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


Addendum to Precautionary SAGE meeting on Covid-19, 22nd January 2020 Held in 10 Victoria St, London, SW1H 0NN
This addendum clarifies the roles of the SAGE attendees listed in the minute. There are three categories of attendee. Scientific experts provide evidence and advice as part of the SAGE process. HMG attendees listen to this discussion, to help inform policy work, and are able to provide the scientific experts with context on the work of government where appropriate. The secretariat attends in an organisational capacity. The list of attendees is split into these groups below.
Attendees
Scientific experts: Patrick Vallance (GCSA), Chris Whitty (CMO), Charlotte Watts (CSA DfID), Jonathan Van Tam (Deputy CMO), Neil Ferguson (Imperial), Carole Mundell (CSA FCO), Peter Horby (Oxford), Christine Middlemiss (CVO DEFRA), James Rubin (King’s College), Cathy Roth (DFID), Jeremy Farrar (Wellcome), Phil Blythe (CSA DfT), Pasi Penttinen (ECDC), David Lalloo (LSHTM), Maria Zambon (PHE), Ben Killingley (UCL), John Edmunds (LSTHM), Jim McMenamin (Health Protection Scotland).
Observers and Government officials: Rupert Shute (dCSA HO), Kavitha Kishen (DfT), Stuart Wainwright (GoS), Tasha Grant (CCS), Samantha Harris (GoS).
Secretariat: [redacted]
Names of junior officials and the secretariat are redacted.
Participants who were Observers and Government Officials were not consistently recorded therefore this may not be a complete list.

UPDATED, valid as of 1700 23 January
Precautionary SAGE meeting on Wuhan Coronavirus (WN-CoV) 22 January 2020 Held in 10 Victoria St, London SW1H 0NN
Situation update

  1. DHSC provided an update on current declared cases, deaths and geographic spread.
  2. China has recently revised case definitions. This makes comparisons difficult.
  3. It was reported that diagnostic testing capability in Wuhan is overwhelmed.
  4. There is considerable uncertainty around the data, with almost certainly many more cases than have been reported; a reasonable worst case cannot be made reliably under such circumstances.
  5. WHO has received some environmental sampling from Wuhan: information on the zoonotic reservoir may be forthcoming shortly.
  6. *** Following the meeting, authorities in Wuhan announced the suspension of public transport, including outbound trains and flights, from 0200 GMT 23 January. ***

Current understanding of WN-CoV

  1. There is evidence of person-to-person transmission. It is unknown whether transmission is sustainable.
  2. The incubation period is unclear – but appears to be within 5 to 10 days; 14 days after contact is a sensible outer limit to use.
  3. It is highly probable that the reproductive number is currently above 1.
  4. It is currently estimated that the mortality rate for WN-CoV is lower than for SARS, but it is too early to reliably quantify that rate.
  5. There is insufficient information currently on the genetic strain to comment on WN-CoV’s origin.
  6. There is no evidence yet on whether individuals are infectious prior to showing symptoms.
  7. There is no evidence that individuals are more infectious when symptoms are more severe, but that is likely.
  8. There appears to be very little genetic diversity in WN-CoV based on sequences available so far.
  9. It is reasonable to argue – based on lessons from MERS and SARS, and consistent with exported cases of WN-CoV – that individuals returning from Wuhan are no longer at risk if they show no symptoms after 14 days.

Summary and review of NERVTAG conclusions

  1. NERVTAG does not advise port of entry screening, irrespective of the current limited understanding of the epidemiology.
  2. NERVTAG does not advise use of screening questionnaires, pilot declarations or requiring confirmation of exit screening at Wuhan.
  3. NERVTAG does support public health information efforts via leaflets, posters and broadcast messengers to passengers.
  4. SAGE supports NERVTAG’s position both on the value of port screening and on monitoring measures.
  5. SAGE would review its position on port screening only if a simple, specific and rapid test was available and was deployable at scale across the UK. Temperature and other forms

of screening are unlikely to be of value and have high false positive and false negative rates.
Transport-related issues

  1. The European Centre for Disease Prevention and Control (ECDC) has just published “Risk assessment guidelines for infectious diseases transmitted on aircraft (RAGIDA) ­Middle East Respiratory Syndrome Coronavirus (MERS-CoV)”.
  2. ECDC advises use of MERS guidelines for the current outbreak, but acknowledges the limitations of its evidence base.

UK health readiness and planning

  1. The UK currently has good centralised diagnostic capacity for WN-CoV – and is days away from a specific test, which is scalable across the UK in weeks. The sensitivity of the test is currently unknown. There are conflicting reports of the sensitivity of diagnostic tests from upper respiratory tract sampling.
  2. DHSC is developing advice for UK healthcare workers on testing potentially infected individuals.
  3. SAGE agreed that DHSC and PHE criteria for testing potentially infected individuals were appropriate, i.e. those with symptoms or signs of WN-CoV, and a history of travelling to or living in Wuhan in the 14 days prior to symptom onset, including those who accessed Wuhan healthcare facilities. SAGE advised that DHSC and PHE should be ready to revise those criteria as the situation evolves.
  4. DHSC and PHE also preparing plans for isolating potentially infected individuals and the follow up of contacts.

ACTION: CMO to share the latest iteration of the PHE isolation plan for suspected cases and contacts with some of the SAGE participants, in particular behavioural scientists, to get their view of its proportionality and advice on how to communicate uncertainty, in order to improve subsequent versions.
ACTION: CMO/DHSC and PHE to consider how NHS primary care facilities might respond to an increase of cases and potential cases.
ACTION: CMO/DHSC and FCO to work together to ensure consistent messaging on travel advice to/from Wuhan.

  1. There are no practical preventative actions that HMG might undertake ahead of Chinese New Year.
    Triggers for escalating HMG response
  2. Of DHSC’s current triggers, there has been infection of healthcare workers and probably some sustained human-to-human transmission, but not geographical spread unconnected to Wuhan.
  3. SAGE agreed that HMG should review its response either in the case of onward spread of WN-CoV person to person outside of China or a severe confirmed case in the UK.
  4. SAGE is unable to say at this stage whether it might be required to reconvene.

Summary of actions CMO to share the latest iteration of the PHE isolation plan for suspected cases and contacts with some of the SAGE participants, in particular behavioural scientists, to get their view of its proportionality and advice on how to communicate uncertainty, in order to improve subsequent versions.
CMO/DHSC and PHE to consider how NHS primary care facilities might respond to an increase of cases and potential cases.
CMO/DHSC and FCO to work together to ensure consistent messaging on travel advice to/from Wuhan.
Attendees
SAGE participants: Patrick Vallance, Chris Whitty, Charlotte Watts, Jonathan Van Tam, Neil Ferguson, Carole Mundell, Peter Horby, Christine Middlemiss, James Rubin, Cathy Roth By phone: Jeremy Farrar, Phil Blythe, Pasi Penttinen, David Lalloo, Maria Zambon, Ben Killingley, John Edmunds, Jim McMenamin

[the remaining minutes (to meeting 41 on 11 June 2020) 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.

Which English city could be next for a Leicester-like lockdown? 2 July New Analysis

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:

  1. Towns such as Leicester may not understand why they are being locked down, as the maps at the Coronavirus data service do not show anything particularly unusual about Leicester;
  2. Other towns may see that they have relatively high case levels on the Coronavirus data service, causing unnecessary alarm;
  3. Having data at a coarse geographical area (currently Upper Tier Local Authorities) does not allow outbreaks in towns and villages to be identified;
  4. 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.

For more information, please contact me at d.a.robertson@lboro.ac.uk
or follow me on Twitter @Dr_D_Robertson

Locations of High COVID Activity (Week 26 Data) – Where could the next Leicester-like lockdown be?

In the week 26 Public Health England surveillance report, this map was produced.

PHE Surveillance Report 25 June Figure 9: Weekly rate of COVID-19 cases per 100,000 population tested under Pillar 1 and 2, by upper-tier local authority, England (box shows enlarged maps of London area)

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:

PHE Surveillance Report Week 26 Figure 9: Weekly rate of COVID-19 cases per 100,000 population tested under Pillar 1 and 2, by upper-tier local authority, England

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.