Report 9

On March 16th Neil Ferguson’s team published “Report 9” which changed government policy and triggered a “lockdown” a week later. The results of his simulation showed that the number of COVID  patients would soon overwhelm the ~4000 ICU bed capacity in the NHS. The code that produced his results has now been made available and I have spent the last few days struggling to get it working. Here are the first results I get after running Ferguson’s “Report 9″model.

COVID simulation for UK if left “unmitigated”

and in yet more detail.

Predicted “unmitigated” deaths using R0=2.4 IFR = 0.9% as used in report 9.

I was surprised to see the date of the peak predicted by the model because in reality the epidemic  occurred about a month earlier (starting March 1). So it looks like Ferguson originally thought that we had much more time to prepare for this emergency than in reality we did have.

The main impact of this report were the  measures he proposed to suppress the epidemic thereby avoiding “overwhelming the NHS” and “save lives”. I have spent the last 3 days struggling to get his code working and it has been a bit of a nightmare. The released procedure as was published on GITHUB could only really be run on a supercomputer,  while instead I have an iMac! There are 4 types of suppression interventions.

  1. PC – School and University closures, restaurants, bars, non-essential shops etc.
  2. CI – case isolation (7 days)
  3. HQ – Household quarantine (14 days)
  4. SD – Social distancing (at various levels)

The newly released “report9” process proposes to run the Covid-Sim model 10 times (multi-threaded) and then take the average. (The main reason to run it 10 times is because you get slightly different values each time).  In addition to this there are an additional 45 combinations of intervention strength and 4 different values of R0  (2.0, 2.2, 2.4, 2.6 ) to run. This makes a grand total of 180  CovidSim batch jobs, which is equivalent to 1800 single threaded runs! This can only really be run on a supercomputer. The full suite of combinations is basically impossible to run on my iMAC. So instead I decided  to restrict all my combinations to a single run (instead of 10) and to use only R0=2.4 because this was used in his original paper.  This produces a more reasonable set of 60 sequential runs which still took me about 2 days to finally finish while getting a headache. Here are the results I get for one  typical 4 level intervention scenario, more or less  corresponding to those shown in report 9.

Impact of 4 suppression scenarios on predicted deaths. The green curve more or less represents the lockdown measures the UK consequently adopted. Note that the dates are  a month later than what actually occurred. The maximum peak in deaths/day reached in the green scenario is ~ 400

Intervention detail. I am not yet quite sure why the second peaks appear yet !

The full lockdown measure finally adopted is shown in green resulting in a smaller peak in deaths after about 28 days followed by a long tail. So how do these prediction compare to what actually happened in reality. UK lockdown measures were introduced on March 23rd a month earlier than envisaged above. Here are the daily deaths in hospitals (excluding care homes) as reported by the NHS.

UK Hospital deaths by actual date

This indeed shows the same shape but twice as many deaths occurred than expected, yet at no time were ICU beds overwhelmed. The outbreak occurred a month earlier than Ferguson predicted. This  seems to be because there were far more infections in the community than were originally thought. It is now estimated that R0 was actually 3 instead of 2.4.

Hindsight is a wonderful thing, but it seems pretty clear that the UK  should probably have locked down a week earlier, and as a result total deaths probably would have been halved.

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5 Responses to Report 9

  1. Hugo says:

    Around 60% of Corona deaths reported are people older than 80.
    What I wonder, what happened to regular deaths because of age / other sicknesses than Corona. Like hart, cancer end regular and influenza, dementia ad suicide. Those statistics disappeared ?

  2. Fred Byrne says:

    I have difficulty with cause of death. One hears from various sources that death fromn corona virus is assumed if the virus is mentioned as conributory or as a principle cause of death. This may be very misleading. For example, if I have a weak heart and I am subjected to a sudden shock, say a sudden noise like an explosion and my heart pegs out. Did I die from the explosion or from a heart attack? Recently an elderly friend was admitted to hospital with pneumonia. He was recovering very well but suddenly died from a massive heart attack. His death was attributed to his heart attack as though pneumonia had absolutely nothing to do with it. It could have been the other way about; admitted with a heart attack but died from pneumonia. So a corona victim with a weak heart dies . From which did he die? The statistics are unclear. To my mind all present analyses are unclear and unhelpful we must wait for maybe months or years before we get a handle on any of this.

    • Clive Best says:

      I agree with you. Unfortunately the statistics in the UK are rather opaque as there was little or no testing outside of hospitals until recently. The ONS figures for excess deaths in general must exaggerate the Covid deaths because the lockdown may itself be the cause of many knock on deaths, especially in Care Homes.

      I am looking now at just the COVID specific Hospital deaths in England and comparing those to Fergusons model. The results show everyone was rather complacent at the start including Ferguson !

      • Börje Månsson says:

        The secondary peaks in the numbers of deaths in the simulation probably are an effect of clustering. If there are clusters in the in the population with different R0 then the first peak comes from the cluster with the highest R0 and the cluster with second highest R0 comes after that. Also the spread between clusters is slower than within a cluster.

  3. brianrlcatt says:

    Two points. Obs one is that the major difference between the options as regards deaths is when schools and colleges are added to the closures. Where all the young people who largely don’t die are. How so? Is this credible, unless they immediately visit the unprotected and largely ignored care homes.

    To the second point: This doesn’t need a model. The decisions made by government as to delay and emphasis in fact made things as bad as they could be short of no action, by leaving the most likely to be infected unprotected while focussing on protecting the people who would later have to look after these avoidable deaths in people who should have been protected first. SO nonsensical.

    Government action was “to protect the NHS” – from what/how? They did the opposite as far as minimising emergency admissions by the infected elderly. They maximised them.

    The majority the NHS would have to take into intensive care were in care homes, the most vulnerable to infection, held captive and unprotected awaiting infection by unprotected staff and visitors while the NHS was protected – from what?

    Not from the relatively few younger patients who mostly don’t die, very few as % of their demographic. So this deliberate choice led to the maximisation of the eventual numbers of critically ill admissions to intensive care from the most at risk population, hardly protecting anyone, neither the NHS nor the vulnerable aged. An very obvious and logical failure of reason. Not even guided by common sense, never mind the guessed science from dodgy models.

    It seems government policy was to sacrifice the old and vulnerable to be seen to be doing something to protect the relatively non vulnerable public, while abandoning the unprotected vulnerable to full exposure, resulting in maximum infections in this group with the highest mortality, using the delay while they incubated the disease to provide PPE to the NHS? What kind of logic is that?

    Protecting the vulnerable in care homers should always have been the first step to reducing deaths and protecting the NHS from the need to treat them at all, from the knowledge available at the time.

    Have I got this wrong somewhere?

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