Coronavirus (COVID-19): state of the epidemic - 18 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 01 February is between 0.8 and 1.0. The lower limit and upper limit of the R value have remained unchanged since the last published figure (Figure 1) ^{[2] [3]}.

As at 1 February 2022, the UKHSA's consensus view was that the incidence of new daily infections in Scotland was between 204 and 377 per 100,000 people. This equates to between 11,200 and 20,600 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 1 February was between -3% and 1%. The upper and lower limits have increased since the previous week^{[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 increased in the two weeks up to 13 February 2022, but the trend was (statistically) uncertain in the most recent week. The estimated percentage of people testing positive for Covid-19 in the private residential population is 4.17% (95% credible interval: 3.69% to 4.64%)^[9], equating to around 1 in 25 people (95% credible interval: 1 in 25 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 the Covid-19 Infection Survey daily positivity estimates for Scotland fluctuating in recent weeks, and showing early signs of levelling off in the most recent week. By comparison, the Scotland weekly case rate by specimen date has levelled off since around 18 January, with a slight decrease in the latest two weeks.

In the week 6 to 12 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 for Covid-19 decreased in the most recent week: 4.49% (95% credible interval: 4.34% to 4.64%), equating to around 1 in 20 people (95% credible interval: 1 in 25 to 1 in 20).
• In Wales, the percentage of people testing positive for Covid-19 continued to decrease in the most recent week: 3.71% (95% credible interval: 3.19% to 4.27%), equating to around 1 in 25 people (95% credible interval: 1 in 30 to 1 in 25).
• In Northern Ireland, the percentage of people testing positive for Covid-19 increased in the two weeks up to 12 February 2022, but the trend was uncertain in the most recent week; the estimated percentage of people testing positive is 7.99% (95% credible interval: 7.05% to 8.98%), equating to around 1 in 13 people (95% credible interval: 1 in 14 to 1 in 11)^{[10] [11]}.

In Scotland, the trend over time for the estimated percentage of people testing positive for Covid-19 in private residential households were uncertain for all age groups in the most recent week due to wide confidence intervals. Meanwhile, weekly PCR or LFD case rates by specimen date across Scotland continue to see a slight decrease with some difference between age groups^[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 Covid-19 levels have shown an upturn, with the week ending on 14 February recording levels of 88 million gene copies per person per day (Mgc/p/d), up from 51 Mgc/p/d the previous week (ending 7 February). This moderate increase in wastewater viral levels is observed across many of the local authorities in Scotland^[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, and their shedding properties. 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 5 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.

By reporting date^[16], an average number of 6,270 cases confirmed by either PCR only, LFD only or both PCR and LFD tests were reported per day in the week leading up to 16 February. The seven-day average number of daily reported cases levelled off between mid to late January, and has been slightly decreasing since. In the most recent week there continued to be a slight decrease of 7% from the daily average of 6,744 cases reported in the week leading up to 9 February (Figure 4)^[17].

For comparisons over time it is more reliable to look at case rates by specimen date^[19]. Up until 5 January, case rates by specimen date were only identifiable for cases confirmed by a PCR test, but following the change in testing policy, case rates by specimen date are now available for cases confirmed either by PCR or LFD test. Comparisons over this time period must be made with caution, as changes might reflect changes in testing behaviour rather than changing infection levels.

Following a sharp drop in the weekly rate of PCR or LFD confirmed Covid-19 cases after the testing policy change on 5 January, the rate of decrease has slowed since mid-January. By specimen date, the seven-day combined PCR and LFD case rate continued to decrease in Scotland in the week leading up to 12 February. There were 794 weekly combined PCR and LFD cases per 100,000 population in the week to 12 February, which is a slight 4% decrease from 828 weekly cases per 100,000 on 5 February and a 9% decrease from 871 weekly cases on 15 January (Figure 5)^[20]. This remains a high case rate compared to previous phases of the pandemic in Scotland.

As at 12 February, the highest combined PCR and LFD weekly case rates by specimen date per 100,000 were seen among those aged 20 to 39, at 1,118 weekly cases per 100,000, followed by those aged 40 to 49, 19 and younger, and 50 to 59. The lowest case rates were seen among those aged 60 to 69, 70 to 79, and 80 or older. All age groups for people younger than 50 years old had a higher weekly case rate per 100,000 than the Scottish average in this week.

There are some differences in the trend of weekly case rates over time between age groups. With the exception of those aged 19 or younger, weekly case rates were decreasing across all age groups in early January. In mid-January weekly case rates levelled off among those aged 20 or older, but in the most recent week leading up to 12 February there has been a slight increase in case rates for all age groups aged 50 or over compared to the week leading up to 5 February.

Among those aged 19 or younger, weekly PCR or LFD case rates by specimen date increased from mid-January, peaking on 26 January with 1,620 weekly cases per 100,000 (Figure 6)^[22]. The overall weekly case rate for those aged 19 or younger has since decreased to 886 per 100,000 in the week to 12 February. The weekly case rates decreased for all age bands younger than 20, apart from 16 to 17 where it remained similar to the previous week ^[23].

For those aged 19 or younger, the highest combined PCR and LFD weekly case rates by specimen date per 100,000, as of 12 February, were observed amongst those aged 18 to 19, followed by those aged 5 to 11, 12 to 13, and 16 to 17. The lowest weekly case rates were seen among those aged 14 to 15, 2 to 4, and 1 or younger.

Due to different case definitions across the UK, comparisons between countries cannot be made at this time. Cases data from Scotland and Northern Ireland includes both PCR and LFD test results. Cases data from Wales includes both PCR only 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, with 28 tests per 1,000 people in the week leading up to 16 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 fluctuated between 17.2% and 18% in the two weeks to 9 February, and has increased to a 18.8% PCR positivity rate in the week to 16 February^[25]. 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^[26]. The weekly total of tests reported in the week to 13 February decreased by 5% from the previous week leading up to 6 February. There were 714,319 reported tests in the week to 13 February (Figure 7)^[27].

YouGov survey results have shown that on 15 to 16 February, 52% of respondents had taken a LFD/antigen test and 9% a PCR test in the past week^[28]. Of those who had taken a LFD/antigen test, 45% recorded the result of their last LFD/antigen test online and 50% did not record the results online^[29].

Scottish Contact Survey asks whether people use Lateral Flow Device tests and if so how often. Approximately 76% of individuals had taken at least one lateral flow test within the last 7 days for the survey pertaining to the 3 February - 9 February, decreasing from 78% two weeks prior ^[30].

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^[31]. The SCS^[32] 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 previous publications on the most recent updates on reinfections in Scotland.