Mapping and Nowcasting the Covid-19 Epidemic in British Local Authorities

2020-09-30T00:00:00+00:00

Yee Whye Teh, Avishkar Bhoopchand, Peter Diggle, Bryn Elesedy, Bobby He, Michael Hutchinson, Ulrich Paquet, Jonathan Read, Nenad Tomasev, Sheheryar Zaidi

As the UK pivots to a more localised strategy to manage the Covid-19 epidemic, it is important to understand localised rates of transmissions and incidences. This can be a component of an effective monitoring system and allows to more quickly identify hotspots where there are elevated levels of transmissions. It can also be a useful tool for the public to understand where infections are growing and to adopt appropriate behaviours.

We have developed a system to estimate localised rates of transmissions, and to use these to do daily short-term forecasts of the size of the Covid-19 epidemic in local authorities.

Our system is based on a Bayesian statistical model for estimating the effective reproduction number $R_t$ in individual local authorities. Estimating $R_t$ reliably across small areas with low case counts is difficult because of the low information content in the data, interactions across areas, as well as because of sensitivities to random local events. Further description of our method can be found here.

We used publicly available data on positive tests from the combined Pillars 1 and 2 of UK’s testing strategy. Unfortunately, due to the unclear relationship between the number of positive tests and true incidence rates, predictions of the system cannot be directly interpreted as predictions of true transmission and incidence rates. However, we believe it can be used, along with other indicators based potentially on other data sources, to build a fuller and more timely picture of the state of the Covid-19 epidemic in each local authority as it unfolds. Further details of the limitations of the system can be found here.

Our system complements a number of other publicly available systems for tracking the Covid-19 epidemic in British local authorities:

epiforecasts.io applies the EpiEstim R package, based on Cori et al, to national and regional positive test count data, after suitable preprocessing.
BDI Local Covid Tracker also applies EpiEstim to preprocessed positive test count data, at both upper-tier and lower-tier local authority levels.
Imperial College covid19local applies the Bayesian semimechanistic model of Flaxman et al 2020 as implemented in the epidemia R package to individual local authorities, using death and positive test count data.
PHE/Cambridge Nowcasting uses Bayesian inference on an age-specific transmission model described in Birrell et al applied to regional death count data. This was updated weekly until August 6, 2020.

There are a number of important next steps for the project:

Evaluating the accuracy of predictions of the system using historical data, potentially using seroprevalence data.
Extending the model to include delay distributions between infection to symptom onset and to test specimen being taken.
Extending the model to different type of observations, including deaths, hospitalisations, seroprevalence and symptom onsets.

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Definitions for terms in the map:

Case is an infected individual who has tested positive on the given date, under either Pillar 1 or Pillar 2 of the UK’s testing strategy.
Rt denotes the reproduction number: how many secondary cases a single primary case will result in on average. Rt greater than 1 implies the size of the epidemic is increasing exponentially, and less than 1 means it is shrinking.
Cases (Per 100k) denotes either the historical weekly reported number of cases under Pillars 1+2, normalised by population size, the predicted number in the future weeks.
P(Rt>1) denotes the probability that Rt is larger than 1 given the observed case counts.

School is the Best Place for Children

2020-08-14T00:00:00+00:00

This post was originally prepared for 29th July 2020.

School is the best place for children during the pandemic and the Government should prioritise keeping schools open wherever possible. Our report, published on 24^th July 2020 outlined why.

The Government’s announcement that all pupils will return to school after the summer break following six months of home or “blended” schooling has naturally left parents and guardians anxious. Earlier plans for a return in June were challenged on safety grounds by headteachers, unions and experts and many households are juggling home-schooling and their own work and family commitments.

The costs to children from school closures are considerable, and the infection risk from opening schools is likely lower than activities like going to the pub or the gym. Evidence to date suggests that in open schools, the risks to pupils from Covid-19 are low. Children are very unlikely to develop serious complications from the virus. There is a very rare childhood complication from the disease, which affects black and minority ethnic children to a greater degree, however, this is extremely uncommon. Children can pass on the disease, so there are some risks to parents and teachers, but, the risks of transmission within schools can be reduced through enhanced cleaning and distancing, and wearing face coverings.

It is definitely harmful for children to be absent from school for long periods. Most pupils in the UK have lost around 12 weeks of face-to-face learning, about a third of a year. This will have a significant negative impact on children’s achievement, particularly for socio economically disadvantaged children who have fewer resources at home and those for whom remote teaching has been limited. The impact is likely to be greater for younger children too, given the evidence that children who get a good start to their schooling tend to learn more easily later on.

Unless we help children recover from missed schooling, the consequences may last a lifetime. If young people enter the labour market with poorer skills, they will be at risk of permanently lower earnings and will be more likely to live in poverty. Quantifying this effect is difficult. However, it is estimated that without action to address the effects, from the mid-2030s and for the 50 years following that, around a quarter of the entire workforce will have lower skills, lowering the overall economic growth rate.

The negative impact of school closures is not restricted to loss of learning. Evidence suggests that closures will have also had lasting consequences on children’s physical and mental health. Evidence from the impact of school holidays suggests that children are less active and have worse diets as a result of being out of school. Moreover, social isolation and a lack of contact with peers impacts negatively on children’s mental health, particularly adolescents. The impact is likely to be even greater for those with pre-existing mental health conditions and from poor households.

Keeping schools open is also the key to unlocking the rest of the economy, allowing parents to leave teaching to teachers and return to their own jobs. If schools do not return full time or we have repeated lockdowns, the impact on parents, and particularly women, will be considerable.

What does the Government need to do before schools open?

While we are advocating for children to return to school as soon as possible and for schools to remain open thereafter, the Government must do everything feasible to ensure that this can be done as safely as possible.

The most critical step is to ensure low community transmission of the virus. If local outbreaks occur, then other facilities such as pubs or gyms where the risk of transmission is high should be closed, before considering school closures.

Realistic guidance and substantial extra resources such as PPE, cleaning products, and extra supply teachers must be made available to ensure schools can minimise infection risk. We also need effective surveillance with a suitable test-trace-isolate system that enables a rapid response to outbreaks and that can cope with the predicted increased caseload in the winter.

As we have observed in Leicester, future lockdowns are likely to be local. The Government must provide a clear set of scenario-based objective criteria that trigger actions, including school closures. Our report provides an example set of scenarios. There must also be a clear delineation of responsibilities among the numerous agencies involved in making decisions. Communication with school leaders, teachers and parents needs to be effective, clear and unified.

The Government must also prepare for winter by urgently collecting data that will help us better understand this virus, particularly in children. Scientists are still uncertain about the susceptibility and infectiousness of children, but cases of child-to-adult transmission appear to be relatively uncommon. Local monitoring is needed to provide real-time data on infection rates, enabling local responses. Only this week, Health Protection Scotland launched a public dashboard of COVID-19 to help the public (and schools) understand prevalence by local area. We also need to mitigate the learning loss. To do that, we need anonymous assessment of the impact of closures on educational achievement and pupil mental health. Again this week, the Department for Education announced plans to research the impact of this pandemic on “the academic development of youngsters” including the recovery of lost learning. We also need to know more about how to keep schools open safely. This requires evaluation of the different strategies used in schools to reduce infection risk.

This is a lot to do in the next few weeks, but we believe that schools should be at the centre of the Government’s COVID-19 strategy. Otherwise, we risk our children continuing to pay too high a price for managing this pandemic.

Royal Society DELVE Initiative

Mapping and Nowcasting the Covid-19 Epidemic in British Local Authorities

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School is the Best Place for Children