Coronavirus (COVID-19) state of the epidemic - 5 November 2021

State of the Epidemic in Scotland – 5 November 2021

Background

This report summarises the current situation on the Covid-19 epidemic in Scotland. It brings together the different sources of evidence and data about the epidemic in Scotland at this point in time, why we are at that place, and what is likely to happen next. This summarises the data up to and including 4 November 2021 on Covid-19 in Scotland. This updates the previous publication published on 29 October^[1]. The information in this document helps the Scottish Government, the health service and the wider public sector respond to the epidemic and put in place what is needed to keep us safe and treat people who have the virus.

This edition of the State of the Epidemic summarises current data on Covid-19 at a national and local level, and how Scotland currently compares to the rest of the UK. It looks at the vaccination program in Scotland and its impact. Information is provided about variants of concern and what impact these may have. Bringing this information together in one place gives the opportunity to better understand the current state of the epidemic in Scotland.

Please note that PCR testing might have been affected by half-term holidays throughout October. Testing and case numbers during the period 28-31 October 2021 may have been affected by a data flow issue at the Glasgow lighthouse laboratory, this was cleared on the 31 October. The backlog of NHS Scotland Pillar 1 lab test results that Public Health Scotland were unable to report on 2 November due to an issue affecting data flow on the afternoon of 1 November, were included in newly reported figures on 3 November.

Key Points

• The reproduction rate R in Scotland, as of 19 October, is estimated as being between 0.9 and 1.1. Both the lower and upper limits have increased since last week.
• An average of 2,786 cases were reported per day in the 7 days to 4 November. This compares to the daily average of 2,436 recorded on 28 October (week on week comparison may be affected by data flow issue).
• There were 324 weekly cases per 100,000 in the week to 1 November (by specimen date). This is lower than the most recent peak (825 weekly cases per 100,000 on 6 September) and lower than the peak in July (425 weekly cases per 100,000 recorded on 3 July). 7 day case rates have remained relatively stable in recent weeks.
• Case rates have decreased for those aged 60-79 and 80+ and have increased slightly or plateaued for other age bands in the week to 1 November. As of 1 November, the highest case rates were observed amongst those aged under 20, followed by 40-59, 20-39, 60-79 and 80+.
• As determined through the latest weekly ONS survey, the trend in the percentage of people testing positive for COVID-19 in the private residential population is uncertain in the most recent week in Scotland (24 to 30 October 2021).
• Latest modelled estimates suggest that as of 19 October there were between 63 and 96 new daily infections per 100,000 people in Scotland.
• There were 133 deaths registered in Scotland where coronavirus was mentioned on the death certificate in the week ending 31 October.
• Average hospital admissions (3-week rolling average) related to Covid-19 in children have decreased in all age groups, except for 0-1 year olds, compared to the previous three-week period.
• Clackmannanshire currently has the highest weekly case rate in Scotland reporting 587 weekly cases per 100,000 in the week to 1 November 2021, followed by Na h-Eileanan Siar with 483 weekly cases per 100,000, Orkney with 473 weekly cases per 100,000, and East Ayrshire with 470 weekly cases per 100,000 population. All local authorities reported over 200 weekly cases per 100,000 population in the last week, except for Shetland. Shetland reported the lowest case rate with 184 weekly cases per 100,000 in the same period.
• Nationwide, Covid-19 levels in wastewater have shown an increase since last week (20th to 26th October), increasing by approximately 20%.
• Hospital occupancy has been fluctuating over the past weeks. ICU occupancy appears to have plateaued. There continues to be uncertainty over hospital occupancy and intensive care in the next three weeks.
• Over 4.3 million people in Scotland have been given a first vaccine against SARS-CoV-2, over 3.9 million have received a second dose, and over 800,000 people have received a booster or dose 3 by 4 November.
• The Delta variant remains the dominant strain in Scotland. Prevalence rates of AY.4.2 (Delta+) have increased in recent weeks in both Scotland and England. Clinical implications of Delta+ are still to be determined.

Method

This report brings together a wide range of publically available figures from a range of data sources. These include publications by Scottish Government, Public Heath Scotland, National Records of Scotland and Office for National Statistics along with scientific publications and SAGE and UKHSA summaries where appropriate to summarise the state of the epidemic in Scotland in a given week. We also provide information on public attitudes to the virus from weekly YouGov polling surveys.

The national picture

The latest R value for Scotland, as of 19 October (using data to 1 November)^[2], was between 0.9 and 1.1 (Figure 1), with a growth rate of between -3% and 1%. Both lower and upper limits of R value have increased since last week.

An average of 2,786 cases were reported per day in the 7 days to 4 November. This compares to the daily average of 2,436 recorded on 28 October (week on week comparison may be affected by data flow issue)^[3]. In the week 23 October to 29 October 2021, there were 330 cases (PCR testing only) per 100,000 amongst the unvaccinated individuals, compared to 296 cases per 100,000 for those that had been vaccinated with two doses^[4]. Our current position is 324 weekly cases per 100,000 in the week to 1 November (by specimen date)^[5]. This is lower than the most recent peak of 825 weekly cases per 100,000 on 6 September and lower than the previous peak of 425 weekly cases recorded on 3 July (see Figure 2). 7 day case rates have remained relatively stable in recent weeks.

The number of locations where the levels of SARS-CoV-2 in wastewater are monitored has increased to 110 sites around Scotland. In contrast to Covid-19 case records, virus shedding into wastewater is a biological process. This means that wastewater data is unaffected by factors that impact whether testing is done. Nationwide, Covid-19 levels in wastewater have shown an increase since last week (20th to 26th October), increasing by approximately 20%.

Case rates have decreased for those aged 60-79 and 80+ and have increased slightly or plateaued for other age bands in the week to 1 November. As of 1 November, the highest case rates were observed amongst those aged under 20, followed by 40-59, 20-39, 60-79 and 80+ (Figure 3).

Not everyone who has the virus will be tested, as many people do not realise they have Covid-19, or they have mild symptoms and do not come forward. Latest modelled estimates suggest that, as at 19 October, the incidence of new daily infections in Scotland was between 63 and 96 new infections per 100,000^[7]. This equates to between 3,400 and 5,200 people becoming infected each day in Scotland.

Hospital occupancy has been fluctuating over the past weeks. ICU occupancy appears to have plateaued. The number of people in hospital with confirmed Covid-19 for less than 28 days peaked at 2,053 on 22 January and decreased to a low of 58 on 6 May^[8]. This has since increased and as of 4 November there were 896 patients in hospital with Covid-19. This compares to 932 people in hospital on 28 October (Figure 4). The latest data from PHS shows 657 admissions to hospital for people with confirmed Covid-19 in the week to 31 October compared to 675 in the week to 24 October^[9]. In the 4 weeks to 29 October 23.8% of acute Covid-19 hospital admissions were in unvaccinated individuals^[10]. For context, as of 28 October, 92.5% of adults aged 18+ (90.2% of those aged 12+) have had at least one dose of the vaccine. Overall, individuals in the oldest age groups were most likely to be hospitalised. The age-standardised rate of hospital admissions per 100,000 were higher in unvaccinated individuals compared to vaccinated individuals in the four weeks to 29 October. Unvaccinated individuals were 2.3 times more likely to be in hospital with Covid-19 compared to individuals that had received two doses of vaccine in the period 23-29 October^[11].

As the population is increasingly vaccinated, more of the patients in hospital will be fully or partially vaccinated. Therefore, it is important that we can differentiate between patients in hospital because of Covid-19 rather than with Covid-19. Public Health Scotland estimates that as at July 2021, 75% of acute hospital admissions had a primary diagnosis of Covid-19. The trend decreased from 78% in January 2021 to a low of 66% in April 2021, but has since increased^[12].

There were 133 deaths registered where Covid-19 was mentioned on the death certificate in the week to 31 October. This is an increase of 2 (+2%) in the number of deaths from the previous week, and 80% lower than the peak in April 2020 (663 deaths). The proportion of deaths in care homes decreased from 60% in April 2020 to 16% in the week to 31 October, with 21 deaths occurring in care homes^[14]. In the week ending 31 October, deaths involving coronavirus have increased in those aged 15-44 (from 2 to 4 deaths) and 75-84 (from 35 to 43 deaths) compared to week ending 10 October. Deaths decreased in those aged 45-64 (from 24 to 18 deaths), 65-74 (from 25 to 24 deaths), and those aged 85+ (from 45 to 44 deaths). Deaths remained at 0 in those aged under 15 in the same period^[15] (Figure 5). From 29 December 2020 to 22 October 2021, 71.5% of Covid-19 deaths were in unvaccinated individuals^[16]. Amongst those individuals who have been vaccinated with two doses of Covid-19 vaccine, 78.9% of the confirmed Covid-19 deaths occurred in the 70+ age group^[17].

How Scotland compares with the rest of the UK

The ONS Covid-19 Infection Survey estimates that in the week 24 to 30 October 2021 the estimated percentage of the population living in private residential households testing positive for Covid-19 in Scotland was 1.25% (95% credible interval: 1.00% to 1.55%). The trend in the percentage of people testing positive for COVID-19 in the private residential population is uncertain in the most recent week in Scotland. Estimates for the week 24 to 30 October in the other UK nations are as follows: 2.02% (95% credible interval: 1.91% to 2.13%) for England, 2.39% (95% credible interval: 1.92% to 2.92%) for Wales and 1.49% (95% credible interval: 1.09% to 2.02%) for Northern Ireland. This equates to around 1 in 80 people in Scotland, 1 in 50 in England, 1 in 40 in Wales and 1 in 65 in Northern Ireland^[18].

The ONS Covid-19 Infection Survey estimated that in the week beginning 27 September 2021, 91.3% (95% CI: 89.6% to 92.7%) of the adult population living in private residential households in Scotland would have tested positive for antibodies against SARS-CoV-2, as a result of having the infection in the past or being vaccinated. This compares to 92.2% in England (95% CI: 90.9% to 93.3%), 90.0% in Wales (95% CI: 87.9% to 91.7%) and 90.8% in Northern Ireland (95% CI: 86.7% to 93.3%)^[19].

An estimated 1.9% of the population living in private residential households in the UK were experiencing self-reported long Covid symptoms (symptoms persisting for more than four weeks after the first suspected coronavirus (Covid-19) infection that were not explained by something else) in the 4 weeks ending 2 October 2021. In Scotland, 92,000 people (1.75% of the respective population) living in private households self-reported long Covid symptoms for this period. This compares to 1.90% in England, 1.56% in Wales and 1.43% in Northern Ireland^[20].

Average daily deaths in Scotland (3 per 1 million population) in the week to 4 November are similar to Wales (3 per 1 million), above England (2 per 1 million) and below Northern Ireland (4 per 1 million)^[21]. Average daily cases in Scotland (510 per 1 million) in the week to 4 November are below Wales (814 per 1 million), Northern Ireland (608 per 1 million) and England (580 per 1 million)^[22].

Situation by local authority within Scotland

Clackmannanshire currently has the highest weekly case rate in Scotland reporting 587 weekly cases per 100,000 in the week to 1 November, followed by Na h-Eileanan Siar with 483 weekly cases per 100,000, Orkney Islands with 473 weekly cases per 100,000, East Ayrshire with 470 weekly cases per 100,000, West Lothian with 435 weekly cases per 100,000, and Aberdeenshire with 430 weekly cases per 100,000 population. All local authorities reported over 200 weekly cases per 100,000 population in the last week, except for Shetland (Table 1). Case rates have decreased in Edinburgh, Clackmannanshire, Dundee, East Dunbartonshire, East Lothian, East Renfrewshire, Falkirk, Fife, Glasgow City, North Lanarkshire, Perth and Kinross, Renfrewshire, South Ayrshire, Stirling, West Dunbartonshire and West Lothian over the last week. However, there are still very high levels (150+ weekly cases per 100,000) of case rates across Scotland (Figure 6). Shetland has the lowest case rate in Scotland, reporting 184 weekly cases per 100,000 in the week to 1 November^[23].

Table 1: Total new weekly cases per 100,000 population to 1 November 2021, in order of prevalence

Local authority	Total new cases in the week, per 100,000 population	Change since previous week
Clackmannanshire	587	-29
Na h-Eileanan Siar	483	+204
Orkney Islands	473	+27
East Ayrshire	470	+61
West Lothian	435	-10
Aberdeenshire	430	+30
Argyll and Bute	414	+97
Scottish Borders	381	+88
Angus	379	+41
Stirling	368	-68
North Lanarkshire	368	-49
Dumfries and Galloway	358	+61
South Lanarkshire	350	+38
Fife	349	-84
Dundee City	347	-19
Falkirk	346	-11
North Ayrshire	337	+44
Aberdeen City	330	+32
East Dunbartonshire	326	-17
Highland	321	+2
Midlothian	319	+59
Moray	309	+18
West Dunbartonshire	300	-42
Inverclyde	293	+5
South Ayrshire	285	-12
East Lothian	278	-83
Renfrewshire	253	-45
East Renfrewshire	250	-26
City of Edinburgh	242	-20
Perth and Kinross	242	-94
Glasgow City	216	-16
Shetland Islands	184	+109
Scotland	324	-6

The most recent modelling predicts, based on data up to 1 November, that for the week commencing 14 November 2021, there are 31 local authorities (Shetland being an exception) which are expected to exceed 50 cases per 100,000 population with at least 75% probability. 29 local authorities (Na h-Eileanan Siar, Orkney and Shetland being the exceptions) are also expected to exceed 100 cases per 100,000 with at least 75% probability. Clackmannanshire is the only local authority which is expected to exceed 300 cases per 100,000 population with at least 75% probability^[24].

Children and Education

Schools resumed in Scotland by the week ending 20 August and universities resumed by end of September. The majority of children and young people have returned to full time education. Throughout October schools have been on half-term holidays, which may have an effect on testing.

The total number of Covid-19 cases in young people aged under 22 has levelled off over the last week (4,567 cases recorded in the week to 24 October compared to 4,583 cases in the week ending 31 October). 7 day case rates per 100,000 have levelled off amongst all ages, except for 12-15 year olds, in the week ending 31 October (Figure 7). The percentage of cases made up of children under 12 was 60.4% (2,768 cases) in the week to 31 October, a slight increase from the previous week^[25]. The percentage of cases made up of 18-21 year olds was 10% (458 cases) in the week to 31 October which is unchanged from the week ending 24 October. Following the return of universities, there is no evidence of an uptick in cases in the 18-21 year age group.

The rate of testing increased amongst those aged 2-4, 5-11, and 18-19, decreased or remained the same amongst other age groups in the week ending 31 October. Test positivity rates have decreased in age groups 5-11 and 12-15, however increased or plateaued in other age groups in the same period. In the week ending 31 October, the proportion of positive cases who report having been in an education setting in the 7 day period prior to the onset of symptoms has increased to 13.1%, compared to 7.8% in the week ending 24 October. Hospital admissions (3 week rolling average) in children and young adults decreased amongst all age groups, except for 0-1 year olds, in the period 7-27 October compared to the previous three-week period (30 September – 20 October).

Vaccine uptake in 17-21 year olds as at 25 October was 79.9% for the first dose and 61.1% for the second dose^[26]. Please note that under half of Scottish students are in this age category and only Scottish students (i.e. registered with a GP in Scotland) are included in the figures. Covid-19 infection survey estimated that up to the week beginning 27 September 2021, the percentage of 16-24 year olds in the community population in Scotland testing positive for antibodies increased to 95.4%^[27].

Looking ahead

Changes in patterns of mixing and adherence to restrictions will impact on future case numbers. The Scottish Contact Survey measures times and settings that people mix where they could potentially spread Covid-19.

Average contacts have decreased by 13% in the last two weeks (comparing surveys pertaining to 7th October - 13th October and 21st October - 27th October) with a current level of 4.1 daily contacts.

Mean contacts within the work and other setting (contacts outside home, school and work) have decreased in the last two weeks by 20% and 17% respectively. Contacts within the home have remained at a similar level over the same period.

Those aged between 30-39 and 50-59 reported an increase in overall contacts whereas all remaining age groups reported a decrease. Changes across the age groups are driven by contacts within the work place with the exception of the 18-29 age group, with their decrease driven by a reduction in contacts within the other setting.

The proportion of individuals using public transport increased from approximately 23% to 28% while individuals visiting another’s home rose from 44% to 48% in the last two weeks.

Self-reported compliance with the current regulations and guidance has decreased since January but remains at a high level. On 2-3 November, 67% of people reported ‘complete’ or ‘almost complete’ compliance^[28].

Hospital occupancy has been fluctuating over the past weeks. ICU occupancy appears to have plateaued. There continues to be uncertainty over hospital occupancy and intensive care in the next three weeks (Figure 8)^[29].

Vaccinations are continuing and 90.2% of the 12+ population in Scotland has now been vaccinated with the first dose^[31]. The first vaccines were administered on Tuesday 8 December and 4,318,790 people had received their first dose by 4 November 2021^[32].

By age group, almost 100% of individuals aged 55+, 97% of those aged 50-54, 92% of those aged 40-49, 84% of those aged 30-39, 78% of those aged 18-29, 76% of those aged 16-17, and 55% of those aged 12-15 have received their first vaccination (Figure 9).

Almost 100% of individuals aged 60+, 97% of those aged 55-59, 94% of those aged 50-54, 87% of those aged 40-49, 77% of those aged 30-39, 68% of those aged 18-29, 17% of those aged 16-17, and 1% of those aged 12-15 have received their second dose.

71% of individuals aged 80+, 75% of those aged 75-79, 66% of those aged 70-74, 25% of those aged 65-69, 14% of those aged 60-64, 11% of those aged 55-59, 10% of those aged 50-54, 8% of those aged 40-49, 5% of those aged 30-39, 3% of those aged 18-29, 0% of those aged 16-17, and 0% of those aged 12-15 have received their dose 3 or booster vaccination.

Overall, 3,911,105 people (81.8% of those aged 12 and over) had received their second dose and 858,646 people have received their dose 3 or booster vaccine by 4 November^[33]. There remains a low level of deaths amongst the vaccinated individuals (Figure 5).

The proportion of people surveyed who said they have been vaccinated for Covid-19 is high. 91% of all respondents have already received at least their first vaccine dose. Of those not vaccinated (and small base must be noted), 6% report they are likely to be vaccinated when a vaccine becomes available to them^[34].

How the virus is changing

The variant of concern Delta, also referred to as VOC-21APR-02 (first identified in India) is more transmissible than Alpha variant ^{[35] [36] [37]}. It quickly replaced Alpha (VOC-20DEC-01), first identified in the UK, as the dominant strain in Scotland, and 98,054 cases have now been identified as Delta to 3 November 2021. A sublineage of Delta, AY.4.2, has been classified as VUI-21OCT-01, and 3,593 cases have now been identified in Scotland.

To date there are five ‘variants of concern’ (VOCs) and twelve ‘variants under investigation’ (VUIs)^[38]. There is a concern that some of these new variants may partially escape immunity, from both natural infection and from vaccines currently being deployed and we are monitoring the evidence on this^{[39] [40] [41]}. Up to 3 November there have been 62 genomically confirmed cases of the variant Beta/VOC-20DEC-02 (first detected in South Africa), and 23 cases of Gamma in Scotland. Genomically confirmed cases of other VOCs and VUIs remain low, there have been no new cases of other VOCs or VUIs in the last week (Figure 10). There remains uncertainty regarding the impact of the Delta variant on severity of illness, treatment or reinfections. As more data is analysed we shall become more certain of the impact of Delta on infections, hospitalisations and disease severity and long term vaccine protection effects.

The effectiveness of vaccines

A large study from the University of Oxford and Office of National Statistics shows that with Delta, Pfizer-BioNTech and Oxford-AstraZeneca vaccines still offer good protection against new infections, but effectiveness is reduced compared with Alpha^[43]. Public Health England analysis shows that vaccines are highly effective against hospitalisation from Delta variant with similar vaccine effectiveness against hospitalisation seen with the Alpha and Delta variants at 93% and 96% respectively after two doses of vaccine. There was a 14% absolute reduction in vaccine effectiveness against symptomatic disease after a single vaccine dose with Delta compared to Alpha, and a smaller 10% reduction in effectiveness after 2 doses. Vaccine effectiveness against symptomatic disease is high for both Alpha (89%) and Delta after two doses (79%)^[44]. EAVE II data from Scotland also shows that both the Oxford–AstraZeneca and Pfizer–BioNTech Covid-19 vaccines are effective in reducing the risk of SARS-CoV-2 infection and Covid-19 hospitalisation in people with the Delta variant, but effectiveness against infection appeared to be diminished when compared to those with Alpha^[45]. The latest data released from the EAVE II study revealed that vaccination is over 90% effective at preventing deaths from the Delta variant of Covid-19 (Pfizer-BioNTech 90% effective, Oxford-AstraZeneca 91%)^[46]. The vaccine effectiveness expert committee recently published their consensus view on the effectiveness of different vaccines on infections, symptomatic disease, and severe disease^[47]. The protective effects of vaccines wanes over time, and recently the Joint Committee on Vaccination and Immunisation (JCVI) gave advice on a booster programme to re-vaccinate adults against Covid in the UK^[48].

Next steps

The Scottish Government continues to work closely with Public Health Scotland and modelling groups to monitor what happens following the high number of cases in Scotland this week and how this effects the course of the epidemic.

Each week this report will provide an overview of the current Covid-19 situation in Scotland. This will include real time data on case rates, hospitalisations and deaths and how Scotland’s figures compare to those from the rest of the UK.

Modelling can tell us where the epidemic is likely to be heading. Local data and data by age group can highlight where problems arise, which can help in addressing some of these issues. In the coming weeks the roll out of the vaccine will continue to be monitored along with the impact of this on case rates and deaths among different age cohorts. Investigations are ongoing by NERVTAG, SPI-M, SAGE, UKHSA, Public Health England and Public Health Scotland regarding the impact of new variants and of vaccination; this will be reflected here as work is undertaken.