Maps – Dr Duncan Robertson

We Are Still Not Doing Enough Testing: A Case Study of New York and Liverpool Schools

The Wall Street Journal is reporting that “New York City on Wednesday will close public schools and nonessential businesses in parts of Brooklyn and Queens that have registered a week-long spike in coronavirus cases”

Let’s look at New York and then compare to a UK city, Liverpool.

Cases are high in some New York boroughs. Up to 216 cases per 100,000 per week. But school closures are also being implemented in areas with 89 cases per 100,000 (source: New York Times)

Let’s compare with Liverpool. Here is the latest @PHE_uk report. Liverpool has cases of 238 cases per 100,000 in a week. Which is slightly higher than the highest rate ZIP code in NYC.

But remember, Liverpool’s figures are for the whole local authority.

Let’s dig a little deeper into Liverpool. Here’s the map. We can see some areas with incidence in excess of 1200 cases per 100,000. That’s very high. And don’t forget this is detected cases. The number of cases will be much higher.

But how do we know that there hasn’t been enough testing? We look at positivity. Positivity is the number of people who test positive divided by the number of people tested. And this is what NYC uses to determine whether schools should be closed.

If an area of NYC has positivity greater than 3% – three in every 100 tests being positive – then schools close. What does positivity tell us? Whether enough tests are being performed.

“the World Health Organization recommended in May that the percent positive remain below 5% for at least two weeks before governments consider reopening.” (Johns Hopkins University)

So, given that positivity is set at a threshold of 3% for school closures in NYC and WHO suggest 5% before reopening, this begs the question – What is the positivity in Liverpool?

Just under 15%, according to the latest published data (PHE week 40 reporting). Which means that around 15% of all tests in Liverpool come back positive. That’s *very high*. And means not enough testing is being carried out. And this is a problem.

This is just an example of a city with large positivity. Extra testing capacity has been sent to Liverpool presumably due to students returning to universities there. This is not a Liverpool problem – it’s a national problem.

Heatmaps of COVID Cases in England

Click here to link to Loughborough University press release

Public Health England have released their data on cases split by age and week. We can turn these into a map visualizing the transmission of the epidemic through ages of cases and through time.

We do this by plotting a three-dimensional chart, a heatmap, where the x axis shows time (split into weeks) and the y axis shows the age of individuals who test positive (split roughly into 10-year groups). The colour of the chart shows the number of cases in each age/week cell.

We work out the cases per 100,000 (a standard epidemiological way of presenting incidence numbers) by finding the population in each age group and dividing the cases by that number (population estimates are from 2018).

The beginning of the epidemic

We can see clearly the very high incidence in the over 80s. We now know that many of these were in care homes (although many were in the community). By 28 June (the last day of this chart), the numbers in each age cohort were relatively low, with an incidence of 18 per 100,000 in the over 80s, but a maximum of 11 cases per 100,000 in the under 80s.

The resurgence

We have produced a new heatmap and scaled the reds to the maximum numbers – so the reds in this heatmap (up to 46 cases per 100,000 in 20 to 29 year-olds) are not as high as the reds in the first heatmap (where we saw a maximum incidence of 232 cases per 100,000 in the over 80s)

What we do see however is a movement from young people (20 to 29-year-olds) to the remainder of the working population (certainly up to 60 year-olds).

Based on data from France, the US, and Spain, that I expect that cases will move to the more vulnerable older population, with the very real risk of hospitalizations and deaths increasing over the weeks ahead. Public Health England has already detected new cases in care homes, and we need to be extremely vigilant and aware to ensure we do not repeat the mistakes of the early part of the epidemic.

Update 18 September

Latest version of my heatmap – shows cases established in the working population and the over-80s.

Read here to explain why this is a problem: Should We Be Concerned About COVID Transmission In Young People? Yes.

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.