Updates
Model and report changes
- Over January 2022 our model has been redesigned to incorporate the booster vaccination campaign and to be able to capture, in an unbiased way, the ecological effects of the emergence and subsequent dominance of the omicron variant. In particular, we have stratified the entire model by vaccination status so that we can more accurately capture the impacts of waning immunity. The duration of immunity following infection is assumed to have a mean of around 18 months, but this falls rapidly around the time of the emergence of omicron to account for the immune escape of this variant. The waning of vaccine-derived immunity is captured through an assumed drop in vaccine efficacy at this time.
- We have extended the use of serological sampling data to use samples taken beyond the first wave of the pandemic. The samples are those collected by NHS Blood and Transplant using the Roche-N assay, which measures the prevalence of infection-acquired antibodies in the population.
- The model also accounts for a different susceptibility to infection in each adult age group (no prior information is used); and for the under-15s, (using prior information from Viner et al, 2020, which estimates children to be less likely to acquire infection when in contact with an infectious individual).
- The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly since the outset of the Survey in May 2020 for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths.
- The underlying probability of an unvaccinated individual dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) is allowed to change gradually over the course of 30 days every (approximately) 100 days. This is designed to reflect fluctuations due to seasonal effects, demand on healthcare services or the emergence of new virus variants of differing severity.
- The ‘Epidemic summary’ only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme - it is an average of a lower rate of death in vaccinated individuals and a higher rate among the unvaccinated.
- The attack rate table shows the proportion of individuals to have ever been infected over the course of the pandemic. Under any “Infections” tab, what is presented is the totality of all infections, including reinfections, and will therefore show values higher than the attack rate might suggest.
Updated findings
- The estimated number of new daily infections on the 23rd February across England is 99,500 (74,000–136,000, 95% credible interval). The daily infection rate is estimated to be 178 per 100k population per day nationally. The highest rate is currently in the South West (SW) with 280 infections per 100K population followed by London (GL) with 208 infections per 100K population and the West Midlands (WM) at 199. These rates correspond to 15,700, 18,500 and 11,700 daily infections respectively. There is then a drop to the East of England (EE) (175), South East (SE) (173), East Midlands (EM)(154) and the North East (NE) (NE) (142). Rates of infection are estimated to be much lower in the North West (NW) than elsewhere, with 44 per 100K population. Note that a substantial proportion of these infections will be asymptomatic.
- The daily number of deaths is declining, such that the expected number of deaths halves every 38 days at its current rate. We forecast between 76 and 164 deaths per day by the 16th of March.
- This week we believe the national Rt to be less than 1, depressed currently by the ongoing half-term school holiday period over the last two weeks, resulting in near certainty that Rt < 1 with only the SW having a probability of Rt>1 that is greater than 10%.
- The growth rate for England is -0.02 (-0.04– -0.01) per day. This means that, nationally, the number of infections is declining, corresponding to an Rt of around 0.8.
- Our estimates for the attack rate, that is the proportion of the regional populations who have ever been infected, have GL and NE at 61%. WM and EM are all also above the national average with 57% and 54% respectively.
- Note that the deaths data used are only very weakly informative on Rt over the last two weeks. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to significant revision.
Interpretation
Across England, the daily number of deaths are falling steadily. Estimates for PCR-positive infection prevalence are uniformly declining across all regions of the country. Combined with the knowledge that over the last two weeks there has been reduced epidemic activity across the country due to the staggered half-time school holidays, it is no surprise that estimates for Rt are currently low at around 0.8.
The current period of decline is still to a level of incidence far higher than at the time of our last published report. Since then, our results show that the Omicron variant has infected over 15 million individuals in the last three months. Our current estimate is that 30% of all infections are re-infections.
We estimate that infection with the Omicron variant is less likely to result in death. Over the period covered by Omicron, the overall IFR has changed little, but this masks age-specific IFR estimates that are falling for each age group. The overall IFR staying constant therefore suggests that the balance of COVID infection is shifting to more vulnerable (i.e. older) groups. Plots of the IFR over time show that we are currently estimating the most steep decline in IFR in the younger age groups. Following this drop, the overall IFR is 0.12% (0.11%–0.12%), highest in the over-75s at 2.3% (2.2%–2.5%), a drop of around 25% from that which was estimated in our last report.
Summary
Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.
Methods
We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.
Data sources
We use:
- Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
- the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
- NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
- Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
- Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.
Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).
- Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
- Information on contacts between different age groups from:
- A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
- Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
- The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
- Data from the Department for Education describing the proportion of children currently attending school.
- Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.
Epidemic summary
Current \(R_t\)
Value of \(R_t\), the average number of secondary infections due to a typical infection today.
Attack rate
The percentage of a given group that has been infected.
Change in infections incidence
Growth rates
NB: negative growth rates are rates of decline. Values are daily changes.
England |
-0.03 |
-0.04 |
-0.01 |
East of England |
-0.04 |
-0.08 |
-0.01 |
East Midlands |
-0.04 |
-0.08 |
0.00 |
London |
-0.03 |
-0.07 |
0.01 |
North East |
-0.05 |
-0.09 |
0.00 |
North West |
-0.06 |
-0.11 |
-0.02 |
South East |
-0.04 |
-0.08 |
0.00 |
South West |
-0.02 |
-0.05 |
0.02 |
West Midlands |
-0.03 |
-0.08 |
0.00 |
Yorkshire and The Humber |
-0.04 |
-0.09 |
0.00 |
Halving times
Halving times in days, if a region shows growth than value will be NA.
England |
25.93 |
16.00 |
115.70 |
East of England |
16.90 |
8.21 |
116.90 |
East Midlands |
17.69 |
8.04 |
NA |
London |
25.36 |
9.31 |
NA |
North East |
14.92 |
6.99 |
147.62 |
North West |
10.49 |
5.88 |
44.56 |
South East |
17.54 |
8.09 |
423.85 |
South West |
39.27 |
13.34 |
NA |
West Midlands |
19.77 |
8.44 |
NA |
Yorkshire and The Humber |
15.39 |
7.62 |
NA |
Doubling times
Doubling times in days, if a region shows decline then the value will be NA.
England |
NA |
NA |
NA |
East of England |
NA |
NA |
NA |
East Midlands |
NA |
663.20 |
NA |
London |
NA |
68.33 |
NA |
North East |
NA |
NA |
NA |
North West |
NA |
NA |
NA |
South East |
NA |
NA |
NA |
South West |
NA |
33.15 |
NA |
West Midlands |
NA |
205.86 |
NA |
Yorkshire and The Humber |
NA |
301.19 |
NA |
Change in deaths incidence
Growth rates
NB: negative growth rates are rates of decline. Values are daily changes.
England |
-0.02 |
-0.03 |
-0.01 |
East of England |
-0.02 |
-0.04 |
0.00 |
East Midlands |
-0.02 |
-0.04 |
0.00 |
London |
-0.02 |
-0.04 |
0.01 |
North East |
-0.03 |
-0.05 |
0.00 |
North West |
-0.04 |
-0.05 |
-0.02 |
South East |
-0.02 |
-0.04 |
0.01 |
South West |
0.00 |
-0.02 |
0.03 |
West Midlands |
-0.02 |
-0.04 |
0.01 |
Yorkshire and The Humber |
-0.03 |
-0.05 |
0.00 |
Halving times
Halving times in days, if a region shows growth than value will be NA.
England |
36.41 |
25.74 |
71.53 |
East of England |
33.34 |
17.92 |
NA |
East Midlands |
29.30 |
16.32 |
NA |
London |
43.88 |
18.79 |
NA |
North East |
22.64 |
14.00 |
143.93 |
North West |
16.53 |
12.32 |
37.49 |
South East |
34.80 |
18.08 |
NA |
South West |
338.72 |
29.42 |
NA |
West Midlands |
35.89 |
17.71 |
NA |
Yorkshire and The Humber |
23.66 |
14.58 |
145.68 |
Doubling times
Doubling times in days, if a region shows decline then the value will be NA.
England |
NA |
NA |
NA |
East of England |
NA |
200.48 |
NA |
East Midlands |
NA |
197.25 |
NA |
London |
NA |
58.86 |
NA |
North East |
NA |
NA |
NA |
North West |
NA |
NA |
NA |
South East |
NA |
130.53 |
NA |
South West |
NA |
23.92 |
NA |
West Midlands |
NA |
79.33 |
NA |
Yorkshire and The Humber |
NA |
NA |
NA |
## The execution of the prevalence code block will proceed if
## prev.dat exists and this is TRUE
## it is not an external report and this is FALSE
Infections and deaths
The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (23 Feb).
Prob \(R_t > 1\)
The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.
Copyright © MRC Biostatistics Unit, University of Cambridge