There is a new ‘variant’ clearly identified today, P.1. And it is worth saying a little about what we have learned about it, and from the variants we have identified so far… 1/quite_a_few
First these are not simple ‘mutants’. Mutations happen all the time and most mean nothing much and either persist at low levels or are removed by selection. The variants are characterized by *multiple* mutations – one of the reasons we call them variants and not mutants 2/n
Those multiple mutations are in parts of the genomes that are not exactly the same, but they overlap to a really pretty marked degree (esp the receptor binding domain). This looks like convergent evolution in which different lineages find the same solution by different routes 3/n
(Think bats and birds and their wings for an eg of far more distantly related things coming to a similar solution. One of my rules of evolution is there's usually more than one way to skin a cat, and we can learn from the different ways evolution has skinned cats in the past) 4/n
The variants we are thinking about now all arose independently, but they have things in common. Notably a mutation in the spike protein at the 501 amino acid position. We write it N501Y as shorthand 5/n
Now N501Y is a mutation that has been reported lots of times, because it has happened lots of times (the many millions of cases worldwide do provide the opportunity to mutate) but hasn’t always taken off. Why not if it is allegedly so awesome? (<-rhetorical question) 6/n
It is worth noting that in each of the currently identified variants, this mutation exists alongside *many* others in the same protein and elsewhere in the genome. Almost like it’s not strong enough on its own and needs its friends for support 7/n
This is a comment on a couple things in evolution. First if a mutation happens all the time and is good, why is it not everywhere already? It should have outcompeted everything. One possibility why not is, it has negative impacts too and there is a trade off 8/n
And the fact that mutations at one place in a protein have an impact depending on what else is going on in the protein. They can and do interact. A mutation might be awesome in one context, and meh in another 9/n
It is telling that all the variants reported so far contain *many* mutations over expectations. It suggests quite strongly that the regular rate of evolution is not equal to the task of producing them. That said, they *have* emerged so how did that happen? 10/n
Well they don’t emerge often. There are certainly more than the 3 identified to date, yet to be found. But how many millions of infections have happened in the meantime since the start of the pandemic? 11/n
In some contexts, like this (which I worked on w many smarter people) the clock rate (sort of but not quite the same as the mutation rate) is clearly faster in patients who are chronically infected.… 12/n
This is reasonable. For the virus to survive in a host it needs to adapt which drives a higher clock rate. So the ‘variants’ may have spent time evolving in a context like that. Not necessarily *that*one (chronically infected patients) but one w similar selective pressures 13/n
And variants matter. Look at the UK. Not just now but over the next month which I expect to be terrible (please do check back – will be very surprised if I am wrong). B.1.1.7 is rampant now and the consequences will be horrific 14/n
But the crucial message remains that this is a respiratory virus with ways to control it. There are countries that *have* controlled it. If yours has not, ask why not. Those who cannot work from home deserve protection too, and that starts with keeping transmission low 15/end

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More from @BillHanage

15 Jan
I’ve thought long and hard about this. There is a constellation of circumstantial evidence around the most recently identified variant P.1, and what has been happening in Manaus, Brazil which makes me very seriously concerned. A thread 🧵
First Manaus has already been very hard hit by the pandemic. News reports in earlier stages told of rushed burials and bodies piling up…
The crucial thing was the rapid rates of transmission, not really mitigated by ‘flattening the curve’ any. total per capita mortality was not as high as might be expected elsewhere, but only because the age structure of the population in Manaus skews young…
Read 13 tweets
14 Jan
The UK has other problems for the next month or so, but this decision in my opinion hugely misses the point of rapid testing for schools or other places 1/n…
Imagine you only detect 75% of true cases of infection. Well, you just cut the risk of transmission in school by 75% and that's not nothing. What about the remaining 25%? Use masks as well. Anything that makes it through the rapid test now has to beat the mask 2/n
Two masks actually, if everyone is using them. This article with @j_g_allen and @jenkinshelen explains why this is important 3/n…
Read 9 tweets
9 Jan
It has been a long tiring and, in many ways, terrifying week in the US. The events in DC have nevertheless obscured the growing public health crisis, which even with vaccines available can be expected to get WORSE over the short term - a thread
Where are we right now? Daily deaths cleared 4000 this week. That will get worse. How do I know? Because the deaths are the results of infections in the past, and infections got worse in the last few weeks. I'm so sorry, but it is coming
The amounts of infection now are so high, and the comparative vaccination rates so low, that we have to be prepared for a coming surge into healthcare across the nation. It is already going to be bad enough. It might well be worse given the threat of more transmissible variants
Read 10 tweets
5 Jan
Everyone who thinks I just offer snark and the occasional bit of science. Let me please remind you how seriously I take this. People too close to me have died, too many of them. Too many have suffered the chronic nightmare of long covid
many more have treated the sick, and some have become infected. Some have been severely ill. Some still are
folks need to stop denying gravity and start seeing what is before their eyes. This virus is dangerous to *enough* that we need to take strong action to slow it down
Read 4 tweets
5 Jan
This is relevant to the situation in the UK and elsewhere schools have been open with minimal infection control. Forget December, we knew *enough* in July to start preparing for the winter 1/n
You want schools open? Really? You have a few advantages, especially with younger kids who are less susceptible than older kids and adults. But that's not enough on its own. As in so many things here you see the advantage when you put multiple interventions together 2/n
You can improve ventilation. You can use masks. I know some of you don't *want* to wear masks but pick your battles for chrissakes. Test. Build confidence that you are doing everything to minimize transmission in schools and its consequences, instead of denying it happens 3/n
Read 6 tweets
3 Jan
This is an interesting article. While it’s talking about the poor (frankly bizarro) management in the U.K. and schools in particular it has wider relevance 1/n…
The issue is that it has been clear since the spring that the long term management of the pandemic would require serious sustained action, and no rapid return to ‘normal’. However as we are all aware that has *not* been the messaging 2/n
The article lists reasonable suggestions for schools. These aren’t exhaustive. I’m not commenting here on how well they’d work or how feasible they’d be, but rather that *this* is the type of thinking that is required. And notably, people have been advocating for it for ages 3/n
Read 6 tweets

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