BlueSkiesResearch.org.uk: So near and yet not quite…

There’s been quite an amazing turnaround since my last blog post. At the time I wrote that, the Govt was insisting that schools would open as planned (indeed they did open the very next day), and that another lockdown was unthinkable. So my grim simulations were performed on that basis.

Of course, the next evening, we had another u-turn… schools shut immediately and many other restrictions were introduced on social mixing. Even so, most of the experts thought we would be in for a rough time, and I didn’t see any reason to disagree with them. The new variant had been spreading fast and no-one was confident that the restrictions would be enough to suppress it. Vaccination was well behind schedule (who remembers 10 million doses by the end of the year?) and could not catch up exponential growth of the virus.

Just after I posted that blog, someone pointed me to this paper from LSHTM which generated broadly similar results with much more detailed modelling. Their scenarios all predicted about 100k additional deaths in the spring, with the exception of one optimistic case where stiff restrictions starting in mid-December, coupled to very rapid vaccination, could cut this number to 30-40k. Given that we were already in Jan with no lockdown and little vaccination in sight, this seemed out of reach. Here is the table that summarises their projections. Note that their “total deaths” is the total within this time frame, not total for the epidemic.

However, since that point, cases have dropped very sharply indeed. Better than in the most optimistic scenario of LSHTM who anticipated R dropping to a little below 1. Deaths have not peaked quite yet but my modelling predicts this should happen quite soon and then we may see them fall quite rapidly. The future under suppression looks very different to what it did a couple of weeks ago.

So this was the model fit I did back on 3rd Jan, which assumes no lockdown. Left is cases, right is deaths which rises to well over 1k per day for a large part of early 2021.

And here are the cumulative median infections and deaths corresponding to the above, with some grid lines marked on to indicate what was in store up to the end of Feb (for infections) and end of March (for deaths). As you can see, about 100k of the latter in this time frame (ie 186-73 = 113k additional deaths).

Here now are the graphs of the latest model fit showing the extremely rapid drop in cases and predicted drop in deaths assuming a 6 week lockdown:

And here is the resulting median projection for total cumulative infections and deaths as a direct comparison to the previous blog post:

It’s a remarkable turnaround, and looks like we are on track for about 114-86 = 28k additional deaths (to start of April), which is far lower than looked possible a couple of weeks ago. It seems plausible that an large part of the reason for the striking success of the suppression is that the transmission of the new variant was predominantly enhanced in the young and therefore closing schools has had a particularly strong effect. The assumption that lockdown lasts for 6 weeks, and what happens after it, is entirely speculative on my part but I wanted to test how close we were to herd immunity at that point. Clearly there will be more work to be done at that time but it shouldn’t be so devastating as at present, unless we lose all our immunity very rapidly.

So that’s looking much better than it was. However it’s also interesting to think about what might have happened if the Govt had introduced the current restrictions sooner. Moving the start of the lockdown back by three weeks generates the following epidemic trajectory:

and the resulting cumulative infections and deaths look like:

Due to the automatic placing of text it’s not so easy to read but we end up with about 84000 deaths total (to end of March) which is fewer than we’ve already had.

So the additional 30k deaths seems to be the price we paid for Johnson’s determination to battle the experts and save Christmas.

BlueSkiesResearch.org.uk: Not even half-way there

NB: below calculation was made and published on Monday 4th, when schools had just been opened and before the latest lockdown was announced, so we can hope that it is too pessimistic, but the situation is still very challenging.

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Lots of talk from politicians and others that, while not exactly triumphalist, is certainly very positive and enthusiastic about the prospect of vaccinating ourselves out of trouble. Here’s one of the earliest "light at the end of the tunnel" articles for example. And with the new Oxford/AZ vaccine there is renewed excitement.

Sorry to pour a little bit of cold water on the mood but a bit of perspective is called for.

Here is what my modelling suggests for the progress of the outbreak though the population so far and into the future. It’s not a pretty sight. The total number that may be infected between now and the start of March (less than 2 months away) is more than the entire number that have been infected so far right from the start of the outbreak last Feb/March.

According to these calculations, roughly 15 million have been infected, and a total of roughly 36 million may be by the time it’s over. That is, we have significantly more infections to come, than we have seen so far. And far more than we got in the first wave last spring, when probably something like 10% (my modelling actually says 8%) of the population was infected.

If there ever was a time to stay at home and minimise all unnecessary contact, it most surely is now.

With this rate of spread, vaccinating a few million over the next couple of months has a relatively minor effect. It may reduce the death rate significantly towards the end of this period (and will certainly help the small minority of highly vulnerable people who receive it), but won’t stop the disease spreading widely.

I need to add a few disclaimers about the modelling. This result plotted above is the median of my latest ensemble fit of a simple SEIR model to historical data on deaths and cases. I’ve been modelling the progress of the outbreak for months now and though the model is rather primitive and approximate it has done a pretty decent job of simulating what is actually quite a simple process. If each infected person passes the disease on to more than one other (on average), then the disease grows exponentially, if they pass it on to less than one (on average) then it shrinks exponentially. The more difficult bits (that my model is too simple to attempt) is to predict the effect of specific restrictions such as closing schools or pubs, or determining how many young vs old people get ill. When just looking at total numbers, this simple SEIR model (when carefully used) works better than it probably should.

This simulation, while it fits the historical data well, may not account adequately for the added virulence of the newer strain that has recently emerged. It also assumes that we don’t have an extremely strict lockdown that successfully suppresses the outbreak in the very near future. Reality could end up better than this, or it could end up worse, but I’m pretty confident that the basic message is robust. People are getting infected at a huge rate right now. Stay at home if you can.