On Mon, 23 Mar 2020 at 00:23, John Whittington
<[log in to unmask]> wrote:
> The possibility I asked about, of the virus having been spread
> globally before we'd even heard of it (i.e. in December or earlier),
> seems less likely, since it was really mid-February before most
> countries started reporting cases, particularly given that many
> countries (like Italy) have allegedly 'traced' the onset of their
> problem (in Feb) to a (direct or indirect) 'import' from China at the
> time.
>
> Having said that, given that the virus must have been around in China
> for at least some time before they became aware of it, it would again
> seem pretty likely that infected people would have travelled from
> China to places all over the world back in December.
>
> So, I guess it all comes down to "who knows?" !
One way to study this is to compare the genomes of virus samples taken
in different places, and try to reconstruct a phylogenetic tree.
My non-expert understanding of how this works: the more genetically
similar two samples are, the closer they're related, ie the more recent
their last common ancestor. With an estimate for the rate at which
genetic mutations occur, it's possible to estimate how long ago two
strains diverged. By looking at which mutations different strains have
in common, it's possible to reconstruct a phylogenetic tree showing how
all the strains are related. If a cluster of closely related strains is
found in a particular region, and related strains aren't found
elsewhere, it suggests that the divergence occurred in that region. So
the estimated dates for divergence of that group from other strains, and
for divergence between different strains in the group, give an idea of
when the virus was present in the region.
This site does that with SARS-CoV-2 (it also has datasets for some other
viruses):
https://nextstrain.org/ncov
I don't understand this well enough to offer a detailed analysis, but if
you click on ‘play’ in the ‘transmissions’ map, it plays out the
reconstructed pattern of geographical transmissions, with a moving
window along the date axis of the phylogenetic tree showing when these
transmissions are estimated to have occurred. This mostly shows
transmission from China to other countries starting in late December or
early January. But there's a dot in the UK right from the start of the
data (25th November) – I'm not sure what to make of that.
Best wishes,
Andy
PS. I've only been lurking on the list so far, but I've found the
discussions about the pandemic really interesting and useful, and I'd be
happy for them to stay on the list. Thanks to everyone who's
contributed.
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