Michael Levitt’s analysis of European Covid-19 data

Deaths graphs from EurMoMo allow the calculation of Excess deaths

Introduction

I promised in an earlier blog post to present Prof. Michael Levitt’s analysis of Covid-19 data published on the EuroMOMO site for European health data over the last few years.

EuroMOMO

EuroMOMO is the European Mortality Monitoring Project. Based in Denmark, their website states that the overall objective of the original European Mortality Monitoring Project was to design a routine public health mortality monitoring system aimed at detecting and measuring, on a real-time basis, excess number of deaths related to influenza and other possible public health threats across participating European Countries. More is available here.

The Excess Deaths measure

We have heard a lot recently about using the measure of “excess deaths” (on an age related basis) as our own Office for National Statistics (ONS) work on establishing a more accurate measure of the impact of the Coronavirus (SARS-CoV-2) epidemic in the UK.

I think it is generally agreed that this is a better measure – a more complete one perhaps – than those currently used by the UK Government, and some others, because there is no argument about what and what isn’t a Covid-19 death. It’s just excess deaths over and above the seasonal, age related numbers for the geography, country or community concerned, attributing the excess to the novel Coronavirus SARS-CoV-2, the new kid on the block.

That attribution, though, might have its own different issues, such as the inclusion (or not) of deaths related to people’s reluctance to seek hospital help for other ailments, and other deaths arising from the indirect consequences of lockdown related interventions.

There is no disputing, however, that the UK Government figures for deaths have been incomplete from the beginning; they were updated a few weeks ago to include Care Homes on a retrospective and continuing basis (what they called “all settings”) but some reporting of the ONS figures has indicated that when the Government “all settings” figure was 35,341, as of 19th May, the overall “excess deaths” figure might have been as high as 55,000. Look here for more detail and updates direct from the ONS.

The UK background during March 2020

The four policy stages the UK Government initially announced in early March were: Containment, Delay, Research and Mitigate, as reported here. It fairly soon became clear (after the outbreak was declared a pandemic on March 11th by the WHO) that the novel Coronavirus SARS-CoV-2 could not be contained (seeing what was happening in Italy, and case numbers growing in the UK, with deaths starting to be recorded on 10th March (at that time only recorded as caused by Covid-19 with a positive test (in hospital)).

The UK Government have since denied that “herd immunity” had been a policy, but it was mentioned several times in early March, pre-lockdown (which was March 23rd) by Government advisers Sir Patrick Vallance (Chief Scientific Adviser, CSA) and Prof. Chris Whitty (Chief Medical Officer, CMO), in the UK Government daily briefings, with even a mention of 60% population infection proportion to achieve it (at the same time as saying that 80% might be loose talk (my paraphrase)).

If herd immunity wasn’t a policy, it’s hard to understand why it was proactively mentioned by the CSA and CMO, at the same time as the repeated slogan Stay Home, Protect the NHS, Save Lives. This latter advice was intended to keep the outbreak within bounds that the NHS could continue to handle.

The deliberations of the SAGE Committee (Scientific Advisory Group for Emergencies) are not published, but senior advisers (including the CSA and CMO) sit on it, amongst many others (50 or so, not all scientists or medics). Given the references to herd immunity in the daily Government updates at that time, it’s hard to believe that herd immunity wasn’t at least regarded as a beneficial(?!) by-product of not requiring full lockdown at that time.

Full UK lockdown was announced on March 23rd; according to reports this was 9 days after it being accepted by the UK Government as inevitable (as a result of the 16th March Imperial College paper).

The Sunday Times newspaper (ST) published on 24th May 2020 dealt with their story of how the forecasters took charge at that time in mid-March as the UK Government allegedly dithered. The ST’s Insight team editor’s Tweet (Jonathan Calvert) and those of his deputy editor George Arbuthnott refer, as does the related Apple podcast.

Prof. Michael Levitt

Michael (a Nobel Laureate in Computational Biology in 2013) correctly forecast in February the potential extent of the Chinese outbreak (Wuhan in the Hubei province) at the end of March. I first reported this at my blog post on 24th March, as his work on China, and his amazingly accurate forecast, were reported that day here in the UK, which I saw in The Times newspaper.

On May 18th I reported in my blog further aspects of Michael’s outlook on the modelling by Imperial College, the London School of Hygiene and Tropical Medicine (and others) which he says, and I paraphrase his words, caused western countries to trash their economies through the blanket measures they have taken, frightened into alternative action (away from what seems to have been, at least in part, a “herd-immunity” policy) by the forecasts from their advisers’ models, reported as between 200,000 and 500,000 deaths in some publications.

Michael and I have been in direct touch since early May, when a mutual friend, Andrew Ennis, mentioned my Coronavirus modelling to him in his birthday wishes! We were all contemporaries at King’s College, London in 1964-67; they in Physics, and I in Mathematics.

I mentioned Michael’s work in a further, recent blog post on May 20th, when I mentioned his findings on the data at EuroMOMO, contrasting it with the Cambridge Conversation of 14th May, and that is when I said that I would post a blog article purely on his EurtoMOMO work, and this post is the delivery of that promise.

I have Michael’s permission (as do others who have received his papers) to publicise his recent EuroMOMO findings (his earlier work having been focused on China, as I have said, and then on the rest of the world).

He is senior Professor in Structural Biology at Stanford University School of Medicine, CA.

I’m reporting, and explaining a little (where possible!) Michael’s findings just now, rather than deeply analysing – I’m aware that he is a Nobel prize-winning data scientist, and I’m not (yet!) 😀

This blog post is therefore pretty much a recapitulation of his work, with some occasional explanatory commentary.

Michael’s EuroMOMO analysis

What follows is the content of several tweets published by Michael, at his account @MLevitt_NP2013, showing that in Europe, COVID19 is somewhat similar to the 2017/18 European Influenza epidemics, both in total number of excess deaths, and age ranges of these deaths.

Several other academics have also presented data that, whatever the absolute numbers, indicate that there is a VERY marked (“startling” was Prof. Sir David Spiegelhalter’s word) age dependency in the risk factors of dying from Covid-19. I return to that theme at the end of the post.

The EuroMOMO charts and Michael’s analysis

In summary, COVID19 Excess Deaths plateau at 153,006, 15% more than the 2017/18 Flu with similar age range counts. The following charts indicate the support for his view, including the correction of a large error Michael has spotted in one of the supporting EuroMOMO charts.

Firstly, here are the summary Excess Death Charts for all ages in 2018-20.

FIGURE 1. EuroMOMO excess death counts for calendar years 2018, 2019 & 2020

The excess deaths number for COVID19 is easily read as the difference between Week 19 (12 May ’20) and Week 8 (27 Feb ’20). The same is true of the 2018 part of the 2017/18 Influenza season. Getting the 2017 part of that season is harder. These notes are added to aid those interested in following the calculation, and hopefully help them in pointing out any errors.

The following EuroMOMO chart defines how excess deaths are measured.

FIGURE 2. EuroMOMO’s total and other categories of deaths

This is EuroMOMO’s Total (the solid blue line), Baseline (dashed grey line) and ‘Substantial increase’ (dashed red line) for years 2016 to the present. Green circles mark 2017/18 Flu and 2020 COVID-19. The difference between Total Deaths and Baseline Deaths is Excess Deaths.

Next, then, we see Michael’s own summary of the figures found from these earlier charts:

Table 3. Summary for 2020 COVID19 Season and 2017/18 Influenza Season.

Owing to baseline issues, we cannot estimate Age Range Mortality for the 2017 part of the Influenza season, so we base our analysis on the 2018 part, where data is available from EuroMOMO.

We see also the steep age dependency in deaths from under 65s to over 85s. I’ll present at the end of this post some new data on that aspect (it’s of personal interest too!)

Below we see EuroMOMO Excess Deaths from 2020 Week 8, now (on the 14th May) matching reported COVID Deaths @JHUSystems (Johns Hopkins University) perfectly (better than 2%). In earlier weeks the reported deaths were lower, but Michael isn’t sure why. But it allows him to do this in-depth analysis & comparison with EuroMOMO influenza data.

FIGURE 4. The weekly EuroMOMO Excess Deaths are read off their graphs by mouse-over.

The weekly reported COVID19 deaths are taken from the Johns Hopkins University Github repository. The good agreement is an encouraging sign of reliable data but there is a unexplained delay in EuroMOMO numbers.

Analysis of Europe’s Excess Deaths is hard: EuroMOMO provides beautiful plots, but extracting data requires hand-recorded mouse-overs on-screen*. COVID19 2020 – weeks 8-19, & Influenza 2018 – weeks 01-16 are relatively easy for all age ranges (totals 153,006 & 111,226). Getting the Dec. 2017 Influenza peak is very tricky.

(*My son, Dr Tom Sutton, has been extracting UK data from the Worldometers site for me, using a small but effective Python “scraping” script he developed. It is feasible, but much more difficult, to do this on the EuroMOMO site, owing to the vector coordinate definitions of the graphics, and Document Object Model they use for their charts.)

Figure 5. Deaths graphs from EurMoMo allow the calculation of Excess deaths

FIGURE 5. The Excess deaths for COVID19 in 2020 and for Influenza in 2018 are easily read off the EuroMOMO graphs by hand recording four mouse-overs.

The same is done for all different age ranges allowing accurate determination of the age range mortalities. For COVID19, there are 174,801 minus 21,795 = 153,006 Excess Deaths. For 2018 Influenza, the difference is 111,226 minus zero = 111,226 Excess Deaths.

Michael exposes an error in the EuroMOMO charts

In the following chart, it should be easy to calculate again, as mouse-over of the charts on the live EuroMOMO site gives two values a week: Actual death count & Baseline value.

Tests on the COVID19 peak gave a total of 127,062 deaths & not 153,006. Plotting a table & superimposing the real plot showed why. Baseline values are actually ‘Substantial increase’ values!! Wrong labelling?

Figure 6. Actual death count & Baseline value

In Figure 6, Excess Deaths can also be determined from the plots of Total and Baseline Deaths with week number. Many more numbers need to be recorded but the result would be the same.

TABLE 7. The pairs of numbers recorded from EuroMOMO between weeks 08 and 19

TABLE 7. The pairs of numbers recorded from EuroMOMO between weeks 08 and 19 of 2020 allow the Excess Deaths to be determined in a different way than from FIG. 5. The total Excess Deaths (127,062) should be the same as before (153,006) but it is not. Why? (Mislabelling of the EuroMOMO graph? What is “Substantial increase” anyway and why is it there? – BRS).

FIGURE 8. Analysing what is wrong with the EuroMOMO Excess Deaths count

FIGURE 8. The lower number in TABLE 7 is in fact not the Baseline Death value (grey dashed line) but the ‘Substantial increase’ value (red dashed line). Thus the numbers in the table are not Excess Deaths (Total minus Baseline level) but Total minus ‘Substantial increase’ level. The difference is found by adding 12×1981** to 127,062 to get 153,006. This means that the baseline is about 2000 deaths a week below the red line. This cannot be intended and is a serious error in EuroMOMO. Michael has been looking for someone to help him contact them? (**(153,006 – 127062)/12 = 25944/12 = 2162. So shouldn’t we be adding 12×2162, Michael? – BRS)

Reconciling the numbers, and age range data

Requiring the two COVID19 death counts to match means reducing the Baseline value by 23,774/12 = 1,981**. Mouse-over 2017 weeks 46 to 52 gave the table below. Negative Excess Deaths meant 2017 Influenza began Week 49 not 46. Michael tried to get Age Range data for 2017 but the table just uses 2018 Influenza data. (**see above also – same issue. Should be 25944/12 = 2162? – BRS)

TABLE 9. Estimating the Excess Deaths for the 2017 part of the 2017/18 influenza season

In TABLE 9, Michael tries to estimate the Excess Deaths for the 2017 part of the 2017/18 Influenza season by recording pairs of mouse-overs for seven weeks (46 to 52) and four age ranges. Because the Total Deaths are not always higher than the ‘Substantial increase’ base level, he uses differences as a sanity check. The red numbers for weeks 46 to 48 show that the Excess Deaths are negative and that the Influenza season did not start until week 49 of 2017.

TABLE 10. We try to combine the two parts of the 2017/18 Influenza season

TABLE 10 commentary. We try to combine the two parts of the 2017/18 Influenza season. The values for 2018 are straightforward as they are determined as shown in Fig. 5. For 2017, we need to use the values in Table 9 and add the baseline correction because the EuroMOMO mouse-overs are wrong, giving as they do the ‘Substantial increase’ value instead of the ‘Baseline’ value. We can use the same correction of 1981**(see my prior comments on this number – BRS) deaths per week as determined for all COVID19 data but we do not know what the correction is for other age ranges. An attempt to assume that the correction is proportional to the 2017 number of deaths in each age range gives strange age range mortalities.
Thus, we choose to use the total for 2017 (21,972) but give the age range mortalities just from the deaths in 2018, as the 2017 data is arcane, unreliable or flawed.

Michael’s concluding statement

COVID19 is similar to Influenza only in total and in age range excess mortality. Flu is a different virus, has a safe vaccine & is much less a threat to heroic medical professionals.

Additional note on the age dependency of Covid-19 risk

In my earlier blog post, reporting the second Cambridge Conversation webinar I attended, the following slide from Prof. Sir David Spiegelhalter was one that drew the sharp distinction between the risk to people in different age ranges:

Age related increase in Covid-19 death rates

Prof. Spiegelhalter’s own Twitter account is also quite busy, and this particular chart was mentioned there, and also on his blog.

This week I was sent this NHS pre-print paper (pending peer review, as many Coronavirus research papers are) to look at the various Covid-19 risk factors and their dependencies, and to explain them. The focus of the 20-page paper is the potential for enhanced risk for people with Type-1 or Type-2 Diabetes, but the Figure 2 towards the end of that paper shows the relative risk ratios for a number of other parameters too, including age range, gender, deprivation and ethnic group.

Risk ratios for different population characteristics

This chart extract, from the paper by corresponding author Prof. Jonathan Valabhji (Imperial College, London & NHS) and his colleagues, indicates a very high age-related dependency for Covid-19 risk, based on the age of the individual. The risk ratio for a white woman under 40, with no deprivation factors, and no diabetes, compared with a control person (a 60-69 year old white woman, with no deprivation factors, and no diabetes) is 1% of the risk. A white male under 40 with otherwise similar characteristics would have a risk of 1.94% of the control person.

Other reduction factors apply in the two 10-year age bands between 40-49 and 50-59, for a white woman (no deprivations or diabetes) in those age ranges of 11% and 36% of the risk respectively.

At 70-79, and above 80, the risk enhancement factors owing to age are x 2.63 and x 9.14 respectively.

So there is some agreement (at least on the principle of age dependency of risk, as represented by the data, if not the quantum), between EuroMOMO, Prof. Michael Levitt, Prof. Sir David Spiegelhalter and the Prof. Jonathan Valabhji et al. paper; that increasing age beyond middle age is a significant indicator of enhanced risk to Covid-19.

In some other respects, Michael is at odds with forecasts made by Prof. Neil Ferguson’s Imperial College group (and, by inference, also with the London School of Hygiene and Tropical Medicine) and with the analysis of the Imperial College paper by Prof. Spiegelhalter.

I reported this in my recent blog post on May 18th concerning the Cambridge Conversation of 14th May, highlighting the contrast with Michael’s interview with Freddie Sayers of UnHerd, which is available directly on YouTube at https://youtu.be/bl-sZdfLcEk.

I recommend going to the primary evidence and watching the videos in those posts.

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