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RaTG13, which is the closest known relative of SARS-CoV-2 at full genome level, was sampled (just) in a R. affinis (bat) specimen in Yunnan Province... which is about 1,500 km away from Hubei, the epicenter of the first Covid-19 cluster.

So, what if anything is known about the speed with which viruses spread geographically among bats, particularly R. affinis? Basically, do we have any idea how long it would take a virus to "travel" in (R. affinis) bat populations 1,500 km?

A paper still in draft estimates that the most recent common ancestor of SARS-CoV-2 and RaTG13 "lived" around 2009.

the inferred the time to the most recent common ancestor in the recombinant region of the clade leading to RaTG13 and SARS-CoV-2 is no later than 2009 (2003-2013, 95% HPD limit).

I'm trying to figure out if this time frame is compatible in some sense with the speed with which viruses are known to spread in bat populations.

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  • $\begingroup$ You can make SIR model acquire the diffusion equation characteristics by adding the spatial variables. That will give you the spatial diffusion (spread) speed. $\endgroup$
    – Hans
    May 3 '20 at 1:38
  • $\begingroup$ Look at the sarbecovirus phylogeny and add the precise locations and years. @Hans we don't have any model for how the different bat caves/species exchange viral strains from years to years, we need to built it directly from the sparse data.. $\endgroup$
    – reuns
    May 4 '20 at 6:37

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