Our paper ‘Challenges on the interaction of models and policy for pandemic control’ has been published in the journal Epidemics.
The COVID-19 pandemic has seen infectious disease modelling at the forefront of government decision-making. Models have been widely used throughout the pandemic to estimate pathogen spread and explore the potential impact of different intervention strategies. Infectious disease modellers and policymakers have worked effec-tively together, but there are many avenues for progress on this interface. In this paper, we identify and discuss seven broad challenges on the interaction of models and policy for pandemic control. We then conclude with suggestions and recommendations for the future.
Hadley L., Challenor, P., Dent, C., Isham, V., Mollison, D., Robertson, D. A., Swallow, B., Webb, C. R. (2021) ‘Challenges on the interaction of models and policy for pandemic control’, Epidemics, 37, https://doi.org/10.1016/j.epidem.2021.100499
This was originally published on Twitter on 9 January 2021.
The Government is making the same mistakes as it did in the first wave. Except with knowledge.
The Government’s strategy at the beginning of the pandemic was to ‘cocoon’ the vulnerable (e.g. those in care homes). This was a ‘herd immunity’ strategy. This interview is from March.
This strategy failed. It is impossible to ‘cocoon’ the vulnerable, as Covid is passed from younger people to older, more vulnerable people. We can see this playing out through heatmaps. e.g. these heatmaps from the second wave.
The Government then decided to change its strategy to ‘preventing a second wave that overwhelms the NHS’. This was announced on 8 June in Parliament. This is not the same as ‘preventing a second wave’.
The Academy of Medical Sciences published a report on 14 July ‘Preparing for a Challenging Winter’ commissioned by the Chief Scientific Adviser that set out what needed to be done in order to prevent a catastrophe over the winter period.
Around this time, the Great Barrington Declaration was published. This changed the rhetoric from ‘herd immunity’ to ‘focused protection’. This was and remains non-mainstream from a scientific point of view, but was popular amongst a group of commentators.
Cases were increasing rapidly, and SAGE (the Scientific Advisory Group for Emergencies) called for a ‘circuit breaker’.
At the same time, a focused protection-supporting group of scientists were invited to Downing Street to present the alternate view. Politically, this enabled this headline to be written.
A new variant was discovered with increased transmissibility. This caused a ‘lockdown’ as the NHS was now in crisis mode and there was ‘a material risk of the NHS in several areas being overwhelmed’. The Government’s second strategy is failing.
However, this ‘lockdown’ is not stringent. Many more people are allowed to send their children to school allowing the virus to mix in children and their parents.
The Prime Minister made a strange comment on 6 January. The word ‘cocoon’ was back. Remember that from March?
Matt Hancock has now given an interview setting out the Government’s new, third, strategy.
The strategy is about ‘manageable risk’. Risk to those that may die or live with the effects of catching Covid, or risk to the Government?
We are now back to vaccinating the vulnerable – focused protection if you will.
It appears that the Government has adopted a hybrid strategy – vaccination for the ‘vulnerable’, and herd immunity or focused protection for those that are not. There is no discussion of vaccinating children and the under-50s. It is clear that many more lives will be lost.
Update 10 January 2021
I am pleased to say that Matt Hancock stated today that all adults will be offered a vaccine by Autumn. This is good news. There is a race between vaccination and infection. It is important that restrictions (the ‘cry freedom’ quote) are not released prematurely.
It wasn’t meant to be like this. Remember the Alert Levels (the ‘Nandos chart’)? The whole idea of that was to set some sort of policy – a roadmap if you will – of how we get out of a national lockdown. Introducing… Covid Alert Levels. 12 May 2020.
And remember this? The gentle ski slope of calm. ‘R less than 1 caseload decreasing’ Ah, simpler times.
This was about the same time as the ‘science bit’.
We’ve also had the shiny new: – Joint Biosecurity Centre – National Institute for Health Protection – The Contain framework and lots of other things that seem to have been good ideas at the time.
That Contain framework was a good one. Basically if you get to 50 cases per 100,000 your local authority gets on to a watchlist and restrictions come in. Leicester took the brunt of this one.
Each week, a watchlist was created of the local authorities that were nearing the 50-or-so cases per 100,000 threshold, and they were placed on a list. New restrictions came into force. Trafford was Mentioned in Dispatches with only 32 cases per 100,000
Of course, experts have been banging on about the reckless way that restrictions were lifted – with no basis in science. 10pm closure times for pubs, that sort of thing. Of course, SAGE has experts coming out of its ears, who could have advised on this sort of thing
Of course, they *did* advise on this sort of thing. Here’s the warning to the Government from ‘The Science’ on 14 July (worth a read).
Despite warnings from the Deputy Chief Medical Officer that releasing restrictions too early will backfire spectacularly, the Government pressed on relasing things. We were happy, we ate out to help out. We spread the virus.
Turns out that focus groups and popular policies aren’t necessarily the best way of doing strategy. (I wrote about this in the Financial Times in March).
So, the Government came up with a new shiny Tier Level thing. A new Nandos chart, with extra mild and mild removed. Like the Nandos chart, we start with ‘medium’. Sounds lovely. That’s most of the country.
Problem is that *every single local authority in the country’ has a higher than Trafford that managed to get itself on the Contain watchlist.
So, we now have High and Very High Tier levels. Problem is, of course, that all this procrastination means that the virus is still doubling. If the growth rate is 5%, that means doubling every two weeks.
So, we’re seeing – patients admitted to hospital increasing 30% week on week – deaths increasing 50% week on week
And of course, Test and Trace has failed completely.
We’re now back to another mess of Very High Tier 3 restrictions, not uniform at all as per the plan, but different depending on where you are.
And… we’re back to where we started – uncontrolled virus spread with a mess of differing local restrictions. Maybe we could do some Powerpoints and Blue Sky Thinking and re-invent the Nandos scale and call it the Scoville scale. Because things are getting extra hot out there.
Here is the heatmap of cases for PHE week 41 using week 40 data.
Studies in Spain, France, and the US have all shown that although the second wave may start in young people, it will inevitably move to older people.
The remarkable thing about this disease is that the death rate increases massively with age.
Students are unlikely to die of Covid-19, although some may, and we are still unsure about the long-term health consequences from catching the disease.
The heatmap of cases shows how the disease has travelled through the age groups. As you go from left to right through the weeks, you can see a gradual rise upwards through the population.
These figures should be seen as a minimum. Lack of testing capacity has meant that not everyone can get a test. For example, we do not know whether delays in testing may be concentrated in certain groups such as care home residents.
The latest figures (which will be revised upwards as new cases are recorded) show a very worrying number of cases in the over-80s.
A case rate of 53 per 100,000 over-80s is very concerning. The Department of Health and Social Care have this week stopped publishing the COVID-19 surveillance report which broke down numbers of people with the disease. However, we can estimate that over 1,000 over-80s tested positive last week. Given the very high fatality rate in over-80s, we can confidently predict that over 100 over-80s will die of infections caught in the last week.
This is one of many reasons why interventions are so critical – by not clamping down hard on the disease now, we will sleep walk into a situation as bad or worse than the first wave. The mid-July Academy of Medical Sciences report commissioned by the Chief Scientific Adviser set out a reasonable worst case scenario of 119,000 deaths in this second wave excluding those in care homes. We have a choice as to whether we as a nation repeat the mistakes of the past.
We also know that we are not doing enough testing as the positivity rate is so high (7% overall for Pillar 2 tests and up to 15% in some areas such as Liverpool) (see this thread)
So, how do we go about estimating R? Here’s a post I wrote in January explaining R in relation to Covid-19 (which then didn’t have an official name) in relation to Covid-19 (which then didn’t have an official name)
To estimate R, we carry out surveys – which means you pick a representative group of people, either households or individuals, and test them repeatedly. There are two main surveys: ONS and REACT
ONS excludes student halls of residence, as ‘only private residential households, otherwise known as the target population in this bulletin, are included in the sample. People in hospitals, care homes and other institutional settings are not included’. This is confirmed here.
The REACT survey uses GP lists to generate its sample of people who are tested. But of course, new students are only just registering with their GPs, and it is unclear when the GP lists were pulled for the latest study (Round 5 of REACT-1, 18-26 Sep)
We know that halls of residence are a significant driver of transmission.
We may be systematically under-sampling from halls of residence and therefore systematically underestimating R.
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.
Today’s analysis shows 22 cases per 100,000 in the over-80s population in England.
To put this into context, the Government uses a rate of 20 cases per 100,000 in order to determine (with other factors) whether you should self isolate when you return from a country with this incidence of Covid-19.
An interpretation would be: if you went to a country consisting of only over-80s, you would have to self-isolate when returning to the UK.
One thing civil servants learn is to write things down. Here is Academy of Medical Sciences 14 July report commissioned by the UK Chief Scientific Adviser. For the record.
It sets out what was known in July, and clearly sets out what the Government needed to do at the time. Straight off the bat, we have the executive summary.
Line one: “July and August must be a period of intense preparation for our reasonable worst-case scenario for health in the winter that we set out in this report, including a resurgence of COVID-19, which might be greater than that seen in the spring.”
Here are the challenges expected under a reasonable worst case scenario: 1. A large resurgence of COVID-19 nationally, with local or regional epidemics 2. Disruption of the health and social care systems 3. A backlog of non-COVID-19 care 4. A possible influenza epidemic
And sets out what we should have done: – public engagement – extensive public information campaign – tailoring guidance – and…
Here we go: “Significantly expanding the capacity of the TTI programme to cope with increasing demands over the winter and ensure that it can respond quickly and accurately.”
Improving public health surveillance: “Maintaining a comprehensive, population-wide, near-real-time, granular health surveillance system to ensure rapid identification, investigation and management of local COVID-19 outbreaks across community, work, and health and social care”.
But why does this matter? What would happen if we got this wrong? “Even scenarios with Rt in the 1.1-1-5 are likely to stretch the NHS”
But look at the caveat that goes with that estimate “The latest published figures represent the situation over the past few weeks rather than today. These estimates do not yet fully reflect any very recent changes in transmission due to, for example, the reopening of schools…”
Now re-read the @uksciencechief‘s report “Even scenarios with Rt in the 1.1-1-5 are likely to stretch the NHS”
But what is this reasonable worst case scenario? Back to the report. Oh, and there’s talk of R being 1.7 again:
“infections could be expected to rise gradually with a peak in hospital admissions and deaths of a similar magnitude to the first wave (Figure 4). This is projected to occur in January/February, coinciding with a period of peak demand on the NHS….
“The broader shape of the epidemic curve reflects the lower Rt assumed, but would result in an estimated total number of hospital deaths (excl. care homes) between September 2020 and June 2021 of 119,900 … over double the number occurring during the first wave in spring 2020
Here is the full report. It’s worth a read. And this is what I wrote at the time of publication: ‘don’t say we weren’t warned’.