We have done a sort of blog post/tutorial on local molecular clocks to look at an interesting latency phenomenon in Ebola virus in non-human hosts. This is work in progress based on genomes published recently by DRC/INRB from current and recent outbreaks. http://beast.community/ebov_local_clocks.html …
Question - latency up to beginning of outbreak makes sense, but that hypothesis can be directly tested (given data). I.e., what's the clock within each of the two DRC outbreaks? I assume probably the same as other outbreaks? (i.e., close to larger tree).
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If yes, then we know that latency is a function of the (reservoir?) host, and not actually something intrinsic to a particular (DRC) Ebola virus lineage. Completely what we would expect, but nice to explicitly test (especially given, ehm, certain papers...).
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I think it may be a mechanism that the virus has used to persist in the reservoir - sweeps through a population (roost?) and if it isn’t able to move on to another, then much later it can re-emerge from an older bat to infect all of the new naive bats that have been accumulating.
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The point of the post is that the best fit is that there was a period of latency back in shared lineages (and then became non-latent). It has to be replicating to produce new infections (either in the non-human or human).
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