Actually I don’t know anything? @K_G_Andersen do you know?
Could be intact genomes (unlikely) with otherwise dead particles for all I know.
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Assuming it's a "standard" qRT-PCR with ballpark 150bp product, there are more unknowns than knowns with the detection of it - especially when not followed up further (as I assume)
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Negative qPCRs turning positive would suggest active virus - even if at very low level. NHP papers suggest actively replicating virus for a v. long time and from human studies we know that survivors can sometimes be infectious 500 days out. Very difficult question...
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Als antwoord op @K_G_Andersen @LubanLab en
Not completely throwing out virus persistence... but *leaning out of window* at the moment nobody could reject the idea of self replicating defective genomes or even host-virus fusion genes, as were found for some viruses, either
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Als antwoord op @_b_meyer @K_G_Andersen en
Because I would assume a flair up in infections if actual virus was shed, or would expect at least some virus isolations from patients, not just from NHPs. So far we only hear about RNA, but no virus or simply viral proteins
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Als antwoord op @K_G_Andersen @LubanLab en
I'm aware of some transmissions, even long after initial infection. But I'm wondering whether all PCR detections are full-length replicating virus? Reason as example is that the new paper you linked seems quite high in numbers, compared with results here:https://www.nejm.org/doi/pdf/10.1056/NEJMoa1511410?articleTools=true …
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Als antwoord op @_b_meyer @K_G_Andersen en
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
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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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Als antwoord op @K_G_Andersen @LubanLab en
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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Als antwoord op @K_G_Andersen @LubanLab en
Well, happy DNA hunting
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