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Coronavirus Covid-19 Herd Immunity Imperial College Michael Levitt Office for National Statistics ONS PHE Public Health England Superspreader Sweden

Model update following UK revision of Covid-19 deaths reporting

Introduction

On August 12th, the UK Government revised its counting methodology and reporting of deaths from Covid-19, bringing Public Health England’s reporting into line with that from the other home countries, Wales, Northern Ireland and Scotland. I have re-calibrated and re-forecast my model to adapt to this new basis.

Reasons for the change

Previously reported daily deaths in England had set no time limit between any individual’s positive test for Covid-19, and when that person died. 

The three other home countries in the UK applied a 28-day limit for this period. It was felt that, for England, this lack of a limit on the time duration resulted in over-reporting of deaths from Covid-19. Even someone who had died in a road accident, say, would have been reported as a Covid-19 death if they had ever tested positive, and had then recovered from Covid-19, no matter how long before their death this had happened.

This adjustment to the reporting was applied retroactively in England for all reported daily deaths, which resulted in a cumulative reduction of c. 5,000 in the UK reported deaths to up to August 12th.

The UK Government say that it is also to report on a 60-day basis (96% of Covid-19 deaths occur within 60 days and 88% within 28 days), and also on the original basis for comparisons, but these two sets of numbers are not yet available.

On the UK Government’s web page describing the data reporting for deaths, it says “Number of deaths of people who had had a positive test result for COVID-19 and died within 28 days of the first positive test. The actual cause of death may not be COVID-19 in all cases. People who died from COVID-19 but had not tested positive are not included and people who died from COVID-19 more than 28 days after their first positive test are not included. Data from the four nations are not directly comparable as methodologies and inclusion criteria vary.

As I have said before about the excess deaths measure, compared with counting deaths attributed to Covid-19, no measure is without its issues. The phrase in the Government definition above “People who died from COVID-19 but had not tested positive are not included…” highlights such a difficulty.

Model changes

I have adapted my model to this new basis, and present the related charts below.

  • Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, on March 23rd, modified in 5 steps by -.3%, -0% -0% and -0% successively
  • Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, modified in 5 steps by -.3%, -0% -0% and -0% successively
  • Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, on March 23rd, modified in 5 steps by -.3%, -0% -0% and -0% successively
  • Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, on March 23rd, modified in 5 steps by -.3%, -0% -0% and -0% successively
  • Model forecast for the UK deaths as at August 14th, compared with reported for 84.3% lockdown effectiveness, on March 23rd, modified in 5 steps by -.3%, -0% -0% and -0% successively
  • Chart 12 for the comparison of cumulative & daily reported & modelled deaths to 26th April 2021, adjusted by -.3% on May 13th

This changed reporting basis reduced the cumulative UK deaths to August 12th from 46,706 to 41,329, a reduction of 5,377.

The fit of my model was better for the new numbers, requiring only a small increase in the initial March 23rd lockdown intervention effectiveness from 83.5% to 84.3%, and a single easing reduction to 84% on May 13th, to bring the model into good calibration up to August 14th.

It does bring the model forecast for the long term plateau for deaths down to c. 41,600, and, as you can see from the charts above, this figure is reached by about September 30th 2020.

Discussion

The relationship to case numbers

You can see from the first model chart that the plateau for “Recovered” people is nearly 3 million, which implies that the number of cases is also of the order of 3 million. This startling view is supported by a recent antibody study reported by U.K. Government here.

This major antibody testing programme, led by Imperial College London, involving over 100,000 people, found that just under 6% of England’s population – an estimated 3.4 million people – had antibodies to COVID-19, and were likely to have previously had the virus prior to the end of June.

The reported numbers in the Imperial College study could seem quite surprising, therefore, given that 14 million tests have been carried out in the U.K., but with only 313,798 positive tests reported as at 12th August (and bearing in mind that some people are tested more than once).

But the study is also in line with the estimate made by Prof. Alex de Visscher, author of my original model code, that the number of cases is typically under-reported by a factor of 12.5 – i.e. that only c. 8% of cases are detected and reported, an estimate assessed in the early days for the Italian outbreak, at a time when “test and trace” wasn’t in place anywhere.

A further sanity check on my modelled case numbers, relative to the number of forecasted deaths, would be on the observed mortality from Covid-19 where this can be assessed.

A study by a London School of Hygiene & Tropical Medicine team carried out an analysis of the Covid-19 outbreak in the closed community of the Diamond Princess cruise ship in March 2020.

Adjusting for delay from confirmation-to-death, this paper estimated case and infection fatality ratios (CFR, IFR) for COVID-19 on the Diamond Princess ship as 2.3% (0.75%-5.3%) and 1.2% (0.38-2.7%) respectively.

In broad terms, my model forecast of 42,000 deaths and up to 3 million cases would be a ratio of about 1.4%, and so the relationship between the deaths and cases numbers in my charts doesn’t seem to be unreasonable.

Changing rates of infection

I am not sure whether the current forecast for a further decline in the death rate will remain, in the light of continuing lockdown easing measures, and the local outbreaks.

Both the Office for National Statistics (ONS) and Public Health England (PHE) reported in early July a drop in the rate of decline in Covid-19 cases per 100,000 people in England.

Figure 2: The latest exploratory modelling shows the downward trend in those testing positive for COVID-19 has now levelled off

This was at the same time as the ONS reported that excess deaths have reduced to a level at or below the average for the last five years.

The number of deaths involving COVID-19 decreased for the 10th consecutive week

PHE reports this week that the infection rate is now more pronounced for under-45s than for over-45s, a reversal of the situation earlier in the pandemic. Overall case rates, however, remain lower than before; and although the rate of decline in the case rate has slowed for-over-45s, and is nearly flat now, for under-45s the infection rate has started to increase slightly.

Covid-19 cases rate of decline slows more for under-45s

The impact on the death rate might well be lower than previously, owing to the lower fatality rates for younger people compared with older people.

Herd immunity

Closely related to the testing for Covid-19 antibodies is herd immunity, a topic I covered in some detail on my blog post on June 28th, when I discussed the relative positions of the USA and Europe with regard to the spike in case numbers the USA was experiencing from the middle of June, going on to talk about the Imperial College Coronavirus modelling, led by Prof. Neil Ferguson, and their pivotal March 16th paper.

This paper was much criticised by Prof Michael Levitt, and others, for the hundreds of thousands of deaths it mentioned if no action were taken, cited as scare-mongering, ignoring to some extent the rest of what I think was a much more nuanced paper than was appreciated, exploring, as it did, the various interventions that might be taken as part of what has become known as “lockdown”.

The intervention options were also quite nuanced, embracing as they did (with outcomes coded as they were in the chart below) PC=school and university closure, CI=home isolation of cases, HQ=household quarantine, SD=large-scale general population social distancing, SDOL70=social distancing of those over 70 years for 4 months (a month more than other interventions).

PC=school and university closure, CI=home isolation of cases, HQ=household quarantine, SD=large-scale general population social distancing, SDOL70=social distancing of those over 70 years for 4 months (a month more than other interventions)
PC=school and university closure, CI=home isolation of cases, HQ=household quarantine, SD=large-scale general population social distancing, SDOL70=social distancing of those over 70 years for 4 months (a month more than other interventions)

I had asked the lead author of the paper why the effectiveness of the three measures “CI_HQ_SD” in combination (home isolation of cases, household quarantine & large-scale general population social distancing) taken together (orange and yellow colour coding), was LESS than the effectiveness of either CI_HQ or CI_SD taken as a pair of interventions (mainly yellow and green colour coding)?

The answer was in terms of any subsequent herd immunity that might or might not be conferred, given that any interventions as part of a lockdown strategy would be temporary. What would happen when they ceased?

The issue was that if the lockdown measures were too effective, then (assuming there were any immunity to be conferred for a usefully long period) the potential for any subsequent herd immunity would be reduced with too successful a lockdown. If there were no worthwhile period of immunity from catching Covid-19, then yes, a full lockdown would be no worse than any other partial strategy.

Sweden

I mention all this as background to a paper that was just published in the Journal of the Royal Society of Medicine as I started this blog post, on August 12th. It concerns the reasons why, as the paper authored by Eric Orlowski and David Goldsmith asserts, that four months into the COVID-19 pandemic, Sweden’s prized herd immunity is nowhere in sight.

This is a somewhat polemical paper, as Sweden is often held up as an example of how countries can succeed in combating the SARS-Cov-2 pandemic by emulating Sweden’s non-lockdown approach. I have been, and remain surprised by such claims, and now this paper helps calibrate and articulate the underlying reasons.

Although compared with the UK, Sweden had done little worse, if at all, despite resisting the lockdown approach (although its demographics and lifestyle characteristics are not necessarily comparable to the UK’s), compared with their more similar nearest neighbours, Norway, Denmark and Finland, Sweden has done far worse in terms of deaths and deaths per capita.

I think that either for political or for other related reasons, perhaps economic ones, even some otherwise sensible scientists are advocating the Swedish approach, somehow ignoring the more valid (and negative) comparisons between Sweden and the other Scandinavian countries, as opposed to more favourable comparisons with others further afield – the UK, for example.

I have tried to remain above the fray, notably on the Twittersphere, but, at least on my own blog, I want to present what I see as a balanced assessment of the evidence.

That balance, in this case, strikes me like this: if there were an argument for the Swedish approach, then a higher level of herd immunity would have been the payoff for experiencing more immediate deaths in favour of a better outcome later.

But that doesn’t seem to have happened, at least in terms of outcomes from testing for antibodies, as presented in this paper. As it says “it is clear that nowhere is the prevalence of IgG seropositivity high (the maximum being around 20%) or climbing convincingly over time. This is especially clear in Sweden, where the authorities publicly predicted 40% seroconversion in Stockholm by May 2020; the actual IgG seroprevalence was around 15%.

Concluding comments

As I said in my August 4th post, the outbreaks we are seeing in some UK localities (Leicester, Manchester, Aberdeen and many others) seem to be the outcome of individual and multiple local super-spreading events.

These are quite hard to model, requiring very fine-grained data regarding the types and extent of population interactions, and the different effects of a range of intervention measures available nationally and locally, as I mentioned above, applied in different places at different times.

The reproduction number, R (even nationally) can be increased noticeably by such localised events, because of the lower overall incidence of cases in the UK (something we have seen in some other countries too, at this phase of the pandemic).

While most people nationally aren’t directly affected by these localised outbreaks, I believe that caution – social distancing where possible, for example – is still necessary.

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Adam Kucharski Alex de Visscher Coronavirus Covid-19 David Spiegelhalter Superspreader Worldometers

Model updates for UK lockdown easing points

Introduction

As I reported in my previous post on 31st July, the model I use, originally authored by Prof. Alex de Visscher at Concordia University in Montreal, and described here, required an update to handle several phases of lockdown easing, and I’m glad to say that is now done.

Alex has been kind enough to send me an updated model code, adopting a method I had been considering myself, introducing an array of dates and intervention effectiveness parameters.

I have been able to add the recent UK Government relaxation dates, and the estimated effectiveness of each into the new model code. I ran some sensitivities which are also reported.

Updated interventions effectiveness and dates

Now that the model can reflect the timing and impact of various interventions and relaxations, I can use the epidemic history to date to calibrate the model against both the initial lockdown on March 23rd, and the relaxations we have seen so far.

Both the UK population (informally) and the Government (formally) are making adjustments to their actions in the light of the threats, actual and perceived, and so the intervention effects will vary.

Model adjustments

At present I am experimenting with different effectiveness percentages relating to four principal lockdown relaxation dates, as described at the Institute for Government website.

In the model, the variable k11 is the starting % infection rate per day per person for SARS-Cov-2, at 0.39, which corresponds to 1 infection every 1/0.39 days ~= 2.5 days per infection.

Successive resetting of the interv_success % model variable allows the lockdown, and its successive easings to be defined in the model. 83.5% (on March 23rd for the initial lockdown) corresponds to k11 x 16.5% as the new infection rate under the initial lockdown, for example.

In the table below, I have also added alternative lockdown easing adjustments in red to show, by comparison, the effect of the forecast, and hence how difficult it will be for a while to assess the impact of the lockdown easings, volatile and variable as they seem to be.

DateDay Steps and example measuresChanges to % effectiveness
23rd March52Lockdown starts+83.5%
13th May105Step 1 – Partial return to work
Those who can work from home should do so, but those who cannot should return to work with social distancing guidance in place. Some sports facilities open.
-1% = 82.5%

-4% = 79.5%
1st June122Step 2 – Some Reception, Year 1 and Year 6 returned to school. People can leave the house for any reason (not overnight). Outdoor markets and car showrooms opened.-5% = 77.5%

-8% = 71.5%
15th June136Step 2 additional – Secondary schools partially reopened for years 10 and 12. All other retail are permitted to re-open with social distancing measures in place.-10% = 67.5%

+10% = 81.5%
4th July155Step 3 – Food service providers, pubs and some leisure facilities are permitted to open, as long as they are able to enact social distancing.+20% = 87.5%

-6% = 75.5%
1st August186Step 3 additional – Shielding for 2m vulnerable people in the UK ceases0% = 87.5%
Dates, examples of measures, and % lockdown effectiveness changes on k11

After the first of these interventions, the 83.5% effectiveness for the original March 23rd lockdown, my model presented a good forecast up until lockdown easing began to happen (both informally and also though Government measures) on May 13th, when Step 1 started, as shown above and in more detail at the Institute for Government website.

Within each easing step, there were several intervention relaxations across different areas of people’s working and personal lives, and I have shown two of the Step 2 components on June 1st and June 15th above.

I applied a further easing % for June 15th (when more Step 2 adjustments were made), and, following Step 3 on July 4th, and the end (for the time being) of shielding for 2m vulnerable people on August 1st, I am expecting another change in mid-August.

I have managed to match the reported data so far with the settings above, noting that even though the July 4th Step 3 was a relaxation, the model matches reported data better when the overall lockdown effectiveness at that time is increased. I expect to adjust this soon to a more realistic assessment of what we are seeing across the UK.

With the % settings in red, the outlook is a little different, and I will show the charts for these a little later in the post

The settings have to reflect not only the various Step relaxation measures themselves, but also Government guidelines, the cumulative changes in public behaviour, and the virus response at any given time.

For example, the wearing of face coverings has become much more common, as mandated in some circumstances but done voluntarily elsewhere by many.

Comparative model charts

The following charts show the resulting changes for the initial easing settings. The first two show the new period of calibration I have used from early March to the present day, August 4th.

On chart 4, on the left, you can see the “uptick” beginning to start, and the model line isn’t far from the 7-day trend line of reported numbers at present (although as of early August possibly falling behind the reported trend a little).

On the linear axis chart 13, on the right, the reported and model curves are far closer than in the version in my most recent post on July 31st, when I showed the effects of lockdown easing on the previous forecasts, and I highlighted the difficulty of updating without a way of parametrising the lockdown easing steps (at that time).

Using the new model capabilities, I have now been able to calibrate the model to the present day, both achieving the good match I already had from March 23rd lockdown to mid-May, and then separately to adjust and calibrate the model behaviour since mid-May to the present day, by adjusting the lockdown effectiveness at May 15th, June 1st, June 15th and July 4th, as described earlier.

The orange dots (the daily deaths) on chart 4 tend to cluster in groups of 4 or 5 per week above the trend line (and also the model line), and 3 or 2 per week below. This is because of the poor accuracy of some reporting at weekends (consistently under-reporting at weekends and recovering by over-reporting early the following week).

The red 7-day trend line on chart 4 reflects the weekly average position.

Looking a little further ahead, to September 30th, this model, with the initial easing settings, predicts the following behaviour, prior to any further lockdown easing adjustments, expected in mid-August.

Chart 12 for the comparison of cumulative & daily reported & modelled deaths, on the basis of 83.5% effectiveness, modified in 4 steps by -1%, -5% -10% and +2% successively
Chart 12 for the comparison of cumulative & daily reported & modelled deaths

Finally, for comparison, the Worldometers UK site has a link to its own forecast site, which has several forecasts depending on assumptions made about mask-wearing, and/or continued mandated lockdown measures, with confidence limits. I have screenshot the forecast on October 1st, where it shows 48,268 deaths assuming current mandates continuing, and mask-wearing.

My own forecast shows 47,201 cumulative deaths at that date.

Worldometers forecasts on the basis of mask wearing vs. no mandated measures, with confidence limits
Worldometers forecasts on the basis of mask wearing vs. no mandated measures, with confidence limits

Alternative % settings in red

I now present a slideshow of the corresponding charts with the red % easing settings. The results here are for the same initial lockdown effectiveness, 83.5%, but with successive easings at -4%, -8%, +10% and -6%, where negative is relaxation, and positive is an increase in intervention effectiveness.

  • Chart 12 for the comparison of cumulative & daily reported & modelled deaths to 26th April 2021, on the basis of 83.5% effectiveness, modified in 4 steps by -4%, -8% +10% and -6%% successively
  • Chart 12 for the comparison of cumulative & daily reported & modelled deaths to 30th Sep 2020, , on the basis of 83.5% effectiveness, modified in 4 steps by -4%, -8% +10% and -6%% successively
  • Chart 4 for the comparison of cumulative & daily reported & modelled deaths, plus reported trend line, on the basis of 83.5% effectiveness
  • Model forecast for the UK deaths as at August 8th, compared with reported for 83.5% lockdown effectiveness
  • Model forecast (linear axes) for the UK deaths as at August 8th, compared with reported for 83.5% lockdown effectiveness, modified in 4 steps by -4%, -8% +10% and -6%% successively

The model forecast here for September 30th is for 49, 549 deaths, and the outlook for the longer term, April 2020, is for 52,544.

Thus the next crucial few months, as the UK adjusts its methods for interventions to be more local and immediate, will be vital in its impact on outcomes. The modelling of how this will work is far more difficult, therefore, with fine-grained data required on virus characteristics, population movement, the comparative effect of different intervention measures, and individual responses and behaviour.

Hotspots and local lockdowns

At present, because the UK reported case number trend has flattened out and isn’t decreasing as fast, and because of some local hotspots of Covid-19 cases, the UK Government has been forced to take some local measures, for example in Leicester a month ago, and more recently in Manchester; the scope and scale of any lockdown adjustments is, therefore, a moveable target.

I would expect this to be the pattern for the future, rather than national lockdowns. The work of Adam Kucharski, reported at the Wellcome Open Research website, highlighting the “k-number”, representing the variation, or dispersion in R, the reproduction number, as he says in his Twitter thread, will be an important area to understand.

The k-number might well be more indicative, at this local hotspot stage of the crisis, than just the R reproduction number alone; it has a relationship to the “superspreader” phenomenon discussed for SARS in this 2005 paper, that was also noticed very early on for SARS-Cov-2 in the 2020 pandemic, both in Italy and also in the UK. I will look at that in more detail in another posting.

Superspreading relates to individuals who are infected (probably asymptomatically or pre-symptomatically) who infect others in a closed social space (eg in a ski resort chalet as reported by the BBC on February 8th) without realising it.

The hotspots we are now seeing in many places might well be related to this type of dispersion. The modelling for this would be a further complication, potentially requiring a more detailed spatial model, which I briefly discussed in my blog post on modelling methods on July 14th.

Superspreading might also need to be understood in relation to the opening of schools, in August and September (across the four UK home countries). It might have been a factor in the Israel experience of return to schools, as covered by the Irish Times on August 4th.

The excess deaths measure

There has been quite a debate on excess deaths (often a seasonal comparison of age-related deaths statistics compared with the previous 5 years) as a measure of the overall position at any time. As I said in a previous post on June 2nd, this measure does mitigate any arguments as to what is a Covid-19 fatality, and what isn’t.

The excess deaths measure, however, has its own issues with regard to the epidemic’s indirect influence on the death rates from other causes, both upwards and downwards.

Since there is less travel (on the roads, for example, with fewer accidents), and many people are taking more care in other ways in their daily lives, deaths from some other causes might tend to reduce.

On the other hand, people are feeling other pressures on their daily lives, affecting their mood and health (for example the weight gain issues reported by the COVID Symptom Study), and some are not seeking medical help as readily as they might have done in other circumstances. Both factors tend to increase illness and potentially death rates.

Even as excess deaths reduce, then, it may well be that Covid-19 deaths increase as others reduce. Possibly a crossover with seasonal influenza deaths, later on, might be masked by the overall excess deaths measure.

As I also mentioned in my post on July 6th, deaths in later years from other causes might increase because of this lack of timely diagnosis and treatment for other “dread” diseases, as, for example, for cancer, as stated by Data-can.org.uk.

So no measure of the epidemic’s effects is without its issues. Prof. Sir David Spiegelhalter covered this aspect in a newspaper article this week.

Discussion

The statistical interpretation and modelling of data related to the pandemic is a matter of much debate. Some commentators and modellers are proponents of quite different methods of data recording, analysis and forecasting, and I covered phenomenological methods compared with mechanistic (SIR) modelling in previous posts on July 14th and July 18th.

The current reduced rate of decline in cases and deaths in some countries and regions, with concomitant local outbreaks being handled by local intervention measures, including, in effect, local lockdowns, has complicated the predictions of some who think (and have predicted) that the SARS-Cov-2 crisis will soon be over (some possibly for political reasons, some of them scientists).

Even when excess deaths reduce to zero, this doesn’t mean that Covid-19 is over, because, as I mentioned above, illness and deaths from other causes might have reduced, with Covid-19 filling the gap.

There are also concerns that recovery from Covid-19 as a death threat can be followed by longer-lasting illness and symptoms, and some studies (for example this NHLBI one) are gathering evidence, such as that covered by this report in the Thailand Medical News.

This Discharge advice from the UK NHS makes continuing care requirements for discharged Covid-19 patients in the UK very clear.

It is by no means certain, either, that recovery from Covid-19 confers immunity to SARS-Cov-2, and, if it does, for how long.

Concluding comments

I remain of the view that in the absence of a vaccine, or a very effective pharmaceutical treatment therapy, we will be living with SARS-Cov-2 for a long time, and that we do have to continue to be cautious, even (or, rather, especially) as the UK Government (and many others) move to easing national lockdown, at the same time as being forced to enhance some local intervention measures.

The virus remains with us, and Government interventions are changing very fast. Face coverings, post-travel quarantining, office/home working and social distancing decisions, guidance and responses are all moving quite quickly, not necessarily just nationally, but regionally and locally too.

I will continue to sharpen the focus of my own model; I suspect that there will be many revisions and that any forecasts are now being made (including by me) against a moving target in a changing context.

Any forecast, in any country, that it will be all over bar the shouting this summer is at best a hostage to fortune, and, at worst, irresponsible. My own model still requires tuning; in any case, however, I would not be axiomatic about its outputs.

This is an opinion informed by my studies of others’ work, my own modelling, and considerations made while writing my 30 posts on this topic since late March.