COVID-19: Day 256 Update: I am feeling uneasy

Michael: How are you feeling this week?

Thank you for asking. I am well.

Last week I said: I am having difficulty grasping ‘the big picture’ about what is going on with the pandemic.

This week I still feel the same. But things are becoming clearer. And I think I am beginning to understand the fundamental reason for my unease. It is the unreliability of every single measure of the prevalence of the virus.

Considering this as a measurement problem I realised that…

  • …all the measures we have of the prevalence of the virus are imperfect.

We’ll look at the latest data below, but here I will just summarise how we get to know anything at all about the viral prevalence.

How we measure the viral prevalence:

  • The ONS prevalence survey takes samples from people randomly-selected from around the UK.
    • It tests people whether or not they have symptoms.
    • It samples the adult population reasonably fairly with regard to age, ethnicity, location and social class.
    • But even sampling 25,000 people each week it is not very sensitive.
    • Also, if the geographical distribution of the viral infections is not random (which it isn’t) then the survey can easily miss (i.e. under-sample) ‘hot-spots’.
    • The lag between measurements and analysis is several days to weeks.
  • The death count.
    • Probably the most reliable indicator of the spread of the virus, but even counting bodies is not straightforward.
    • The death count is blind to the amount of infection amongst younger people – in general they don’t die..
    • And it lags the time of active infection by around three to four weeks. So by the time the older infected people start dying – the virus may have already passed through three to four generations of infection and be widespread in the younger community.
  • Hospitalisation.
    • Like deaths, this statistic lags the infection, but by less time than the death count.
    • Like deaths, this statistic is blind to the amount of infection amongst younger people – in general they don’t need to be hospitalised.
  • PCR Tests
    • The PCR swab tests from the tonsils (or nasal passages) test for COVID-19 genetic material. But the tests are themselves imperfect indicators of the amount of virus present and whether it is alive or dead. The tests sometimes detect remnant dead virus fragments, and sometimes fail to detect live virus.
  • Pillar 2 (Community testing)
    • The meaning of the pillar 2 tests changes depending on the testing strategy and protocol.
    • This makes it hard to associate any increases or decreases in the Pillar 2 tests with a sign of increased or decreased prevalence.
    • Mass (Pillar 2) testing in suspected ‘hotspots’ is certainly good for making rapid assessments of areas of known high infection – but the exact significance of the measured prevalence from one hotspot to another is not clear because of differences in community behaviour and testing protocols.
    • The UK testing infrastructure appears to have bottlenecks and its actual performance may be obfuscated for political reasons (examplar). One curious example is that the government still do not clearly distinguish between tests processed, and the number of people tested.
  • Symptom surveys
    • These surveys ask people to fill in an app-based questionnaire daily, reporting any symptoms.
    • Through mass participation, this can detect the onset of infection amongst participating social groups with only a few days delay.
    • But these surveys cannot detect the virus pre-symptomatically,and are only weakly sensitive to the 80% (yes, 80%) of people who are infected a-symptomatically or with only mild symptoms. (Yes, 80% – link).
  • ONS Antibody tests
    • The ONS antibody tests provide an insight into how many people have been infected in the past – the answer is about 6% of the UK population.
    • But there are still unanswered questions about whether all infected people produce an antibody response

Why I feel uneasy.

So in order to get a picture of what is happening look we need to look at all these measures – and each one needs to be interpreted with nuance. And we need to seek a coherent picture that is consistent with all the data.

Additionally the government endlessly changes data formats and presentations to make coherent and consistent analysis difficult. This is possibly deliberate but could also be a result of chaotic incompetence.

Summarising, my unease arises from being unable to establish a coherent narrative about “what is going on”. This is not a narrative that seeks to blame any particular group, but one which just states the facts as well as we know them without any spin.

Indeed. I am writing this to try to clarify my own thoughts.

This week’s nuanced analysis.

Based on the data below I note that:

  • The number of positive cases has risen sharply. The sharpness of the rise is almost certainly an anomaly caused by a change in testing strategy or protocol – it just doesn’t look right! – but there is a consensus that this probably reflects a real rise.
  • There is an increase in the daily rate of deaths – but there has not been any obvious pre-cursor of this in the positive tests.

The government’s ‘policy roulette’ has come up with a “rule of six” and a ‘Moon Shot’ testing programme.

  • The “rule of six” (RO6) represents a continued arbitrary breathtaking assault on our freedom.
    • It is not clear that it will be widely adhered to – especially if it is expected to be adhered to nearer to Christmas (103 days away).
    • The government’s endless U-turns and their disregard for their own commitments gives them little moral authority.
    • But it is clear that the ‘new normal’ we have been experiencing in the last couple of months is not working well enough to suppress the virus.
    • So the RO6 is probably the sort of extreme measure that might significantly affect virus transmission: some disagree.
  • The Moonshot testing programme is nonsense from top to bottom.
    • The existing testing programme is being chaotically mismanaged (link). Making it bigger will likely make a bigger mess.
    • It is likely that a vaccine from one source or another will become available in the early part of 2021 – and it would be much cheaper and more effective than a testing programme.

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 1300 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 and has increased recently: the raw count of positive tests was 55 from 59,222 in the two weeks to 5th September, up from 26 in 45,959 in the preceding two weeks. But this survey lacks the sensitivity to track rapid local increases in prevalance.

Click for larger image.

 

Data #2. Other ONS conclusions

ONS also analyse antibody data and conclude on the basis of just over 7000 tests that – as in previous weeks – roughly 6.02% ± 1.1% of the UK population have already been exposed to the virus.

Data#3. Tests and Deaths

The graph below shows:

  • the number of deaths per day.
  • the number of positive tests 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 looks unfeasibly sharp and is probably the result of a genuine increase in prevalence, coupled with a change in the testing protocol.

In the last couple of weeks the generally downward trend in deaths per day has shown fluctuations and increases whose significance is still not yet clear.

I am puzzled because the rise did not seem to be associated with any corresponding change in positive tests in the preceding weeks.

What to make of all of this?

I don’t know the true story that links all these facts. Worryingly, I don’t think anybody knows what is going on.

But is difficult not to expect several more weeks of increased cases and eventually deaths.

 

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