Bill Hanage+ Your Authors @BillHanage Assoc Prof at Harvard T. H. Chan School of Public Health and Gooner. Currently cosplaying Dr Rieux in some weird re-enactment of La Peste. Tweets are personal May. 02, 2020 3 min read + Your Authors

This preprint has been getting attention. It claims that the SARS-CoV-2 virus is mutating into a more transmissible form as the pandemic wears on. I think those claims are suspect, to say the least  1/n

Major observation: a specific mutation in the spike protein of the virus has been in a higher fraction of cases as the pandemic has worn on in multiple places. Given the role of the spike protein in entry of the virus to cells this might be reasonable. Now for the cold water 2/n

We need to distinguish between selection, in which a variant becomes more common because it leaves more descendants, and founder effects in which a variant becomes more common because it was fortunate rolling the dice 3/n

by that, I mean this variant might have been lucky and got introduced to places outside Wuhan and different approaches to social distancing early on. It's not about the virus, it's the environment and the opportunities for transmission 4/n

The paper distinguishes between orange and blue variants (you don’t need to be tracking the exact mutation or character state for you wonderful nerds following) the orange is the old one, the blue is the more recent one 5/n

The blue mutation is already found in close to 100% of the cases of the early outbreak in North Italy. This might be selection. It might well also be chance, the lucky strain that got out of China. Most outbreaks around the world descend from Europe now 6/n

Meanwhile, China’s extreme interventions appear to have squashed what remained in China and stemmed the dissemination of the other parts of the early viral diversity (w strong caveat that there are far fewer genomes from regions that are not Europe or the US) 7/n

incidentally, the relative lack of genomes from later stages of the pandemic from China and the rest of Asia makes this hard to interpret. More from Iran would also be helpful – right now so far as I can tell there’s maybe one Iran genome on  8/n

By the way that Iran genome is unsurprisingly v close to the root (don’t use time trees for that!). I believe there has been quite a large outbreak in Iran. Knowing more about it including genomes would be good 9/n

Essentially the virus has been mutating, as @XuetingQ and Isaid it would in February. That don’t mean that much. Mutations are what happens when genomes replicate. Comes with the territory like showers with the springtime.  10/n

The increase in the ‘blue’ variant may well reflect a population bottleneck, in which it happens to be the one that gets into the (relatively inattentive) European population and then spreads like wildfire. That's what I *think* happened (<- note opinion not 'science') 11/n

Finally, I could be wrong, I often am. But here is why I think I am not. Look at the data in the preprint for Washington state 12/n

WA was alerted early on through outbreaks in healthcare. It put in serious controls at local and state levels. The orange variant arises, and is followed by the blue (coming in from the east coast and Europe) yet both decline at roughly the same rate 13/n

This is undoubtedly a complicated issue, and one we will learn more about. But right now there are better ways of fighting the pandemic than worrying about different strains defined by one non synonymous SNP 14/end

coda: if anyone who does not know what it is already googles 'non synonymous SNP' I will be delighted. There's a helluva lot of knowledge out there and epidemiology is less complicated than you think. And we will need citizen epidemiologists in the pandemic 👊🏽

You can follow @BillHanage.


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