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.
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
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.
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).
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).
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).
And this breaks down the wards in which most cases were located
with the corresponding map here
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.
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
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.
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.
Public Health England has today released the second tranche of data for COVID tests. This is the most comprehensive data we have for tests as it includes Pillar 1 tests (those conducted by PHE and NHS hospitals) and Pillar 2 tests (those conducted by private companies under NHS Test and Trace).
Some journalists had been using data from coronavirus.data.gov – but this was dangerously misleading as it only revealed Pillar 1 tests – which are now a relatively small proportion of tests. This had led to erroneous league tables based on Pillar 1 data only until the site was updated late on 2 July.
We want to be able to identify possible regions that have the potential to have remedial action taken, for example local ‘lockdowns’, in the future. This does not mean that these areas will be locked down, more that they should be investigated by Directors of Public Health and local journalists. Without specific local knowledge, here are the criteria I have used to identify regions of interest:
HIGH INCIDENCE REGIONS (RED): Greater than 50 cases per 100,000 individuals. While the Joint Biosecurity Centre has not issued public guidelines for this threshold in the UK, Germany has defined 50 cases per 100,000 inhabitants in a week as the number of cases required for a region to apply an ‘emergency brake’ and reimpose restrictions. Areas meeting these criteria could indicate that there is sustained transmission in this area (but see the caveats below).
WATCHLIST REGIONS (AMBER): Between 40 and 50 cases per 100,000 individuals. (The threshold of 40 is chosen based on a qualitative comparison of Barnsley and Bradford in the PHE Leciester epidemiology report.)
RECOVERING REGIONS (GREEN): In a high incidence or watchlist region last week and fewer than 40 cases per 100,000 this week. It is important to bear in mind that no area is recovered from COVID-19, as outbreaks can recur in any region at any time.
A more general point needs to be made about the paucity of publicly available data. Without timely, complete, accurate data available to the public, there are several issues:
Other towns may see that they have relatively high case levels on the Coronavirus data service, causing unnecessary alarm;
Having data at a coarse geographical area (currently Upper Tier Local Authorities) does not allow outbreaks in towns and villages to be identified;
Unitary authorities (such as Leicester – where the city council performs the role of district and county councils) are separated on the maps, but cities such as Oxford (where there is a city council and a separate county council) are included in the data for Oxfordshire, where urban and rural data is evened out, hiding outbreaks in cities.
There are several caveats that need to be emphasized:
The number of tests carried out: when there are low number of tests, there are necessarily low numbers of detected cases. We do not currently have information for the number of tests carried out in each region, so cannot take account of this – it is possible that high cases per 100,000 is due to particularly high levels of testing in that region.
More local testing in locations with known cases: As local outbreaks are detected, extra testing resources may be allocated to towns such as Leicester, with mobile testing stations being set up. There is a feedback loop here meaning that extra cases will be detected – this does not necessarily mean that there is a higher incidence, just that the cases are being detected.
There is a time lag before this data becomes available: The latest data (published today, 2 July 2020) is for cases detected up to 28 June 2020 – so is not in real-time. In addition, there is a further delay between individuals becoming infected and a case being capable of being detected.
Outbreaks in care homes, hospitals and prisons: These need to be treated independently, and are currently included in the data. We know that there are outbreaks in these locations, and PHE report on these (but we don’t know where these outbreaks are taking place). So Pillar 1 and Pillar 2 data by itself does not indicate that there is community spread – this may be confined to these special locations
Local Directors of Public Health are the experts in their local areas: These professionals are experts, know their communities well, and understand the dynamics of transmission far more than can be ascertained by looking at figures in a database. There have been delays in getting this data to local authorities and issues with data quality, but the Prime Minister has promised in the House of Commons that the data is now getting through.
The delay and lack of detail of Pillar 2 results at district council level, or within-local authority breakdowns (as is disclosed for Pillar 1 tests) highlights data weaknesses, compounding the delays in convening the Joint Biosecurity Centre, and the failure of the centralised NHS Test and Trace App. While directors of public health, Public Health England, NHS Test and Trace, the Joint Biosecurity Centre, and the Department of Health and Social care all play their part, the policy for controlling a pandemic rests with central Government and is ultimately the responsibility of the Prime Minister and the Cabinet. Authority can be delegated but responsibility can not.
In the week 26 Public Health England surveillance report, this map was produced.
Leicester is subject to a local ‘lockdown’, but what about the other areas highlighted, and how bad are they compared to Leicester?
This is the data behind the map:
This shows that Bradford, Barnsley, and Rochdale are the next four local authorities in terms of the (Pillar 1 and Pillar 2) COVID rate of infection (cases per 100,000 population).
What is not known however, is whether these are locations of community spread (as is reported in Leicester), or are contained outbreaks in schools or other locations which may indicate that community spread is not taking place and hence lockdowns may not be appropriate in these areas.