Latest Cases Heatmap Analysis: 22 cases per 100,000 over-80-year-olds

Today’s analysis shows 22 cases per 100,000 in the over-80s population in England.

To put this into context, the Government uses a rate of 20 cases per 100,000 in order to determine (with other factors) whether you should self isolate when you return from a country with this incidence of Covid-19.

An interpretation would be: if you went to a country consisting of only over-80s, you would have to self-isolate when returning to the UK.

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Background

Why It Matters

High Resolution Versions:

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White to Red (Colourblind-Safe) Version

Guardian Article

Coronavirus Media Roundup week ended 27 September 2020

Sky News including my cases heatmap analysis at 2:30

Channel 5 News

Quoted in the British Medical Journal
(BMJ 2020; 370 :m3678 doi: https://doi.org/10.1136/bmj.m3678 )

Quoted in The Observer / The Guardian



BBC Local Radio

And interviews on BBC Look North & BBC East Midlands Today; Background to BBC News, Reuters

Coronavirus Media Roundup week ended 20 September 2020

ITV Good Morning Britain

Interviewed on BBC Five Live

Sky News

Analysis shown on ITV Peston

Daily Mail (Mail Online) and Yahoo! News UK

BBC Local Radio (BBC Radio Leicester, BBC Radio Oxford, BBC Radio Berkshire)

and background interviews for BBC, Bloomberg, Reuters.

Civil Servants Write Things Down

One thing civil servants learn is to write things down. Here is Academy of Medical Sciences 14 July report commissioned by the UK Chief Scientific Adviser. For the record.

It sets out what was known in July, and clearly sets out what the Government needed to do at the time. Straight off the bat, we have the executive summary.

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Line one: “July and August must be a period of intense preparation for our reasonable worst-case scenario for health in the winter that we set out in this report, including a resurgence of COVID-19, which might be greater than that seen in the spring.”

Here are the challenges expected under a reasonable worst case scenario:
1. A large resurgence of COVID-19 nationally, with local or regional epidemics
2. Disruption of the health and social care systems
3. A backlog of non-COVID-19 care
4. A possible influenza epidemic

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And sets out what we should have done:
– public engagement
– extensive public information campaign
– tailoring guidance –
and…

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Here we go: “Significantly expanding the capacity of the TTI programme to cope with increasing demands over the winter and ensure that it can respond quickly and accurately.”

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Improving public health surveillance: “Maintaining a comprehensive, population-wide, near-real-time, granular health surveillance system to ensure rapid identification, investigation and management of local COVID-19 outbreaks across community, work, and health and social care”.

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But why does this matter? What would happen if we got this wrong? “Even scenarios with Rt in the 1.1-1-5 are likely to stretch the NHS”

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So, what was R? The UK Government estimated it to be 1.0-1.2 (so say 1.1). That was on 11 September. https://gov.uk/guidance/the-r

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But look at the caveat that goes with that estimate “The latest published figures represent the situation over the past few weeks rather than today. These estimates do not yet fully reflect any very recent changes in transmission due to, for example, the reopening of schools…”

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The REACT survey estimated R to be 1.7 https://imperial.ac.uk/news/203873/largest-covid-19-testing-study-shows-cases/

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Now re-read the @uksciencechief‘s report “Even scenarios with Rt in the 1.1-1-5 are likely to stretch the NHS”

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But what is this reasonable worst case scenario? Back to the report. Oh, and there’s talk of R being 1.7 again:

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“infections could be expected to rise gradually with a peak in hospital admissions and deaths of a similar magnitude to the first wave (Figure 4). This is projected to occur in January/February, coinciding with a period of peak demand on the NHS….

“The broader shape of the epidemic curve reflects the lower Rt assumed, but would result in an estimated total number of hospital deaths (excl. care homes) between September 2020 and June 2021 of 119,900 … over double the number occurring during the first wave in spring 2020

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Here is the full report. It’s worth a read. And this is what I wrote at the time of publication: ‘don’t say we weren’t warned’.

Heatmaps of COVID Cases in England

Click here to link to Loughborough University press release

Public Health England have released their data on cases split by age and week. We can turn these into a map visualizing the transmission of the epidemic through ages of cases and through time.

We do this by plotting a three-dimensional chart, a heatmap, where the x axis shows time (split into weeks) and the y axis shows the age of individuals who test positive (split roughly into 10-year groups). The colour of the chart shows the number of cases in each age/week cell.

We work out the cases per 100,000 (a standard epidemiological way of presenting incidence numbers) by finding the population in each age group and dividing the cases by that number (population estimates are from 2018).

The beginning of the epidemic

We can see clearly the very high incidence in the over 80s. We now know that many of these were in care homes (although many were in the community). By 28 June (the last day of this chart), the numbers in each age cohort were relatively low, with an incidence of 18 per 100,000 in the over 80s, but a maximum of 11 cases per 100,000 in the under 80s.

The resurgence

We have produced a new heatmap and scaled the reds to the maximum numbers – so the reds in this heatmap (up to 46 cases per 100,000 in 20 to 29 year-olds) are not as high as the reds in the first heatmap (where we saw a maximum incidence of 232 cases per 100,000 in the over 80s)

What we do see however is a movement from young people (20 to 29-year-olds) to the remainder of the working population (certainly up to 60 year-olds).

Based on data from France, the US, and Spain, that I expect that cases will move to the more vulnerable older population, with the very real risk of hospitalizations and deaths increasing over the weeks ahead. Public Health England has already detected new cases in care homes, and we need to be extremely vigilant and aware to ensure we do not repeat the mistakes of the early part of the epidemic.

Update 18 September

Latest version of my heatmap – shows cases established in the working population and the over-80s.

Read here to explain why this is a problem: Should We Be Concerned About COVID Transmission In Young People? Yes.

Should We Be Concerned About COVID Transmission In Young People? Yes.

The case numbers for COVID-19 have risen significantly over the last few days and are now at just under 3,000 cases per day.

We have been told by Minsiters and the Deputy Chief Medical Officer that these cases are primarily in young people. So, why should we be concerned
with COVID transmission in young people when they are statistically unlikely to have severe symptoms or be hospitalised or die?

We can look at other countries to see what may happen in the coming weeks.

Various authors have plotted cases vs age vs time. On the x axis is time, on the y axis are ages. Look at weeks S31/S32 (semaine/week 31 and 32). Some incidence in 20-29 year olds. But in week S33, this spreads to 30-70 year olds. And then in week S35 and S36, cases in 70+ year olds.

We have known this for some time. Here is data from Florida from July.
Same thing. Starts with young people and spreads to older age groups.

Here is the UK data for COVID mortality from Public Health England / Joint Biosecurity Centre / NHS Test and Trace. Very few (but some) deaths in young people. So we may not see significant deaths filtering through for a few weeks

Chart 2(b) in the PHE Surveillance report is the one to watch. These data lag by a couple of weeks

but I anticipate cases spreading up through the age pyramid in the next couple of weeks. Which I anticipate will lead to increased hospitalizations in the week after that, and increased deaths a few weeks from that. But this is not inevitable: we need to go back to the fundamental mitigations of social distancing, hand washing, and mask wearing, and not forgetting that the virus is still very much with us.

Update 13 September 2020

Public Health England have released their latest surveillance report and I have made a heatmap for English cases. The data is a week old. We can see high incidence in the 20 to 29 year olds spreading to older ages. I expect this to continue over the coming weeks.

Update 20 September 2020

Here is the heatmap produced for the data published on 18 September. We see an incidence of 20 cases per 100,000 in the over 80s for the most recent week. But look closely at the figure to the left – 21. This is the same as the top right cell in the heatmap above. What is very worrying is that this figure has changed, since PHE publish their data a week in arrears. This imples that indiviuals are having cases included over a week late. This indicates a potential failure in getting these results processed by NHS Test and Trace.


Data Sources for COVID-19 in England – Letter from PHE to Local Authorities

I have received a copy of the following letter from Public Health England to Local Authorities setting out the data sources available to local authories and the public. The letter is dated 9 July 2020 and I have redacted certain information.

This should be useful for people wishing to understand what data is (and was) available on COVID-19 cases in England.

Letter-to-LAs-on-data-access_9-July-2020-REDACTED

Total (Cumulative) Deaths from COVID-19 to 7 July 2020

I have analyzed the death data from coronavirus-staging.data.gov.uk and produced the maps below. These are for total deaths since the beginning of the epidemic (not total cases and not current deaths). Leicester (currently locked down with a large number of cases) does not have a relatively high number of deaths. Areas that are dark green do not imply that they are resistant – just that the epidemic has not reached that area in relatively large numbers.

In London, Tower Hamlets is relatively low, which could be due to the relatively young population in that area and the lack of care homes in the centre of London. It is also interesting to note that parts of London have relaively low deaths despite reportedly high levels of serroprevalence.

COVID-19 Deaths by Population at 6 July 2020

Cumulative COVID-19 deaths per 100,000 population as at 6 July 2020
Zoomed in to London

coronavirus-staging.data.gov.uk has just released death totals per local authority. We can divide these by the population to get deaths per 100,000 population up to 5 July 2020. These data and the analysis is provisional and may be updated.

Group 1: Greater than 100 deaths per 100,000 population

Group 2: Between 80 and 100 deaths per 100,000 population

Group 3: Between 60 and 80 deaths per 100,000 population
Group 4: Between 40 and 60 deaths per 100,000 population
Group 5: Fewer than 40 deaths per 100,000 population

This is what is classified as a death:

For updates, follow me on Twitter @Dr_D_Robertson

Commentary on COVID-19 cases in Leicester

Leicester went into lockdown in early July, with the Statutory Instrument setting out these restrictions published on 3 July (The Health Protection (Coronavirus, Restrictions) (Leicester) Regulations 2020) just before the loosening of restrictions elsewhere in the country.

Public Health England has published an analysis of what is known about the Leiecester outbreak. Diagrams are from the PHE report.

The latest daily case numbers are available at coronavirus.data.gov and are shown below. Note that the latest figures in the data download are not complete, as these will exclude specimens in the post. Also note that the number of positive cases detected will be affected by Leicester being in the news, availability of more testing stations, and the functioning of the NHS Test and Trace service (see update below).

The first thing to note is the mismatch between testing that was disclosed to the public (so called Pillar 1 tests) when a potential lockdown was being discussed by politicians and the total number of tests being conducted (Pillar 1 and Pillar 2 tests). I have discussed why this was a problem here. Since writing, the Government has disclosed total positive tests (but not the number of tests taken) for each location, including Leicester.

Firstly, the number of positive tests rose to 23 June (the chart above updates this slide).

PHE Preliminary Investigation into COVID-19 Exceedances in Leicester (June 2020)

Since then, it appears that the number of positive tests may be falling, but this is preliminary analysis, and we shall know for sure on Thursday when PHE release their updated analysis for the whole country.

The current Leicester cases seem to be through working age people and children (this is where Leicester may be unusual – other outbreaks may be in care homes where the population is older).

PHE Report

This is the spatial analysis of where cases have taken place in Leicester (the left map is Pillar 1 testing and the right map is Pillar 2 testing).

PHE Report

And this breaks down the wards in which most cases were located

PHE Report

with the corresponding map here

PHE Report

It is important to note that testing has been increasing in Leicester, so some of the increase in positive cases may be due to this. William makes the comment below that this may be due to the location of walk-in tests making people from those areas more likely to take tests compared to other areas of the city. There is a feedback effect here, where more positive cases means more testing resources allocated to those areas which means more testing of those areas. Without test data (number of tests in each location), it is not possible to see whether the increased case density is as a result of increased numbers of tests, as we don’t know the percentage of positive cases at each location.

The latest Public Health England national report here with results shown below.

Source: http://www.duncanrobertson.com/2020/07/01/which-city-could-be-next-for-a-leicester-like-lockdown/
Source: http://www.duncanrobertson.com/2020/07/01/which-city-could-be-next-for-a-leicester-like-lockdown/

Leicester cases are now published here:
https://coronavirus-staging.data.gov.uk/cases?areaType=ltla&areaName=Leicester and here is the data from 6 July 2020

coronavirus-staging.data.gov.uk 6 July 2020 data

Update: The .gov.uk analysis seems to average out the 7-day average as +/- 3 days which is misleading, as the recent specimen date tests may not have arrived.

The threshold for lockdown is not publicly disclosed (and there is unlikely to be an absolute threshold as local considerations such as where the outbreak is taking place (for example in a factory or a care home that can be relatively well contained). However, Germany has set a threshold of 50 cases per 100,000 to consider an ’emergency brake’ and reimpose lockdown-like restrictions.

Taking the population of Leicester as 348,300, this would mean that this threshold of 50 cases per 100,000 in a week would be 50 * (348,300 / 100,000) / 7 = 25 cases per day as a threshold. Although of course, the threshold for entering and leaving lockdown are not the same. And Directors of Public Health and journalists, armed with timely and complete data, are far more able to understand what is happening at a local level.

I will provide an analysis of the Public Health England data on Thursday when it is published. For updates, please come back to duncanrobertson.com or follow me on Twitter @Dr_D_Robertson