Testing Pillars

Local confirmed cases now include commercial testing.

On 2nd July, Public Health England updated their COVID-19 reporting. This update meant we can see confirmed cases in both main testing pillars.

This article examines the Leicester lock-down, and confirmed cases in Wiltshire.

Pillars

There are two types of test for SARS-CoV-2: whether you currently have the virus and whether you have had it. Antigen testing is for whether you have the virus.

The UK government has two main ‘pillars’ for its antigen testing programme:

  • Pillar 1: NHS and Public Health England laboratories;
  • Pillar 2: testing by commercial partners.

A confirmed case means a laboratory test gave someone a positive result for SARS-CoV-2.

Before 2nd July, the PHE daily dashboard showed ‘total cases’ for local authorities. There was a major limitation, which was only reflected in the notes:

The UK total is not the sum of the 4 National totals as the pillar 2 cases cannot currently be included in the individual National totals for England, Northern Ireland and Scotland. All other data on this website are based only on cases detected through pillar 1.

As the Financial Times highlight, including ‘pillar 2’ confirmed cases transforms our view. There was an increase in confirmed cases in Leicester.

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‘Pillar 2’ confirmed cases rose, as cases confirmed by the NHS and PHE labs declined. (Image: PHE)

Looking at ‘pillar 1’ confirmed cases gives the wrong impression. This outbreak is visible among the ‘pillar 2’ confirmed cases. The relative scale of the Leicester outbreak may be an artefact of increased testing.

When did Public Health England know?

We can look at the Public Health England surveillance report for week 22. The graph shows ‘pillar 1’ confirmed cases by English local authority:

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The populations are the 2018 ONS mid-year estimates. (Image: PHE)

By week 23 (4th June), the updated graph shows confirmed cases for both testing pillars:

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Note the change in the colour scales. (Image: PHE)

PHE did not publish ‘pillar 2’ confirmed cases by local authority before that date. Those statistics may have been unavailable. That would pose major problems with interpreting confirmed case levels.

One consequence of combining the testing pillars is removing duplicates. Some people had tests from both pillars. This meant PHE counted their positive results twice. The correction reduced the total count by 30,302 confirmed cases.

Check the levels

On 30th June, the Daily Mail reported:

Public Health England (PHE) data shows the London borough of Havering and the entire county of Wiltshire have seen the biggest week-on-week increases in confirmed Covid-19 infections (300 per cent).

A data table showed the levels. Wiltshire Council responded:

However this actually equates to just an increase from one to four new cases.

In both reports, the figures refer to the Public Health England data dashboard. Neither the Daily Mail nor Wiltshire Council recognised the limitation. These figures are only from confirmed cases in NHS and PHE lab tests.

Based on submitted tests up to 4th July, Wiltshire had:

  • 17th — 23rd June 2020: seven cases, by specimen date;
  • 24th — 30th June 2020: seven confirmed cases.
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There may be lag with some tests. These figures are subject to revision. (Image: R Pubs)

By 12th July, the two numbers were seven and eight, respectively.

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Well, that saves me doing it myself. (Image: PHE COVID-19 dashboard — Beta)

Case numbers remain subdued.

Of English local authorities, Wiltshire has a low number of confirmed cases. As of 12th July, there were around 251 confirmed cases per 100,000 people. Public Health England uses the 2018 ONS mid-year population estimate.

The R code for the graph is available on R Pubs and GitHub.

This blog looks at the use of statistics in Britain and beyond. It is written by RSS Statistical Ambassador and Chartered Statistician @anthonybmasters.

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