My guess is that is has to do with the presence of dsRNA in the enterovirus infections.
That is a very plausible hypothesis.
I think that is the mechanism that Tam and Messner proposed in their
paper on coxsackievirus persistence: they found that coxsackievirus B can persist in stable dsRNA forms within cells, and what's more, they found these dsRNA forms possess the
full viral genome, and having this complete genetic package, these dsRNA forms can later spring back to their original viral particle form, thereby rekindling the viral infection again.
The coxsackievirus B dsRNA studied by Tam and Messner is slightly different to the dsRNA studied by Tracy and Chapman, as the latter cannot spring back to their original viral particle form, and can no longer produce viral particles, because as you know, an essential part of their genome needed to manufacture viral particles has been deleted and lost. So this latter type of dsRNA does not contain the full viral genome, but rather a partially deleted viral genome.
I am not clear, though, on the relationship between the full viral genome dsRNA found by Tam and Messner, and the partially deleted viral genome dsRNA found by Tracy and Chapman. I'd like to know: do these two slightly different forms of dsRNA co-exist in the same virally infected cell? And if so, under what circumstances is the full genome dsRNA produced in the cell, and under what circumstances is the partially deleted genome dsRNA produced?
If it is only full genome dsRNA that can act as the "seeds" that allow the coxsackievirus B infection to rekindle and grow back (which would make sense), then perhaps one way to permanently eradicate coxsackievirus B might be to devise a treatment that promotes the formation of the partially deleted genome dsRNA rather than the full genome dsRNA.
That way the dsRNA "seeds" would not contain the full genome needed to rekindle the infection of viral particles, so then once all the viral particles were wiped out by say interferon treatment, they could never grow back again.