Coronavirus (COVID-19): modelling the epidemic (issue no. 71)

Coronavirus (COVID-19): modelling the epidemic in Scotland (Issue No. 71)

Background

This is a report on the Scottish Government modelling of the spread and level of Covid-19. This updates the previous publication on modelling of Covid-19 in Scotland published on 23rd September 2021. The estimates in this document help the Scottish Government, the health service and the wider public sector plan and put into place what is needed to keep us safe and treat people who have the virus.

This edition of the research findings focuses on the epidemic as a whole, looking at estimates of R, growth rate and incidence as well as local measures of change in the epidemic.

In Scotland, the modelled estimate for R is between 0.7 and 1.0, with the growth rate between -4% and -1%.

Key Points

• The reproduction rate R in Scotland is currently estimated as being between 0.7 and 1.0, as of 14th September. The lower and upper limits have decreased since last week.
• The number of new daily infections for Scotland is estimated as being between 162 and 213, per 100,000 people. The lower and upper limits have decreased since last week.
• The growth rate for Scotland is currently estimated as between -4% and -1%.
• Average contacts have increased by approximately 17% in the last two weeks (comparing surveys pertaining to 9th September - 15th September and 23rd September - 29th September) with a current level of 5.4 daily contacts.
• Mean contacts within the workplace have increased by around 75% whereas contacts in the other setting (contacts outside home, school and work) have decreased by 9% in the last two weeks. Contacts within the home have remained at a similar level over the same period.
• All age groups between 18-59 have reported an increase in overall contacts with those aged 18-29 almost doubling in the last two weeks.
• Those aged between 18-39 have reported the biggest increase in interactions with those aged under 18 in the last two weeks.
• The proportion of individuals visiting a pub or restaurant increased from approximately 43% to 45% with individuals visiting a non-essential shop increasing from 39% to 41% in the last two weeks.
• The proportion of contacts reported to have been indoors only has increased from 57% to 67% within the last two weeks whereas the proportion of contacts occurring outside only has shown a decrease over the same period.
• The number of people wearing a face covering where they have at least one contact outside of the home has increased in the last two weeks, increasing from 82 to 87%.
• Hospital and ICU occupancies have plateaued. Hospital occupancy and intensive care use are likely to fall in the coming weeks.
• Modelled rates of positive tests per 100K using data to 27th September indicate that, for the week commencing 10th October 2021, there are 29 local authorities which are expected to exceed 50 cases per 100k with at least 75% probability.
• Of these, eight local authorities are expected to exceed 300 cases per 100k with at least 75% probability. These are Dundee, East Ayrshire, Fife, Glasgow, North Lanarkshire, South Ayrshire, South Lanarkshire and West Lothian.
• There are no local authorities which are expected to exceed 500 cases per 100k with at least 75% probability.
• Nationwide, levels of Covid-19 in wastewater (WW) have continued their decline, decreasing by 18% since last week. This puts WW viral levels somewhat below the July peak, as is the case for the rate of new cases.
• Modelling of long Covid gives estimates that on 17th October 2021 between 1.0% and 2.2% of the population are projected to experience symptoms for 12 weeks or more after their first suspected Covid infection in Scotland. The estimate is unchanged from last week.

Recent cases

Figure 1 shows the number of cases reported in Scotland between July and September 2021^[1]. The vertical dashed lines indicate the cut off points for each of the modelling inputs; after these dates, the number of cases is not incorporated into the outputs.

R, growth rate and incidence are as of 14th September (dashed line 1). The medium term projections by the Scottish Government of infections, hospitalisations and ICU beds, the modelled rates of positive tests per 100k and the long Covid analysis use data to 27th September (dashed line 2). Wastewater data is to 28th September (dashed line 3). Contact pattern data is to 29th September (dashed line 4).

Overview of Scottish Government Modelling

Modelling outputs are provided here on the current epidemic in Scotland as a whole, based on a range of methods. Because it takes a little over three weeks on average for a person who catches Covid-19 to show symptoms, become sick, and either die or recover, there is a time lag in what our model can tell us about any re-emergence of the epidemic and where in Scotland this might occur.

However modelling of Covid-19 deaths is an important measure of where Scotland lies in its epidemic as a whole. In addition, the modelling groups that feed into the UK Health Security Agency (UKHSA) consensus use a range of other data along with deaths in their estimates of R and the growth rate. These outputs are provided in this research findings. The type of data used in each model to estimate R is highlighted in Figure 2.

We use the Scottish Contact Survey (SCS) to inform a modelling technique based on the number of contacts between people. Over time, a greater proportion of the population will be vaccinated. This is likely to impact contact patterns and will become a greater part of the analysis going forwards.

The logistical model utilises results from the epidemiological modelling, principally the number of new infections. The results are split down by age group, and the model is used to give a projection of the number of people that will go to hospital, and potentially to ICU. This will continue to be based on both what we know about how different age groups are affected by the disease and the vaccination rate for those groups to estimate the proportion of cases that will require hospital, and the length of time people that people will stay there.

What the modelling tells us about the epidemic as a whole

The R value and growth rates are estimated by several independent modelling groups based in universities, Public Health England (PHE) and the Joint Biosecurity Centre. Estimates are considered, discussed and combined at the Epidemiology Modelling Review Group (EMRG), which sits within the UKHSA.

UKHSA's consensus view across these methods, was that the value of R as at 14th September^[2] in Scotland was between 0.7 and 1.0 (see Figure 2)^[3].

R is an indicator that lags by two to three weeks and therefore should not be expected to reflect recent fluctuations.

This week the Scottish Government presented two outputs to EMRG. The first uses confirmed cases, as published by Public Health Scotland (PHS), and deaths from National Records Scotland (NRS). The second uses instead wastewater data to estimate the number of cases, and deaths from NRS. Both outputs are shown in Figures 2 and 3.

Source: EMRG

The various groups which report to the EMRG use different sources of data in their models to produce estimates of incidence (Figure 3). UKHSA's consensus view across these methods, as at 14th September, was that the incidence of new daily infections in Scotland was between 162 and 213 new infections per 100,000. This equates to between 8,900 and 11,600 people becoming infected each day in Scotland. The lower and upper limits have decreased since last week.

Source: EMRG

The consensus from UKHSA for this week is that the growth rate in Scotland is between -4% and -1% per day as at 14th September. The lower and upper limits have decreased since last week.

What we know about how people's contact patterns have changed

Average contacts have increased by approximately 17% in the last two weeks (comparing surveys pertaining to 9th September - 15th September and 23rd September - 29th September) with a current level of 5.4 daily contacts as seen in Figure 4. Mean contacts within the work have increased by around 75% whereas contacts in the other setting (contacts outside home, school and work) have decreased by 9% in the last two weeks. Contacts within the home have remained at a similar level over the same period.

Figure 5 shows how contacts change across age group and setting. All age groups between 18-59 have reported an increase in overall contacts with those aged 18-29 almost doubling in the last two weeks. Increases within these age groups are largely driven by increased contacts within the work setting. Mean contacts for individuals over 60 have decreased over the same period

The heatmaps in Figure 6 show the mean overall contacts between age groups for the weeks relating to 9th September - 15th September and 23rd September - 29th September and the difference between these periods.

As seen in Figure 7, the proportion of participants visiting different locations remains at similar levels across the majority of locations. The biggest increases are seen with those using visiting a pub or restaurant and also individuals visiting a non-essential shop. The proportion of individuals visiting a pub or restaurant increased from approximately 43% to 45% with individuals visiting a non-essential shop increasing from 39% to 41% in the last two weeks.

Figure 8 shows the proportion of participants that reported contacts had indoors and outdoors for contacts individually reported for panel B. A contact can be recorded as both indoor and outdoor. The graph also shows contacts reported as outside only and indoor only. The proportion of contacts reported to have been indoors only has increased from 57% to 67% within the last two weeks whereas the proportion of contacts occurring outside only has shown a decrease over the same period.

Figure 9 shows the number of people wearing a face covering where they have at least one contact outside of the home. This has increased in the last two weeks, increasing from 82 to 87%.

From Figure 10, it can be seen that the oldest age group has lower levels of contacts and higher vaccinations than the youngest age groups, they also have the lowest weekly case number comparatively to the younger age groups. Despite that they have higher weekly hospitalization levels to that seen with the younger age groups.

What the modelling tells us about estimated infections as well as Hospital and ICU bed demand

The Scottish Government assesses the impact of Covid-19 on the NHS in the next few weeks in terms of estimated number of infections. Figure 11 shows two projections over the three weeks to 17th October.

'Central' assumes that infections will plateau at the current level. 'Better' assumes that infections will continue to fall^[7].

In the coming weeks it is likely that infections will either decrease or plateau.

Figure 12 shows the impact of the projections on the number of people in hospital. The modelling includes all hospital stays, whereas the actuals only include stays up to 28 days duration that are linked to Covid-19.

Hospital and ICU occupancies have plateaued and are likely to fall in the coming weeks.

Figure 13 shows the impact of the projection on ICU bed demand.

A comparison of the actual data against historical projections is included in the Technical Annex.

What the modelling tells us about projections of hospitalisations and deaths in the medium term

SPI-M produces projections of the epidemic^[10] (Figures 14 and 15), combining estimates from several independent models (including the Scottish Government's logistics modelling, as shown in Figures 11-13). These projections are not forecasts or predictions. They represent a scenario in which the trajectory of the epidemic continues to follow the trends that were seen in the data up to 27th September and do not include the effects of any future policy or behavioural changes.

The delay between infection, developing symptoms, the need for hospital care, and death means they cannot fully reflect the impact of behaviour changes in the two to three weeks prior to 27th September. Projecting forwards is difficult when the numbers of admissions and deaths fall to very low levels, which can result in wider credible intervals reflecting greater uncertainty. The interquartile range can be used, with judgement, as the projection from which estimates may be derived until the 12th October, albeit at lower confidence than the 90% credible interval.

These projections include the potential impact of vaccinations over the next few weeks. Modelling groups have used their expert judgement and evidence from Public Health England, Scottish Universities & Public Health Scotland, and other published efficacy studies when making assumptions about vaccine effectiveness.

What we know about which local authorities are likely to experience high levels of Covid-19 in two weeks' time

We continue to use modelling based on Covid-19 cases and deaths using data to 27th September from several academic groups to give us an indication of whether a local authority is likely to experience high levels of Covid-19 in the future. This has been compiled via UKHSA into a consensus. In this an area is defined as a hotspot if the two week prediction of cases (positive tests) per 100K population is predicted to exceed a threshold, e.g. 500 cases.

The very high peak and subsequent sharp fall in cases in the cities of Edinburgh and Glasgow has resulted in very uncertain model combinations this week, it is therefore likely that the uncertainty is overestimated in these areas and case numbers are in the lower range of the estimate. The continued very low case numbers in Shetland and Orkney has also resulted in a similar situation with case numbers also likely to be in the lower end of the uncertainty range.

Modelled rates of positive tests per 100K using data to 27th September (Figure 16) indicate that, for the week commencing 10th October 2021, there are 29 local authorities which are expected to exceed 50 cases per 100k with at least 75% probability^[11].

Of these, eight local authorities are expected to exceed 300 cases per 100k with at least 75% probability. These are Dundee, East Ayrshire, Fife, Glasgow, North Lanarkshire, South Ayrshire, South Lanarkshire and West Lothian.

There are no local authorities which are expected to exceed 500 cases per 100k with at least 75% probability^[12].

What can analysis of wastewater samples tell us about local outbreaks of Covid-19 infection?

Levels of Covid-19 RNA in wastewater collected at a number of sites around Scotland are adjusted for population and local changes in intake flow rate and compared to 7 day average daily new case rates derived from Local Authority and Neighbourhood (Intermediate Zone) level aggregate data. See Technical Annex in Issue 34 of these Research Findings for the methodology.

Nationwide, levels of wastewater (WW) Covid-19 RNA have continued their decline, falling to around 80 million gene copies per person per day (Mgc/p/d), from around 100 last week (15/9/21 to 21/9/21). This puts WW viral levels somewhat below the July peak, as is the case for the rate of new cases.

Figure 17 shows the national running average trend for the full set of sampled sites, with a small number of unrealistically large outliers excluded. As was the case last week, a new running average-based methodology for visualization of national trends has been introduced (see methodology update in previous issue).

What estimates do we have of the number of people experiencing long Covid symptoms?

The Scottish Government is modelling the number of people likely to experience long Covid symptoms. This gives a projection of estimated self-reported long Covid rates in the future, based on Scottish Government medium term projection modelling, as set out in Figure 18.

This modelling estimates that at 17th October 2021 between 54,000 (1.0% of the population) and 121,000 (2.2%) people are projected to experience symptoms for 12 weeks or more after their first suspected Covid infection in Scotland.

These are preliminary results, further data on rates of long Covid and associated syndromes as research emerges are required.

What next?

The modelled estimates of the numbers of new cases and infectious people will continue to be provided as measures of the epidemic as a whole, along with measures of the current point in the epidemic such as R_t and the growth rate. Further information can be found at https://www.gov.scot/coronavirus-covid-19.

We may report on exceedance in future weeks when the background levels of Covid-19 reduces so that it can be useful in identifying outbreaks.