Last updated on 10th July 2020
The latest data for COVID19 (Coronavirus) cases in England as of Friday 3rd July 2020 show that the number of cases continues to fall but there are some signs here and there that the number of cases is flattening out and may even be increasing in some areas. The next couple of weeks will be important to see if a second wave is on its way.
I plan to update this post every Thursday. You can follow me on Twitter to be told when I have made updates.
The 2 time series for COVID19 Cases in England
Each time series is denoted with a 4 letter code which I will use throughout. Clicking on the 4 letter code will take you to the source data. I have only extracted data for England from these sources but some also cover Scotland, Wales & Northern Ireland.
- PHEs – Public Health England Positive Tests for COVID19 by Date of Specimen – Daily number of positive tests for COVID19 for tests undertaken in an NHS/PHE laboratory. Data is published daily and be broken down by local authority. Data is for “Pillar 1” & “Pillar 2” tests together (see section 1B).
- ONSe – ONS COVID19 Household Infection Survey – Using a random sample of households in England who are tested every week, the % of people infected with COVID19 is estimated on a fortnightly basis. Sample excludes institutional settings such as Hospitals & Care Homes. Data is published weekly on a Thursday.
1 – PHEs – Public Health England COVID19 Positive Tests (Pillar 1 only)
As of 9th July 2020, a total of 248,809 tests gave a positive result for COVID19 in England. The breakdown by the day the specimen was taken is shown in the chart below as bars.
The chart format is identical to that used for the PHEr series in section 1 of my post “Latest Trends for COVID19 deaths in England” and the reader should click on that link if they are not familiar with it. The trend extrapolation method is also the same as explained in that post but in this post I will display the calculation using a different chart format.
Unlike PHEr which was based on the date the death was registered, PHEs is based on the date the specimen was taken. Given that it might take a few days for the specimen to be sent to a laboratory, be tested and then the results to be communicated to PHE, this means that the data for the most recent dates are always being updated. Analysis shows that the last 4 days see the most changes and so these days are not included in the extrapolation.
The chart below uses a vertical log scale to show two things; the cumulative number of positive tests (diamonds) and the difference between the logarithm of the cumulative number and the logarithm of the cumulative number 7 days previously (small circles). Mathematically the second line is the same as the logarithm of the dashed black line in the chart above.
By fitting a straight line through the second line, we can then use that straight line to extrapolate the log of the geometric trend into the future. It is apparent though that a straight line fit is not possible for the whole timeframe. From the end of March to the beginning of June, a straight line fit is apparent as shown by the dashed red line but from 6th June the geometric trend started to diverge and is now following a different straight blue line. The blue line is the fit I am using to extrapolate the number cases into the future which is based on the last 4 weeks of data. It should be emphasised that the total number of cases continues to fall but is doing so at a slower rate than before so this is not changing the fundamental picture.
In the 7 days up to 4th July, a total of 3,672 positive tests were recorded across England. This is down on the previous week and the overall picture is one of a downward trend. However, the PHEs series can be broken down by local authority and individual areas may be seeing an increase in cases. At the regional level, this appears to be the case in the South West though the actual increase is very small and might just be a blip.
Keeping a close eye on local figures is something I am recommending all organisations should be doing. The government has said it will reimpose lockdowns on local areas if it has to and as I write, a local lockdown has been put in place in Leicester. To help you analyse your own area, I have created a spreadsheet which allows you to recreate the above two charts for any area you wish. Click on the link below to download and read the HELP sheet to get started.
Leicester is an Upper Tier Local Authority and if you had selected this at the time of the new lockdown there, you would have got this chart.
Using the last 3 weeks to extrapolate the trend, it was clear at the start of July that the local trend was upwards. Whilst the recent days appear to be lower, remember the last 5 days are subject to a lot of upward revisions.
When the Leicester lockdown was announced it caught a lot of people by surprise. The reason was because until 2nd July, PHE was only publishing Pillar 1 tests for local authorities and the substantial increase in June nearly all came from pillar 2 tests. This has now changed and all data above is now for Pillar 1 + Pillar 2 data together but what does Pillar 1 & 2 mean?
1B – Pillar 1, Pillar 2 & Leicester
If you read the detailed notes about the data supplied by PHE, you will see references to “Pillar 1” and “Pillar 2” testing. The DHSC (Department of Health & Social Care) provides further details but briefly the difference is this –
- Pillar 1 are tests carried out in NHS/PHE laboratories focusing on key workers and those with a clinical need.
- Pillar 2 are tests carried out by commercial laboratories which tend to focus on the wider community.
DHSC compile this data for all 4 nations and publish the combined numbers by day for the whole of the UK as shown in this chart.
You can see that the Pillar 2 testing process started later and it is really only since the middle of May that Pillar 2 got up to speed. Today, more positive tests are being found through Pillar 2 than Pillar 1 though it does appear that both are following similar trends.
The spreadsheet link I gave you earlier now has some extra charts showing number of positive tests per 100,000 population by week. This data is supplied by DHSC and provides a useful variant on the daily charts shown before. For example, the South West (which apparently had an uptick recently is shown here and it is clear that any uptick is from a very low level and not really noticeable.
2 – ONEe – ONS COVID19 Household Infection Survey
For the fortnight up to 5th July 2020, the ONS estimated that 1 in 3900 people are infected with COVID19 in England. The ONS survey is focused on the wider community rather than institutions and as such is similar in scope to the pillar 2 data discussed in the previous section.
The ONS intend to increase the sample size considerably to allow for more granular results. At present, it cannot provide a local estimate given that only 8 people out of a total of 25,662 tested positive for COVID19. Such small numbers are why you have to be very careful before drawing conclusions about the overall trend though it does seem to show a decline over the long term. The margin of error in the estimates are quite large as shown the vertical bars which represent 95% confidence intervals.
The ONSe series has a lot of potential to give good answers to questions we want answered since it is properly designed sample based on statistical principles (I run a training course on Statistical Sampling) but for now it is primarily a national trend tracking tool.
– More posts about COVID19 –
- A very useful guidance to interpreting statistics of COVID19 published by the Royal Statistical Society.
- My collection of links to all kinds of material related to the statistics of COVID19, epidemiological modelling and testing.
- How large a sample is needed in order to decide whether COVID19 restrictions can be lifted? A lot, lot less than you think!
- Latest trends in COVID19 deaths in England using 6 time series
- How many excess deaths will there be as of 19th June? This is my estimate of excess deaths using a statistical model.