples from ME/CFS patients, and detected enterovirus in the muscles. But because muscle biopsies are painful and leave a scar, Dr Chia pioneered a new approach, where he took stomach tissue samples instead, which are not painful.
However, the main issue with the enterovirus theory of ME/CFS is that you also find enterovirus infections in the muscle and stomach tissues of healthy controls. So this suggests that an enterovirus infection of the muscle and stomach tissues cannot be the sole cause of ME/CFS.
Some have argued that ME/CFS might arise when enterovirus enters and infects the brain. It could be that a brain infection is the critical factor which causes ME/CFS, and that the muscle and stomach infections are secondary factors, which may play a role, but the brain is the primary factor.
And certainly, 3 post-mortem studies on enterovirus ME/CFS patients
have found enterovirus in their brain tissues. But we would need many more such post-mortem studies in order to attain statistical significance.
Or it could be that ME/CFS arises when enterovirus enters and infects a particular organ.
So in summary: the main issue with the enterovirus theory is that you find enterovirus in the muscle and stomach tissues of healthy controls as well as ME/CFS patients.