Coronavirus (COVID-19): state of the epidemic - 11 February 2022

Estimated Infection Levels and Case Numbers

Estimated Infection Levels

The reproduction number (R) is the average number of secondary infections produced by a single infected person. If R is greater than one the epidemic is growing, if R is less than one the epidemic is shrinking. The higher R is above one, the more people one infectious person might further infect other people and so the faster the epidemic grows. Please note that R is an indicator that lags by two or three weeks. For more information please visit the UK government website.

The UK Health Security Agency's (UKHSA) consensus estimate for R in Scotland as at 25 January is between 0.8 and 1.0. Both the lower and upper limits of the R value have increased since the last published R value (Figure 1) ^{[2] [3]}.

As at 25 January 2022, the UKHSA's consensus view was that the incidence of new daily infections in Scotland was between 168 and 292 per 100,000 people. This equates to between 9,200 and 16,000 people becoming infected each day in Scotland^{[5] [6]}.

The growth rate reflects how quickly the numbers of infections are changing day by day. It is an approximation of the percentage change in the number of new infections each day. More information can be found on the UK government website.

The latest growth rate for Scotland as at 25 January was between -5% and -1%. The upper limit has remained unchanged since the previous week, and the lower growth limit has increased^{[7] [8]}.

Covid Infection Survey

The Covid-19 Infection Survey is a UK wide study carried out by the Office for National Statistics (ONS) and the University of Oxford. The survey invites private residential households to test whether they have the infection, regardless of whether they have symptoms, using a PCR test. Participants are also asked to provide a blood sample to test for antibodies. This means the study is unaffected by testing policy changes mentioned at the start of this report.

In Scotland, the percentage of people testing positive for Covid-19 in the private residential population in Scotland increased in the week to 5 February 2022. The estimated percentage of people testing positive for Covid-19 in the private residential population is 4.01% (95% credible interval: 3.60% to 4.47%)^[9], equating to around 1 in 25 people (95% credible interval: 1 in 30 to 1 in 20). This is higher than the latest peak of 2.29% recorded in the week to 11 September 2021, and higher than the previous peak of 1.24% recorded in the week to 17 July 2021.

Figure 2 shows that the COVID-19 Infection Survey daily positivity estimates for Scotland levelled off from mid to late January, and have increased in the week to 5 February 2022. By comparison, the seven-day average number of combined PCR or LFD daily reported cases has levelled off since around 18 January, with a slight overall decrease in the most recent week to 9 February.

In the week 30 January to 5 February 2022, estimates for the other nations of the UK are as follows and can be seen in Figure 2.

• In England, the percentage of people testing positive has increased in the two weeks up to 5 February 2022, but the trend is uncertain in the most recent week. The estimated percentage of people testing positive is 5.18% (95% credible interval: 5.03% to 5.34%), equating to around 1 in 19 people (95% credible interval: 1 in 20 to 1 in 19).
• In Wales, the percentage of people testing positive in private residential households decreased in the most recent week: 3.99% (95% credible interval: 3.42% to 4.60%), equating to around 1 in 25 people (95% credible interval: 1 in 30 to 1 in 20).
• In Northern Ireland, the trend in the percentage of people testing positive in private residential households continued to increase in the most recent week: 7.93% (95% credible interval: 6.91% to 9.01%), equating to around 1 in 13 people (95% credible interval: 1 in 14 to 1 in 11)^{[10] [11]}.

In Scotland, estimates for the percentage of people testing positive for COVID-19 in private residential households increased for primary school aged children and those aged 40 and over in the most recent week. The trends were uncertain for secondary school ages and young adults^[12].

Wastewater Estimates

The Scottish Government has been working with the Scottish Environment Protection Agency (SEPA) to detect and analyse fragments of Covid-19 virus RNA in wastewater. The number of locations where the levels of SARS-CoV-2 in wastewater are monitored has increased to 141 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, wastewater (WW) Covid-19 levels remained at their previous levels, with the week ending on 7 February recording levels of 52 million gene copies per person per day (Mgc/p/d), essentially the same as 53 Mgc/p/d the previous week (ending 31 January). There is some slight variability between locations, but it is not yet clear if this forms any systematic pattern^[13].

Compared to before December 2021, wastewater Covid-19 levels appear lower than anticipated given the known levels of Covid-19 activity. This effect may be due to the switchover from Delta variants to the new Omicron variant. Thus, Figure 3 shows only data from after the end of 2021, at which point the Omicron variant already represents almost all cases in Scotland. From this, we see a rapid decline from peak levels in early January with stable wastewater viral levels since late January^[14].

Covid-19 Cases

Please note that on 5 January 2022 people were advised that they no longer need to seek a confirmatory PCR test following a positive lateral flow test. This will impact the number of cases reported from 6 January 2022, and means that comparisons over time need to be made with caution. The Omicron variant represents the dominant variant in Scotland. For more information on the difference between reporting and specimen date, please see this earlier publication.

The seven-day average number of combined PCR or LFD daily reported cases has levelled off since around 18 January. By reporting date^[16], an average number of 6,718 cases confirmed by either a PCR or LFD tests^[17] were reported per day in the week leading up to 9 February. This is a slight decrease of 6% from the daily average of 7,130 cases reported in the week leading up to 2 February (Figure 4)^[18].

By specimen date^[20], the seven-day PCR case rate decreased in Scotland in the week leading up to 6 February. There were 439 weekly PCR cases per 100,000 population in the week to 06 February, which is a 3% decrease from 452 weekly cases per 100,000 on 30 January (Figure 5)^[21]. Covid-19 case data that combines PCR and LFD test results by specimen date will be available in Scotland from 10 February 2022 and will be included in next week's report.

The following age breakdowns include test results by reporting date.

Combined PCR and LFD weekly cases by reporting date (as per data from the PHS Daily Dashboard) show that as of 9 February, the highest combined PCR and LFD weekly case rates by reporting date per 100,000 were observed amongst those aged 20 to 24, followed by those aged 15 to 19, 25 to 44, and 0 to 14. The lowest case rates were seen among those aged 65 to 74, 85 and older, and 75 to 84.

When looking over time, this data shows mixed trends across different age groups. With the exception of those aged 14 or younger, weekly case rates were decreasing across all age groups in early January from high levels of Covid-19 infections in late 2021. Since mid-January, weekly case rates have levelled off among those aged 25 or older, and have remained at similar levels with minor fluctuations throughout the weeks.

Among those aged 14 or younger weekly case rates increased from mid-January, peaking on 27 January (Figure 6)^[22]. The weekly case rate for this age group has since decreased, but in the week to 9 February there has been an 18% increase in the weekly case rate for those aged 15 to 19, and a 42% increase for those aged 20 to 24 years old. However, there are early signs this increase is levelling off^[23].

The trend seen among younger age groups in the data from the PHS daily dashboard aligns with data published on the PHS Education dashboard, which provides a weekly combined PCR and LFD case rate by specimen date. The highest total combined PCR and LFD weekly case rates by specimen date among children and young people (aged under 22) in the week to 6 February 2022, were observed among those aged 18-19, 5-11, 20-21 and 12-15. These four age groups have a higher seven-day combined PCR and LFD case rate than the Scotland average in this time period.

Total combined PCR and LFD weekly case rates per 100,000 among children and young adults in the week leading up to 6 February have decreased for all age groups under 18 compared to the previous week (ending 30 January). In the same time period, the weekly case rate has increased in age groups 18 to 19 by 104%, and in the age group 20 to 21, by 91%. Case numbers in under 12 year olds are currently accounting for 53% of total cases in those under 22 years old^[25].

Due to different case definitions across the UK, comparisons between countries cannot be made at this time. As of 9 February, cases data from Scotland and Wales includes only PCR test results. Cases data from Northern Ireland includes both PCR and LFD results, and cases data from England includes PCR, LFD and LAMP (loop-mediated isothermal amplification) test results.

Additionally, from 31 January 2022, case reporting in England and Northern Ireland has changed to an episode-based definition which includes possible reinfections. Historical data on cases by specimen date from these two countries has been revised back to the beginning of the pandemic, but cases by reporting dates have not. This changing case definition has not yet been implemented for data from Scotland or Wales. Reported case numbers can be found on the UK Government Dashboard.

Due to the different case definitions outlined above, we have not included case comparisons across the four UK nations using data from the UK Government dashboard in this edition of the report. When these definitions are more aligned we will resume reporting on these comparisons. To compare estimated infection levels in private residential households across the UK, please see the previous section on the Covid-19 Infection Survey.

Testing Rates and Positivity

After a period of increase, the seven-day total of conducted PCR tests per 1,000 population peaked at 83 on 7 January 2022, and then decreased to 33 on 23 January. The seven-day total of conducted PCR tests per 1,000 has since plateaued, showing 29 tests per 1,000 people in the week leading up to 9 February.

Showing a similar trend, the proportion of positive PCR tests in the last seven days (test positivity rate) reached 29.4% on 4 January and then sharply decreased to 17.9% on 18 January. The PCR test positivity rate has since plateaued with slight fluctuations throughout the two most recent weeks, with a 17.7% PCR positivity rate on 9 February^[26]. Please note that caution must be exercised when interpreting these figures following changes to the testing policy on 5 January 2022.

After a decrease in the number of LFD tests that were reported between 27 December 2021 and 9 January 2022, there was a peak in reported LFD tests on 16 January 2022, with 810,225 reported tests^[27]. In the week leading up 30 January, the number of reported tests continued to decreased by 2% from the previous week leading up to 23 January. There were 780,869 reported tests in the week to 30 January (Figure 7)^[28].

YouGov survey results have shown that on 18-19 January, 58% of respondents had taken a LFD test and 10% a PCR test in the past week^[29]. Of those who had taken a LFD test, 47% recorded the result of their last LFD test online and 48% did not record the results online^[30].

Scottish Contact Survey asks whether people use Lateral Flow Device tests and if so how often. Approximately 74% of individuals had taken at least one lateral flow test within the last 7 days for the survey pertaining to the 27 January through 2 February, decreasing from 76% two weeks prior. Of those individuals who had taken a lateral flow within the last 7 days, 33% did not report their results ^[31].

There are differences in the results from the YouGov and the Scottish Contact Survey (SCS) which may be likely to be due to differences in sampling and methodology. YouGov is an online survey based on an active sample which is representative of the Scottish population with around 1,000 respondents^[32]. The SCS^[33] is based on a longitudinal survey with a larger sample of around 3,000, with the responses being modelled to represent the Scottish population.

Covid-19 Reinfections

In Scotland, possible reinfections are defined as a positive test 90 days or more after a previous positive test. This amount of time is set in order to be able to distinguish between viral persistence of the primary Covid-19 episode and a true reinfection. The current Covid-19 Case definition only includes the first time a person is infected, but Public Health Scotland is currently reviewing its methodologies and infrastructure to incorporate reinfection reporting routinely in late February 2022, as well as provide revised historical data on hospitalisations and deaths. See more in the PHS Weekly Report.

See last week's publication on the most recent updates on reinfections in Scotland.