Could you give us a little more info here?  Like how did they find
out their Neps had a virus?  Were there symptoms?  If so what?
> Is it possible for an entire species of Nep (pick one with a
> small distribution) to be infected with a virus?
Yes!  Or maybe:  Why not?  Seriously though,  If it is a virus
that is not fatal or causes much illness *and* can past from
the mother plant to the seeds I say the answer is a Yes.
> Is is possible to eliminate the virus from a plant (at least
> propagate it in such a way that the virus doesn't get carried)?
> (Are virii carried with pollen? - maybe we could think of endemic
> virii almost like mitochondria)
Don't know, but most plant viruses do not past from the
mother to the seed.
Dave Evans