China's New Outbreak

China has released genomes of virus samples from their new outbreak in Beijing. These show that they are a strain from Europe, not from Wuhan and/or Hubei.

They're pretty sure that strains are close enough to each other that getting one confers immunity to all of them.

But, this points to the problem that we can't think about this in terms of countries. We're forced to do that because of the way the data is collected, but that isn't the way a pandemic works.

There are now roughly 3,000 strains of COVID-19 out there. The one currently breaking out in Beijing originally developed in Europe (it's closest relatives were most commonly found in England). The thing is, it broke off from those strains perhaps as much as 3 months ago. So it's been simmering somewhere (probably Beijing, but really along any path connecting airports).

The place to go to see this Nextstrain.org (which I linked to about 4 months ago). It's like a family tree.

The oldest strains are on the left. Blue is strains collected in Asia. Each branch is an estimate, based on the number of similar and different mutations between strains, of where each one began. For example, perhaps we start with AAA, which mutates to ABA and ACA, and then the first of those mutates to both ABB and ABC, while the other mutates to ACB and ACC. So it's basically a family tree.

The current outbreak in Beijing is that blue line near the top that extends the furthest to the right (most of the ones near it are in Bangladesh).The olive green color is Europe. So you can see that the European strains break off from those in Asia in late January, mutate most wildly there, and then went back to Asia.

The sense in which this has been circulating for a while, presumably in Beijing, is that those blue lines stretch back into early March. There are over 100 cases there now, and you know how it works: 1, then 2, then 4, then 8, then 16, then 32, then 64. So this has doubled about 6 times before they caught on to it.

This is part of the reason that I am very discouraged that we will ever get thing under control. Strains come and go, but there are just too many out there now, in too many places.

UPDATE

I don't feel that I emphasized this enough. Just because a strain in one place is close to a strain ni another place, it does not mean it "came from there". So China should not blame the UK.

Instead, it means that the strain observed in one location at one point in time, was similar to strains observed in another place at another point in time. There may have been a ton of travel in between, and even development of intermediate strains that were not observed.

Here's a look at the detail, similar to the one above, from a different source:

Combined with the above chart, this indicates that it's probably been a while since relatives of the strain currently in Beijing were in China. And relations were definitely popping up in Germany, England, and Taiwan along the way. But it isn't the same strain in Beijing as in any of those places.

BTW: the GISAID initiative, as of today, has received about 49K submissions of viruses from around the world, but only about 3K of them are different from one another.