COVID-19: Day 262: Update

Summary

My puzzlement at what is happening continues.

  • On the one hand the viral prevalence appears to be increasing and a prudent approach prioritising public-health over the economy would indicate strong action – lock-downs and similar – is required urgently.
  • On the other hand, an increasingly vocal group is arguing that the government are chasing shadows, and that an epidemic explosion similar to that we experienced in the spring is not about to occur.

Worryingly the views about what is happening have a political dimension. So it is easy to find oneself inclined to one camp or the other based on feelings of general sympathy rather than particular facts. Many people are totally fed up with the restrictions and the COVID-related pallava, and would happily just ignore the whole thing. But would that be wise? And would it cause thousands of deaths each day as it did in the spring?

So what is actually happening?

Back in March the virus had spread uncontrolled through the population for a couple of months and was on an exponential rise. It is my understanding that no reasonable person would dispute that, if left uncontrolled,  it could have killed on the order of half a million people. At the peak of the deaths a few weeks after lock-down, about 1000 people a day were dying after an agonising illness.

The consensus is that this was stopped by the ‘lock-down’ and that subsequent measures have contained the virus. The current rate of COVID-related death rates (about 10 a day) is probably acceptable indefinitely until a vaccine arrives.

Since July 4th there has been a slow rise in COVID-19 positive tests per day, and two weeks ago there was a sudden sharp rise. But the interpretation of the rise is open to question:

  • On the one hand the Government take the rise as an indication that the viral prevalence is increasing. They warn that the virus may explode just as it did in March.
  • And on the other hand, critics point out that hospitalisations are not rising and that the protocols for testing have changed – concentrating on areas where the virus is known – creating an ‘echo chamber’ of alarm.

Both these views are probably true, but the cost of locking-down is immense, as is the potential cost of not locking-down soon enough if a lock-down is required.

Before trying to figure out what we should do, we should look at the data…

Data#1. Prevalence

Since late April the ONS prevalence survey has been randomly testing people each week to look for the virus. They then collate their data into fortnightly periods to increase the sensitivity of their tests. Details of their full results are described methodically in this ‘bulletin‘.

Click for a larger image.

The number of people tested and the number of positive tests are given in their table (reproduced above) along with their estimate that on the 5th September 2020 roughly 1 in 770 of the population were actively ill.

Their data – graphed below – suggest that the prevalence has been below the 1 in 1000 level for several months but is now almost certainly above that level: the raw count of positive tests was 87 from 66,717 in the two weeks to 10th September, up from 36 in 51,992 in the preceding two weeks and 22 from 39,998 in the two weeks preceding that.

Click for a larger image.

My conclusion is that viral prevalence in the general population around the 10th September was two to three times what it had been at it its minimum in July and August.

It has probably risen further in the 17 days since the last data point

Data#2. Tests and Deaths

The graph below shows:

  • the number of deaths per day.
  • the number of positive tests per day on the same logarithmic scale. 

The data were downloaded from the government’s ‘dashboard’ site. The deaths refer to deaths within 28 days of a test and the positive tests refer to Pillar 1 (hospital) and Pillar 2 (community) tests combined. All curves are 7-day retrospective rolling averages.

Click for a larger image

The rapid rise in the number of positive tests is probably the result of a genuine increase in prevalence, coupled with a change in the testing protocol i.e. more testing in suspected ‘hot spots’.

In the last couple of weeks the generally downward trend in deaths per day has shown fluctuations and appears to be starting to increase. It is certainly not falling.

Are we on the verge of a viral resurgence? Or Not.

The ONS survey and the testing data indicates an increase in viral prevalence,

But if we plot the number of people hospitalised alongside the test and death data in the graph above, we see that increase in tests has not resulted in a concomitant increase in hospitalisations or use of ventilators.

Click for larger version

The data show that up until the start of July, the data for tests, hospitalisations, ventilations and eventually deaths all followed the same pattern.

But since then the roughly 10 fold increase in positive tests per day has not been matched by similar increases in hospitalisations.

In order to understand the above graph, one needs to understand that although the significance of three of the data streams has remained unchanged across the graph – the significance of a positive test has changed significantly.

To see this it is best to split the above graph down the middle and consider the left and right hand sides separately.

Click for larger version

Let’s consider the left-hand side of the graph first: 

Click for larger version

Here the positive tests arose as the COVID-status of a seriously ill person entering hospital (Pillar 1 testing) was confirmed.

  • Typically patients were already in a a vulnerable group.
  • Typically they had already been ill for 2 to 3 weeks before entering hospital, and around 20% of these people would die within about 3 weeks (link).
  • Thus the link between a positive tests, hospitalisation, ventilator use and death were striking and easy to see.

Now consider the right-hand side of the graph: 

Now most tests are carried out in the community (Pillar 2) and only around 1% are positive.

  • The vast majority of positive tests are amongst people who are not in a vulnerable group and who will never need to go to hospital.
  • Even for people who will eventually become hospitalised, the test will come much earlier in the course of the disease.

What next?

The data are not – in my opinion – decisively clear. This is how I read the graphs.

  • The rising number of Positive tests are consistent with the ONS data on rising prevalence. The significance of the kink at the start of September is not yet clear but is probably a result of a real increase and increased testing in hot-spots.
  • The fall in the number of COVID hospitalisations flattened out at the start of September.
    • This statistic is the difference between admissions and discharges, and so there must have been a rise in the rate of daily admissions beginning around late August/start of September..
  • Curiously, the previously falling number of COVID-patients on ventilators flattened out before the hospitalisation curve. I can’t think why that might be.

What has probably happened is this:

  • The virus has been spreading and increasing in prevalence since July.
  • Summer holidays, and increased activities of all kinds have allowed the virus to spread, mainly amongst younger people.
    • Younger people are less seriously affected and thus have not caused an immediate increase in hospitalizations.
  • With increased activity and the re-starting of schools the spread is now reaching vulnerable groups leading to increased deaths and hospitalisations.

The key question is:

  • With the viral prevalence we now have, and the mode of conducting our lives that we have now adopted – to what rate of hospitalisation and death have we committed ourselves?

I don’t think anyone knows the answer to that question. But we will all find out fairly soon.

2 Responses to “COVID-19: Day 262: Update”

  1. OurTerry Says:

    Great analysis Michael. Am interested in the decoupling of the ventilator and hospitalisation stats – one thing I remember from earlier in the year was that doctors were learning new things about covid-19 very quickly and that many of their initial assumptions about the disease were not correct. At first they assumed it was a bit like other respiratory diseases and that low oxygen levels meant people needed help with their breathing. In fact it appeared their hypoxia was more like altitude sickness and their breathing was fine, and that intubating them might actually be making their condition worse. This was a mysterious development (not sure what the latest thinking is – this was around June) but it led to them putting fewer patients on ventilators. So the different decision-trees leading to intubation have certainly changed, so may lead to the decoupling you describe above.
    https://www.sciencedaily.com/releases/2020/07/200702144732.htm

    • protonsforbreakfast Says:

      Thanks. That is a good point and what I take from it is that ‘hospitalisations’ themselves are probably a better thing to count than ‘ventilations’. I say this assuming that the threshold for admission to hospital has remained relatively stable, but as treatment options have evolved, the number of ventilated patients may have changed with ‘fashion’.

      I am just looking at the effect of false positives on my conclusions – more later.

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