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.

Update 12 October 2020

Latest heatmap. See here for discussion.



Show Your Working: Model Quality Assurance in Government & Letter in Financial Times

School pupils have had a tough year. For those with examinations, such as A-levels, it has been even tougher. The Department for Education decreed that A-levels and GCSEs should not take place due to the COVID crisis.

This meant that an alternative way of allocating grades to students needed to be found.

To set the context, Ofqual, the Office of Qualifications and Examinations Regulation, regulates qualifications, examinations and assessments in England. It is a Non-Ministerial Government Department constituted under the Apprenticeships, Skills, Children and Learning Act 2009. Now, it is evident that, despite being a non-ministerial department, the Department for Education has a responsibility for setting policy.

Therefore, a Memorandum of Understanding exists between Ofqual and DfE setting out how the two organizations will work together. Section 2 sets out responsibilities:

On 31 March, the Secretary of State, Gavin Williamson, wrote to Ofqual, setting out a ministerial direction. These are the salient points in the Direction:

Firstly, there needs to be a calculation, and secondly ‘as far as possible, the qualification standards are maintained and the distribution of grades follows a similar profile to that in previous years’.

This is a very strong constraint, and to be fair, one that Ofqual met in their initial calculated grade. The problem was it was not fair.

Much debate has been generated as to algorithms, models, and their use in Government (and arm’s length bodies such as Ofqual). But this is not a new problem.

In 2012, the West Coast rail franchise was awarded to FirstGroup. Virgin Trains complained, serious errors were found in the model used by DfT, and the award to FirstGroup was cancelled.

This cost taxpayers £54 million, and, as a result, and report was commissioned to prevent this happening again.

In 2013, Nick Macpherson, Permanent Secretary of the Treasury, published a Review of Quality Assurance of Goverment Analytical Models.

Macpherson’s report was operationalized by HM Government by The Aqua Book: Guidance on producing quality analysis for Government.

The Aqua Book recommends that there should be a Senior Responsible Owner for each model (for Government departments and their arm’s length bodies, such as Ofqual).

Ofqual’s model documentation was set out in their 318-page report Awarding GCSE, AS, A level, advanced extension awards and extended project qualifications in summer 2020: interim report, but the model code has not yet been published.

I cannot find any reference to the Aqua book or ‘quality assurance’ in this model documentation.

Here is my letter about this in the Financial Times

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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

Data Sources for COVID-19 Analysis in England

Since the early Number 10 Downing Street press conferences, the data available to analyze the progression of the COVID-19 epidemic in the UK has become somewhat fragmented. This is an overview of the major sources of data.

coronavirus.data.gov.uk

This shows data for testing, cases, healthcare, and deaths, updated daily.

More detail is shown on each data set, for example cases:

which is broken down by Nation, Region, Upper Tier Local Authority (‘UTLAs’ / counties) and Lower Tier Local Authorities (‘LTLAs’ / districts). Note that some councils, such as Leicester, are Unitary Authorities, and are both UTLAs and LTLAs and their data is disclosed in both UTLA and LTLA data sets. Currently, this only shows the latest data, and cases per 100,000 people (making it easier to compare different sized locations).

This data is shown as a map at Middle Layer Super Output Area (‘MSOA’) level (although the colour bar makes interpretation a little difficult) and shows cases per week. The mean population of a MSOA is around 7,200 people, so the key is not very useful.

Data for UTLAs and LTLAs used to be reported by specimen date, but it is not clear where these data are now available.

Public Health England Surveillance Reports

Public Health England (‘PHE’) produce a COVID-19 surveillance report each week. This now shows a list of watchlist local authorities.

These data are shown on a


together with a chart of the number of English cases per week

and the history of the highest rated UTLAs

There is also a report of the number of ‘incidents’ (what are colloquially described as outbreaks) and where they originate from.

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.

Searchable SAGE (Scientific Advisory Group for Emergencies) Minutes on COVID-19

The early minutes of SAGE (the Scientific Advisory Group for Emergencies) were searchable:

However, later minutes are not.

So, if you are searching for, say “asymptomatic transmission”, you won’t find anything. Which is odd, beacuase the SAGE meeting where this was first mooted, on 28 January, is searchable (the documents listed do not link to SAGE minutes). Or maybe it does not search within the documents themselves.

So I have OCR’d the minutes and they are listed at the end of this page.

Spoiler: the phrase ‘asymptomatic transmission’ is mentioned in SAGE minutes

The minutes are available here:https://www.gov.uk/search/transparency-and-freedom-of-information-releases?organisations%5B%5D=scientific-advisory-group-for-emergencies&parent=scientific-advisory-group-for-emergencies

SAGE minutes to meeting 41 (11 June) are on the next page


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

Thinking of Drinking?

The pubs open on Saturday in England, allowing people to mix in confined spaces and potentially transmit COVID-19.

In Friday’s Number 10 briefing, the Chief Medical Officer said
“The biggest risks are when lots of people from completely different households are brought together in close proximity indoors. And whether that’s in a pub or a cricket pavilion that is a high risk activity. And that’s the reason why the really quite onerous social distancing guidelines that are going to cause a significant change to pubs and cause difficulties for many publicans, and we all recognise that, are so essential. There is no doubt these are environments whose principle job it is to bring people together. That’s a great thing to do socially, but it’s also a great thing from the virus’s point of view. And therefore we do have to have a really clear and really disciplined approach to trying to maintain social distancing whilst also enjoying pubs, and this would be true in any other environment”

Which regions of the country are particularly risky? Leicester for a start, where drinking in pubs is banned. Kirklees, Bradford, Blackburn, Rochdale, Rotherham, and Oldham have the next highest cases.

But there are vast swathes of the country that exceed the US Centers for Disease Control threshold for re-opening (10 cases per 100,000 people in a two-week period). While not equivalent, I have used 5 cases per 100,000 people in one week as a cut-off.

I have analyzed the latest Public Health England data to work out which parts of the country exceed these thresholds and plotted them on the map below.

This of course does not mean that other parts of the country are risk-free.

This article was updated on 4 July with the latest data for PHE specimen date for the week to 3 July 2020 inclusive.

Top Local Authorities for COVID-19 Positive Tests

Public Health England have tonight (2 July 2020) released data for the total number of people who have positive COVID-19 results at a local authority level. The data is at https://coronavirus.data.gov.uk/#category=utlas&map=rate. Critically, these include both Pillar 1 (NHS and PHE labs) and Pillar 2 (NHS Test & Trace commercial labs) data.

Here are the cumulative totals for upper tier local authorities ranked from top to bottom ranked by rate (i.e. controlling for population). Leicester is top, followed by Oldham, Barnsley, and Bradford. Note these are the cumulative totals, which doesn’t necessarily mean that there are current outbreaks there.



And here is the data for lower tier local authorities. Leicester (a unitary authority) still top, followed by Ashford, Barrow-in-Furness, and Preston.

Public Health England should be applauded for releasing this data, which will enable us to be far more informed about the epidemiology of the disease at a local level.