I’ve mainly focussed on Vallance, partly because he was the Govt’s Chief Scientific Advisor and also co-Chair of SAGE (along with Whitty) but also because he’s had the most to say, and been the most clearly wrong in what he did say. But it’s also interesting to compare and contrast with other prominent members of SAGE. Prof John Edmunds is one such, I probably don’t need to show his horrendous TV interview of the 13th of March again but will do so anyway. It’s so endearing to see him sneering at Tomas Pueyo after the latter informs him correctly that the doubling time of the pandemic is about 3 days and a catastrophe is unfolding under out noses. No, he replies, you just don’t understand the data, the doubling time is really 5 days, and we mustn’t act too soon (go to 23:15 in the video):
In his recent testimony to the Inquiry, Edmunds says:
the surveillance system was poor, with the data being delayed and hard to interpret – so much so, that estimating the growth rate of the epidemic was difficult (estimates of the doubling time varied from about 3 days to about 5-7 days, depending on what method and data sources were used) and getting an accurate assessment of the overall size of the epidemic was also difficult. The delays and under-reporting (partly due to a lack of testing) might well have led decision-makers to conclude that they had more time to act than was the case.
It would have been more honest of him to say that his interpretation of the data was poor (along with the rest of SAGE) and this lead decision makers to believe they had more time to act. Furthermore, including the estimate of 3 day doubling in that comment above is particularly misleading, as SAGE was not acknowledging the legitimacy of such estimates at the time. Indeed he ridiculed the number when Pueyo suggested in on the evening of 13th March. But this post isn’t really about SAGE’s competence, it is just about establishing what SAGE actually did say at the time.
Edmunds then goes on to say:
Surveillance started to improve after the CHESS (‘COVID-19 Hospitalisation in England Surveillance System’) system was launched in hospitals on around 14-15th March, but it took a little while for the new data-stream to stabilise.
Here we see clear blue water between his testimony and that of Vallance. Remember, Vallance talks of SAGE members having a Road to Damascus conversion over the weekend of 14-15 March due to this new data becoming available. Edmunds does not repeat that claim, presumably because he knows it to be false. Perhaps he does not, however, contradict Vallance quite clearly enough for this contradiction to be obvious to a casual reader – or even those undertaking the Inquiry. He then rapidly passes on to the responsibility decision-makers had for deciding what to do. He admits that “It is certainly possible that had SAGE been earlier, clearer and more urgent in its advice then lockdown could have been introduced earlier.” “Earlier, clearer and more urgent” indeed. He could have added “correct“. But he didn’t.
I’ve sent the following letter to the Public Inquiry, noting the significant and repeated inconsistencies between what Vallance has recently testified about the events in mid-March 2020, and what the contemporaneous documentary evidence of that period actually says. This evidence includes, rather amusingly, Vallance himself in one of the daily PM statements and press conferences. I will of course post any response(s) received.
To: contact@covid19.public-inquiry.uk
To whom it may concern.
I have noticed a discrepancy between the witness statements made to the Inquiry by Sir Patrick Vallance concerning the events of March 2020, and documentary evidence from that period. It primarily concerns the estimation of the doubling time of the pandemic, which was of great importance in planning the policy response to it. The reason why this is important is that changing the estimate of doubling time from 5 days to 3 days would indicate that the problem was far greater, more urgent, and harder to deal with, than was previously thought. It would inevitably lead to an abrupt and urgent change in policy requirements. However, there is no evidence to support the claim made by Vallance that SAGE was calling for urgent and strict action from March 16 onwards, and that the Govt delayed action for a further week.
Vallance’s evidence to the UK Covid-19 Inquiry
To the Inquiry, Vallance stated that he, and other members of SAGE, changed their minds about the growth rate of the pandemic over the weekend of 14-15 March (bold emphasis added by me):
“I think the new understanding on the weekend of 14 and 15 March was that we were much further ahead in the pandemic than we realised, and the numbers that came in that week showed that there were many more cases, it was far more widespread, and was accelerating faster than anyone had expected.”
“We got information on 13 March which unambiguously showed that the pandemic was far more widespread and far bigger and moving faster than we had anticipated“
“The advice given on 18 March was a consequence of our concerns about the rapid doubling time and number of infections”
“A major reason SAGE did not advise earlier and more extensive interventions, for example on 10 March rather than 16 March, was that we were unaware of how widely seeded the virus was in the UK and how short the doubling time had become.”
“I am asked if the models underestimated the spread of the virus early in the pandemic. I think that they did, at least in terms of speed until shortly before the four day period of 13 to 16 March, which I discuss above. This was a function of poor and time delayed data and a consequent under-estimation of the virus’ doubling time.”
The conclusions that we are inescapably being asked to draw from these multiple statements is that (a) SAGE was underestimating the growth rate of the pandemic prior to the weekend of 14/15 March, but corrected their error at that time and (b) the correction of this error was critical in changing their advice from a measured program of mitigation to a much more urgent suppression of the pandemic.
Vallance’s evidence to the House of Commons Science and Technology Committee, July 2020
This mirrors the testimony Vallance gave previously to the House of Commons Science and Technology committee in July 2020:
“When the SAGE sub-group on modelling, SPI-M, saw that the doubling time had gone down to three days, which was in the middle of March, that was when the advice SAGE issued was that the remainder of the measures should be introduced as soon as possible.”
“The advice changed because the doubling rate of the epidemic was seen to be down to three days instead of six or seven days. We did not explicitly say how many weeks we were behind Italy as a reason to change; it was the doubling time, and the realisation that, on the basis of the data, we were further ahead in the epidemic than had been thought by the modelling groups up until that time.”
SAGE minutes of mid-March and other contemporaneous evidence
However, contrary to these claims, the minutes of the SAGE meeting on the 16th March very clearly stated:
“UK cases may be doubling in number every 5-6 days.”
and later that day, Vallance personally repeated the 5 day doubling figure live on TV:
“…the epidemic, you’d expect to double every 5 days or so…”
Two days later, the minutes of the SAGE meeting on the 18th March again stated:
“Assuming a doubling time of around 5-7 days continues to be reasonable, but this is before any of the measures brought in have had an effect; these measures are likely to slow the doubling time even if there is still an exponential curve.”
The first time 3 day doubling was hinted at in any official documentation appears to be the SPI-M-O meeting on the 20th March:
“Nowcasting and forecasting of the current situation in the UK suggests that the doubling time of cases accruing in ICU is short, ranging from 3 to 5 days.”
and this was finally endorsed in the SAGE minutes of the 23rd March:
“The doubling time for ICU patients is estimated to be 3-4 days“
It looks like Sir Patrick may have confused the weekends of 14-15 March, with 21-22 March. For example, the SPI-M meeting he referred to above as taking place prior to SAGE’s change of heart “in the middle of March” is actually documented as having taken place on the 20th March. I hope you will be able to contact him to ask him about these discrepancies.
At the very least, the documentary evidence proves that SAGE was still underestimating the growth rate of the pandemic right through their meetings of the 16th and 18th March, only finally correcting their error on the 23rd. But perhaps a more worrying implication here is that Sir Patrick’s recollection of SAGE’s approach towards mitigation and lockdown at this time is also in error. In fact, the minutes of the meetings of the 16th and 18th appear entirely supportive of the Govt actions at that time, which were to continue with the gradual extension of the measured program of (mostly voluntary) measures. On the 16th:
“SAGE cannot be certain that the measures being considered by HMG will be sufficient to push demand for critical care below NHS capacity but they may get very close under the RWC scenario.
While SAGE’s view remains that school closures constitutes one of the less effective single measure to reduce the epidemic peak, it may nevertheless become necessary to introduce school closures in order to push demand for critical care below NHS capacity. However school closures could increase the risks of transmission at smaller gatherings and for more vulnerable groups as well as impacting on key workers including NHS staff. As such it was agreed that further analysis and modelling of potential school closures was required (demand/supply, and effects on spread).”
and on the 18th:
“SAGE advises that the measures already announced should have a significant effect, provided compliance rates are good and in line with the assumptions. Additional measures will be needed if compliance rates are low.”
They even argued that the measures implemented on the 18th (including the new school closures) were probably adequate to fully suppress the pandemic:
“SAGE reviewed available evidence and modelling on the potential impact of school closures. The evidence indicates that school closures, combined with other measures, could help to bring the R0 number below 1, although there is uncertainty.”
Summary
The claims that the Govt was responsible for a week of delay at this time, and that SAGE was arguing for much more immediate and stringent action, is not supported by a reasonable reading of the evidence. Indeed, SAGE had no reason to be doing this, since they still believed (contrary to Vallance’s testimony above) that the pandemic was doubling at a rate no more rapidly than 5 days (at worst) and furthermore, as they explicitly stated on the 18th, was probably being significantly slowed beyond this figure by existing policies already introduced at that time.
All of the quotations I have given above are directly copied from official documentation available on the Govt’s own web site, other than that taken from the youtube video of the PM statement and press conference of the 16th March which is my own transcription. Please contact me if you require any help in validating the provenance or accuracy any of this evidence.
One thing that all the protagonists (myself included) agree on is that SAGE’s estimate of doubling time in mid-March was of critical importance. Vallancetestified forcefully to this effect in 2020:
When the SAGE sub-group on modelling, SPI-M, saw that the doubling time had gone down to three days, which was in the middle of March, that was when the advice SAGE issued was that the remainder of the measures should be introduced as soon as possible.
And then confirmed in this exchange with a committee member:
Sir Patrick Vallance: Knowledge of the three-day doubling rate became evident during the week before.
Q1080 [ed – this number has changed from the previous time I posted about this] Graham Stringer: Did it immediately affect the recommendations on what to do?
Sir Patrick Vallance: It absolutely affected the recommendations on what to do, which was that the remaining measures should be implemented as soon as possible. I think that was the advice given.
and again:
Sir Patrick Vallance: The advice changed because the doubling rate of the epidemic was seen to be down to three days instead of six or seven days. We did not explicitly say how many weeks we were behind Italy as a reason to change; it was the doubling time, and the realisation that, on the basis of the data, we were further ahead in the epidemic than had been thought by the modelling groups up until that time.
But why does the doubling time matter so much, and is the difference between 3 days and 5 day really important? The point of this post is to answer these questions.
I’ll start by repeating a couple of plots I first made way back in April 2020 when it was just dawning on me what a colossal cock-up SAGE had made of it. These graphs are generated by a simple SEIR model that I’ve shown to reasonably replicate more sophisticated ones. In the below, the blue “calibrated” line uses data up to 14 March to estimate doubling time, which comes out at 3 days. The red “uncalibrated” line uses parameters from Ferguson’s March 16 paper, which has a doubling time of 5 days.
So, one obvious point is that the blue curve does a much better job of predicting what was going to happen (ie, the magenta x, which were not used to calibrate either model). But that’s not the point of this particular post. Rather, it’s just that the predictions for 3d vs 5d doubling are radically different. Here is the longer-term view, now without the logarithmic scaling on the axis:
Note the “we are here” point is mid-March, when the red and blue curves are visually indistinguishable.
There are several reasons why the doubling time matters. Firstly, the estimate of current pandemic size is based on historic data. Edmunds specifically talks of a 12 day delay from infection to illness, to testing, to finally test data reporting. So 100 cases reportedtoday means 100 infections 12 days ago, and that’s 4 doublings at 3d doubling, meaning 1,600 cases now. If the doubling time was only 5d, then the 12 day delay is just over 2 doublings, and we wouldn’t be at 1,600 cases for another 8 days (4 doublings is 20 days, so that means 12 just past and another 8 in the future). So one immediate consequence of a change in perceived doubling time is that we’ve lost just over a week in terms of pandemic progression. (These calculations all ignore the proportion of infections that are undetected, which can reasonably assume to be roughly constant and thus not affect the argument.)
Secondly, the 3d doubling means the pandemic comes much sooner, and (thirdly) reaches a much higher peak, as shown in the 2nd graph above. What was expected some time over the summer, is now happening next month, and it’s going to be a lot worse than expected – getting on for twice as many cases per day at peak.
Finally, the more rapid doubling implies a higher R0-number, and this makes it harder to control. With R0=2.4 (Ferguson’s 16 March number), a reduction of contacts to 40% of normal would control the virus, because 2.4 x 0.4 = 0.96 which is less than 1. Whereas a 3d doubling implies a rather higher R0, let’s say 3.2. This then requires much stiffer action, because 3.2 x 0.4 = 1.28 which is still greater than 1. A reduction to 30% of previous contact levels to get the R number below 1 (3.2 x 0.3 = 0.96 as before) is obviously much tougher to achieve especially given that family members, essential work etc mean we can’t really isolate perfectly. (Quibbling over the exact value of R0 to use doesn’t invalidate the general point that a higher R0 is harder to control.)
So, changing the estimate of doubling time from 5d to 3d would be a real “oh shit” moment for anyone involved in pandemic planning. It means (a) we’ve instantaneously lost 8 days of lead-time, (b) the pandemic peak is going to be coming a month sooner than expected, (c) the peak is going to be almost twice as big as expected, and (d) the control measures we were hoping to use are much less likely to be adequate. Any plan predicated on a 5d doubling time would immediately have to be revisited in the most extreme and urgent manner.
I hope I have convinced my reader that whatever plans were in place in early March under the assumption of a 5 day doubling, the new understanding that the doubling time was instead 3d would cause an abrupt and substantial change of perspective. This, from a scientific perspective, is inevitable and obvious.
Ok I’m going to do a bit of analysis of Vallance’s evidence to the UK Covid-19 Inquiry, focussing specifically on the events of the mid-March 2020 period up to the imposition of the first “lockdown” on 23rd March. On Monday 20th Nov 2023 he was interviewed by the Inquiry and also provided some written testimony. This is broadly speaking a more detailed version of the testimony he provided back in July 2020 to the House of Commons Science and Technology Committee (whichI blogged about at the time) but appears significantly inconsistent with the documentary evidence provided by the minutes of SAGE meetings and other records of that period. If you already agree with me that Vallance misled the S&TC with his testimony in 2020 then you might not find this very interesting, but I think I might as well go over it again as there’s a lot more testimony to consider (including other participants in SAGE).
I’ll break it up into sections in order to make it digestible, and also to avoid me going round in ever decreasing circles. To start with, let’s consider some background concepts…
This module will look at, and make recommendations upon, the UK’s core political and administrative decision-making in relation to the Covid-19 pandemic between early January 2020 until February 2022, when the remaining Covid restrictions were lifted. It will pay particular scrutiny to the decisions taken by the Prime Minister and the Cabinet, as advised by the Civil Service, senior political, scientific and medical advisers, and relevant Cabinet sub-committees, between early January and late March 2020, when the first national lockdown was imposed.
I’m particularly interested in this period, as it’s the time that the expert scientific analysis and advice from SAGE was so woefully inadequate. I’ve blogged about this at length, but just to recap, the scientists were mistakenly thinking that the doubling time of the pandemic was about 5-6 days (various numbers appear in the SAGE minutes) and that we shouldn’t take too stringent measures as there was a genuine risk that by doing so we’d put the pandemic off to the following winter when it would add to the normal seasonal pressures on the NHS. They were quite anxious that we should get through it over the summer of 2020 instead.
Vallance misled the Science and Technology Select Committee a while ago about this, claiming that SAGE had recommended lockdown on the 16th or 18th of March. This is contradicted by the minutes of those meetings, and even if you try to argue that the minutes may not be completely definitive on that, it is also contradicted by his accompanying statement that their change of heart was due to correcting their estimate of the doubling time (to 3 days), which the SAGE minutes document very precisely to the 23rd March. He’s due to give evidence to the UK Covid-19 Inquiry on Monday, so I await with interest to see whether he will correct the record or also mislead them.
This error was not just an inconsequential comment in a committee that no-one cares about, but has been widely reflected in press comment. For example, the usually excellent Lewis Goodall on Xitter:
Doesn’t seem to me that what @uksciencechief said earlier has received as much attention as it should, in the day’s tsunami of news. In saying that SAGE advised the govt to lockdown a week earlier than they did, yet more space is opening up between them. pic.twitter.com/cKuWXlh7vH
I can see I’m going to have to go over all this again. It’s not a task I really face with much enthusiasm, but it doesn’t seem like anyone else is prepared to do it. To say I’m disappointed at the revisionism, sleight-of-hand and downright misleading testimony from several senior scientists to the UK Covid-19 Inquiry would be an understatement. I had naively hoped there might be some element of humility, introspection and self-reflection concerning their errors at the start of the outbreak, but I’ve seen no hint of this. (If anyone wants to reassure me that lessons have been learnt internally, then I’m all ears, but would want to see evidence of this.)
Unfortunately, neither the inquisitors themselves, nor the journalists following the process, nor the array of commentators eagerly quoting the juicy messages, seem to have the will or perhaps the scientific skills to unpick the story. That’s not to say it is hugely complicated, but a basic understanding of the underlying mathematics is vital for piecing together how it all played out, and why. And it’s very clear that most people start out with an agenda and go looking for support, rather than really being interested in understanding the truth. The scientists are delighted to have found a route to blaming the politicians, and the politicians are too focussed on knifing each other to question what the scientists are now claiming the history to be.
That’s not to say I’m perfect (far from it), but on this particular topic, I happen to be correct. A more difficult question, is whether anyone else cares. Anyway, on with the show….
It occurred to me that the talk of perhaps bringing in restrictions some time in the future was probably poorly timed, in that we are probably pretty close to the peak right now and if action is going to be worthwhile, it needs to be pretty much immediate. Having made a few comments to that end on twitter, I thought I should check out my intuition with some calculations. So here they are.
My starting point is that the Omicron variant represented 22% of tests on the 11th Dec (link) and we had about 40k positive tests on that day (link - but see additional note at bottom of post) meaning 9k tested cases which I will assume represents 18k real infections (ie 50% of infections are actually observed) and furthermore I'll assume that these infections happened on the 8th as it must take a little while to feel ill and get tested.
I'm using a doubling time of about 2 days with an underlying R0 number of 6, and another assumption I'm making is that the population is about 50% immune. I'm ignoring the Delta infection which is small in comparison and carries on largely in parallel with Omicron.
So I initialise the model to hit 18k infections on the 8th, and ran it forwards. This is what I get with no action at all, just the natural infection profile of an uncontrolled epidemic:
32 million infections in total, with a daily peak of 2.7 million on the 27th.
If instead we were to introduce severe restrictions now, such that the underlying R0 dropped from 6 to 1.5, the epidemic would be much smaller:
A daily max of about 430k infections and only 4 million in total. Note that the underlying R0 dropping to 1.5 means the effective R value drops to about 0.75 as the population is half immune.
However the Govt seems to be slowly meandering towards the possibility of some restrictions in about a week. If we were to say Boxing Day instead, then we get:
The daily max here is 2.4 million, with the total about 16 million. So even this delayed action does cut the epidemic in half, by shutting it down rapidly from the peak. That's a bit better than my intuition had suggested to me.
The details of these calculations are sensitive to the timing of the peak of course, which depends on all the assumptions I've made. What is not in doubt is that every day makes quite a big difference to the outcome.
Edit: In the time it took me to write this post, the number of cases by specimen date on the 11th has been updated to 46k!
Posting this mostly because some people seem to be under the misapprehension that the UK is doing really well at coping with COVID, at least in comparison to our European neighbours. It's simply not true, though it's hard to discern quite how poorly we are doing from most of the media including the BBC. This article in the FT presents some of the data, and I'll take some more from OWID.
While the rapid start of the vaccination campaign was certainly impressive and genuinely superior to the rest of the EU, we have now been overtaken by many of our neighbours.
That's us 2nd from bottom on that chart of major European nations.
Vaccination of children has been abysmal, both with the stupid delay due to JCVI's shilly-shallying, and then the slow roll-out. Boosters are running at about half the rate that the original vaccination was, so the backlog is growing rapidly.
Our own volunteer-run vacc centre was mothballed a while back, we could be doing a thousand a day no problem, but it's apparently not part of the plan.
Case numbers are far higher here than just about anywhere else in Europe. USA is comparable, which is hardly an endorsement.
And of course plenty of deaths too:
Yes, both France and Spain had a bit of bump in the late summer, but quickly got on top of it, which we haven't bothered to do. There's no sign of any improvement and in fact the recent case numbers are ticking up quite firmly, so we can probably expect deaths to follow. The deaths aren't really the only problem of course, the knock-on effect of pressure on the hospitals affects a much broader range of people who aren't even infected.
In case you are thinking optimistically that just about everyone must have had it by now and the numbers must be about to go down, I've seen it said that some regions of Iraq, the total number of cases to date is substantially higher than the population, i.e. many people have had it twice or more. Immunity doesn't last. Of course the severity of the disease is far lower after vaccination, and hopefully will also drop with prior infection. But it's not going to go away and the reluctance of the govt to take any action to help control the disease probably means we'll be stuck with very high levels for the foreseeable future.
One year on and there's been a slew of articles revisiting the events of the past year. I was going to ask what has prompted this little flurry, but it's obviously the anniversary thing. With increasing pressure for a public inquiry, it seems that some of the key players have been trying to position themselves favourably, so let's have a look at what's been written, versus what the contemporaneous documentation actually says. SAGE minutes can be found here, I think (I downloaded the relevant docs a while back).
“13 March, the government's Scientific Advisory Group for Emergencies (Sage) committee concluded the virus was spreading faster than thought.
But it was Downing Street "modellers in the building", according to one current official, who pored again over the numbers, and realised the timetable that had only just been announced was likely to result in disaster.
The next morning, a small group of key staff got together. Simple graphs were drawn on a whiteboard and the prime minister was confronted with the stark prediction that the plan he had just announced would result in the NHS collapsing under the sheer number of cases.
Several of those present tell me that was the moment Mr Johnson realised the urgency - that the official assumptions about the speed of the spread of this new disease had been wrong.
[...]
On 16 March, the public were told to stop all unnecessary social contact and to work at home if possible.
[...]
For many inside government, the pace of change that week was staggering - but others remain frustrated the government machine, in their view, had failed to move quickly enough.”
The narrative being presented here of ponderous government is significantly misleading.
The govt claimed at the time to be paying close attention to the scientific advice from SAGE, and the specific change to SAGE's assessment on the 13th March was not that the disease was spreading any more rapidly, but merely that the number of infections was higher than previously thought (due to greater importation from abroad). This is a key distinction that anyone numerate should be able to grasp readily. To quote from SAGE minutes on the 13th:
“Owing to a 5-7 day lag in data provision for modelling, SAGE now believes there are more cases in the UK than SAGE previously expected at this point, and we may therefore be further ahead on the epidemic curve, but the UK remains on broadly the same epidemic trajectory and time to peak.
[...]
SAGE was unanimous that measures seeking to completely suppress spread of Covid- 19 will cause a second peak.”
Changing the estimate of the number of cases just brings the peak forward by a few days. Even a factor of 2 is only a single doubling time which they thought to be about 5-7 days at that time. Changing the estimate of the growth rate could (and in fact did) change the timetable and urgency much more significantly, but this didn't happen for another week and a half.
It is not clear who “the modellers in the building” refers to in Kuenssberg's piece, but they are clearly not SAGE. Maybe Cummings had run a few numbers on a spreadsheet but since SAGE was supposed to be an assembly of world-leading experts, it would hardly be appropriate to discard their analyses in favour of his. For that matter, I had also blogged that the mitigation plan was likely to overwhelm the NHS (a conclusion that I reached around the 9th March based on some very simple calculations) but I wouldn't expect Johnson to listen to me either. SAGE minutes are very clear that they still believed the doubling rate to be 5-7 days right up to the 18th March and had described any overload on the NHS as being some way off (albeit a looming problem that would need addressing at some time in the future). They were unanimously (see above) opposed to suppression at this point.
On the 16th, the SAGE meeting changed its advice somewhat and suggested that some social distancing measures (but not school closures) should be implemented promptly:
“SAGE advises that there is clear evidence to support additional social distancing measures be introduced as soon as possible.
[...]
SAGE will further review at its next meeting whether, in the light of new data, school closures may also be required to prevent NHS capacity being exceeded.”
Clearly there was some increased urgency here but NOT any indication that the NHS was under immediate threat, in direct contradiction to Kuenssberg's unattributed claim above that “the prime minister was confronted with the stark prediction that the plan he had just announced would result in the NHS collapsing under the sheer number of cases.” I'm not saying it is impossible that anyone said such a thing, but if they did, they were an isolated voice and certainly not representative of SAGE as a whole.
Immediately following the SAGE meeting on the 16th, the Govt did of course request that people avoid all unnecessary social contact. Admittedly, this instruction had neither legal force nor economic support at that point but SAGE was obviously reasonably satisfied with the adequacy of this plan as can be seen from their minutes of the 18th (at which time they also recommended school closures):
“SAGE advises that the measures already announced should have a significant effect, provided compliance rates are good and in line with the assumptions. Additional measures will be needed if compliance rates are low.”
So it was only in the case of poor compliance that additional measures would be required.
There was no SAGE meeting between 18th and 23rd, which was unfortunate in the circumstances (21-22 being a weekend). On the 23rd, SAGE finally realised that they had got the R number wrong and that as a result the doubling time was much shorter than had been previously believed, making the situation quite desperate. Specifically, the SAGE meeting of the 23rd concluded: “Case numbers could exceed NHS capacity within the next 10 days on the current trajectory” and this statement must be understood in the context of the immediately preceding 20th March SPI-M meeting which noted both: “Any measures enacted would take 2-3 weeks to have an impact on ICU admissions” and also: “If the higher reproduction number is representative of the longer term, then it is likely that additional measures will be required to bring it below one”.
Thus SAGE's underestimate of the R number didn't just mean that the epidemic was coming faster and harder than previously thought: another consequence is that actions that would have been adequate for R=2.4, might not be adequate for R=3. It is quite understandable that this caused alarm within SAGE, but it only happened on the 23rd.
The Govt imposed a legally-enforceable lockdown with much more far-reaching restrictions immediately that evening (23rd March).
Moving on to the next article, in the Guardian, a hagiography of Patrick Vallance:
“But it now seems clear that Boris Johnson, and his advisers, were slow to heed Vallance’s early advice.
Before the 16 March press conference, Vallance chaired a meeting of the Scientific Advisory Group for Emergencies (Sage) in which a collection of experts had advised that the first lockdown should begin immediately.
Johnson did not announce the unprecedented national lockdown until a week later on 23 March in a primetime TV address to the nation.”
This is simply not true as documented above. SAGE asked for relatively modest action around the 16-18th, and the Govt responded promptly. SAGE explicitly assessed on the 18th that the actions were probably adequate and it was only on the 23rd when they realised that they had got the doubling time wrong, that they suddenly realised they had a much larger and more urgent problem on their hands. Vallance also got this wrong in his appearance before the House of Commons Select Committee on Science and Technology.
Most recently, a podcast on the Guardian consisting of an interview of Neil Ferguson. He points very firmly to the data about higher case numbers due to greater importation being what drove the accelerated decision making in mid-March (NB this view is very different from Vallance who very emphatically linked the change in policy advice to the revision of the estimated doubling time - it is simply not possible for both Ferguson and Vallance to both be correct about this). Ferguson mentions this being discussed in the “first weekend in March” which I'm sure must be a simple slip as this would be 7-8th March whereas on the 10th and even 13th SAGE seems pretty sanguine about the situation and does not suggest any need to take immediate action. Assuming he meant the 14-15th March instead, this is far more consistent with SAGE as the minutes of the 16th do certainly suggest some some action should be taken in the light of the new data:
“The science suggests additional social distancing measures should be introduced as soon as possible.”
When asked specifically (at 11m20 in the podcast) “were scientists telling ministers to go earlier?” Ferguson firstly points again to the surveillance data as escalating the decision making process, and then coyly says it was entirely in the Govt's hands as to what actions they took. He could have said, but chose not to, that the Govt followed SAGE's advice promptly and to the letter. And the interviewer didn't pursue the point. While the improved surveillance data undoubtedly played a role in the process, the urgent advice for the most stringent controls only came on the 23rd as a result of the revised estimate of doubling time. You only have to glance at the SAGE minutes to see that they were not shy about offering policy advice throughout the outbreak.
At 16m40 onwards the interviewer says, with reference to the situation in September after schools reopened:
“...once again the advice from scientists was to lock down. But that advice was not heeded. Did that delay once again lead to a higher death rate than we might have seen?”
Without getting into the September story here, any delayed response from the Govt (which I don't dispute was evident in the autumn) could only “once again” have resulted in a higher death rate if there had also been a delayed response to advice to lock down in March. Which there was not, according to the evidence I have outlined.
There is currently lot of debate on how and when we lift restrictions, and the risks of this. There are several unknowns that may affect the outcome. I have extended the model in a couple of simple ways, firstly by including a vaccination effect which both immunises people, and substantially reduces the fatality rate of those who do get ill, and also by including a loss of immunity over time which is potentially important for longer simulations. The magnitudes of these effects seem highly uncertain, I’ve just made what seems like plausible guesstimates. I use a vaccination rate of 0.5% per day which is probably in the right ballpark though my implementation is extremely simplistic (NB this is the rate at which people move from the vulnerable to the immune category, so it directly accounts for the imperfect performance of the vaccine itself). As well as this, I’m assuming the fatality rate for those infected drops down to 0.3% as vaccination progresses through the most vulnerable groups, since we’ve heard so many good things about vaccination preventing serious illness even in those who do get ill. This value must also account for the proportion of victims that have not been vaccinated at all, so it’s really a bit of a guess but the right answer has to be significantly lower than the original fatality rate. The loss of immunity in this model occurs on a 1 year time scale, which in practice due to model structure means 1/365 = 0.27% of the immune population return to the vulnerable state each day. I don’t claim these numbers are correct, I merely hope that they are not wrong by a factor of more than about 2. In the long term in the absence of illness, the balance between vaccination and loss of immunity loss would lead to about 1/3rd of the population being vulnerable and 2/3rds being immune at any given time. This is just about enough to permanently suppress the disease (assuming R0=3), or at least keep it at a very low level.
The model simulates the historical trajectory rather well and also matches the ONS and REACT data sets, as I’ve shown previously, so I think it’s broadly reasonable. The recent announcements amount to an opening of schools on the 8th March, and then a subsequent reopening of wider society over the following weeks and months. In the simulations I’m about to present, I’m testing the proposition that we can open up society back to a near-normal situation more quickly. So after bumping the R number up on the 8th March I then increase it again more substantially, putting the underlying R0 number up to 2.5 in the ensemble mean, close to (but still lower than) the value it took at the start of last year, with the intention being to simulate a return to near-normal conditions but with the assumption that some people will still tend to be a bit on the cautious side. So this is a much more ambitious plan than the Govt is aiming for. I’m really just having a look to see what the model does under this fairly severe test. Here is the graph of case numbers when I bump the R number up at the end of April:
And here is the equivalent for deaths, which also shows how the R number rises:
So there is another wave of sorts, but not a terrible one compared to what we’ve seen. In many simulations the death toll does not go over 100 per day though it does go on a long time. Sorry for the messy annotations on the plots, I can’t be bothered adjusting the text position as the run length changes.
If we bring the opening forward to the end of March, it’s significantly worse, due to lower vaccination coverage at that point:
Here the daily deaths goes well over 100 for most simulations and can reach 1000 in the worse cases. On the other hand, if we put off the opening up for another couple of months to the end of July, the picture is very much better, both for cases:
and deaths:
While there are still a few ensemble members generating 100 deaths per day, the median is down at 1, implying a substantial probability that the disease is basically suppressed at that point.
I have to emphasise the large number of simplifications and guesstimates in this modelling. It does however suggest that an over-rapid opening is a significant risk and there are likely benefits to hanging on a bit longer than some might like in order that more people can be vaccinated. My results seems broadly in line with the more sophisticated modelling that was in the media a few days ago. To be honest it’s not far from what you would get out of a back-of-the-envelope calculation based on numbers that are thought to be immune vs vulnerable and the R0 number you expect to arise from social mixing, but for better or worse a full model calculation is probably a bit more convincing.
While the Govt plan seems broadly reasonable to me, there are still substantial uncertainties in how things will play out and it is vitally important that the govt should pay attention to the data and be prepared to shift the proposed dates in the light of evidence that accrues over the coming weeks. Unfortunately history suggests this behaviour is unlikely to occur, but we can live in hope.
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.
