I assume detection by qRT-PCR only? brings back the standard question of is it full-length genomic RNA? Is there live virus? - potential for defective genome to switch on survival pathways and to persist.
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wondering whether immune-privileged site would favour prolonged production/replication of defective genomes that are not cleared by immune system as would happen elsewhere in patient
Yeah, don't think most PCR detections are replicating virus - likely only in a (small?) subset of cases. The whole immune-privileged / persistence issue is a very interesting one, and I honestly don't know what to think. Peculiarly linked to a v. low evo rate of the virus. Huh?!
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yes, the low evolution/mutation rate throws me too. .... is it because low replication? different selective pressure? weird things happening (like viral "RNA" replicated by cell? or something that is thought in Arenas - there might be a DNA form somewhere)? who knows
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The NHP studies from
@guspalpogeng suggest ongoing replication - which is very intriguing given the low (pretty much absent) evolutionary rate. I can't pretend I understand what's going on
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Have been playing around with the DNA idea too - not willing to rule it out... 
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Male reproductive tract is unique, virus persistence can occur in a micro-environment shaped by testosterone even in the immunologically non-privileged sites i:e accessory sex glands. We know from our model virus EAV, it persist for up to 10 years .. may be to life long in the RT
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