I had to put on chest waders to get back here and it sure wasn't like sloshing through a pristine trout stream. Where do people find this crap? And why? Anyway, two things. First, non-infectious viral debris ls like the genome remnants left over after adaptive immunity kicks in and there's residual clean up on aisle 5. Chopped up viral RNA, RTPCR will amplify it just fine as long as the primer binding sites are there. But that comes at the end of the acute phase of the infection. Certainly does not precede it like I suspect you may be thinking. Second, its a decent article. The idea that long-haulers have some sort of persistent chronic infection lingering in immune privledged cells after the acute phase is over is likely to be right in some way, shape, or form, IMO. As I understand it (I'm not an immunologist but can generally keep up) much of the pathways involved in innate immunity, which will constantly be trying to go after the virus that managed to avoid clearance through adaptive immunity, funnels down to persistent inflammation. My sister, who is otherwise generally healthy, has an underlying thyroid condition, and she's a managing long-hauler. Doesn't surprise me a bit. For hepatitis C, mentioned in the article, a lot of these pathways are starting to be understood at a molecular level.
