Coronavirus (COVID-19): state of the epidemic - 1 April 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 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 15 March is between 0.9 and 1.1. The lower and upper limits of the R value have both decreased since the last published figure (Figure 1)^{[3] [4]}.

UKHSA was unable to form a consensus view on the incidence of new daily infections in Scotland as at 15 March^[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 15 March was between -1% and 2%. The upper and lower growth limits have both decreased since the previous week^{[7] [8]}.

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 continued to increase. The week ending on the 29 March saw levels of around 297 million gene copies per person per day (Mgc/p/d), an increase of around a half from 200 Mgc/p/d the week ending 22 March (Figure 2)^[9].

While there are increases in wastewater Covid-19 levels across most of Scotland, three local authorities have decreased their levels over the past week. Decreases were reported in Dumfries and Galloway, Inverclyde and Perth and Kinross. Please note that comparisons for Moray, Na h-Eileanan Siar and Shetland Islands are not possible due to sampling coverage.

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. This means the study is unaffected by testing policy changes in early 2022. Participants are also asked to provide a blood sample to test for antibodies.

In Scotland, the percentage of people testing positive for Covid-19 as estimated by the Covid-19 Infection Survey increased over the most recent two weeks, but the trend is uncertain in the most recent week (20 to 26 March), as seen in Figure 3^[13]. Recent increases in estimated infection levels in Scotland have correlated with the increasing prevalence of the Omicron BA.2 variant in Scotland since early February.

The estimated percentage of people testing positive for Covid-19 in the private residential population in the week 20 to 26 March in Scotland is 8.57% (95% credible interval: 7.89% to 9.27%)^[14], equating to around 1 in 12 people (95% credible interval: 1 in 13 to 1 in 11). In the latest four weeks, the estimates of positivity have surpassed the previous peak from early January 2022.

In the week 20 to 26 March 2022^[15], estimates for the other nations of the UK are as follows and can be seen in Figure 3:

• In England, the percentage of people testing positive continued to increase: 7.56% (95% credible interval: 7.36% to 7.75%), equating to around 1 in 13 people (95% credible interval: 1 in 14 to 1 in 13).
• In Wales, the percentage of people testing positive continued to increase: 6.97% (95% credible interval: 6.24% to 7.73%), equating to around 1 in 14 people (95% credible interval: 1 in 16 to 1 in 13).
• In Northern Ireland, the trend in the percentage of people testing positive is uncertain: 6.70% (95% credible interval: 5.77% to 7.68%), equating to around 1 in 15 people (95% credible interval: 1 in 17 to 1 in 13).

In Scotland, the trend in the percentage of people testing positive was uncertain in all age groups in the most recent week^[16]. Meanwhile, the case rates (including reinfections) by specimen date show a decrease in all age groups in the week to 27 March compared to the previous week, in line with the overall decreasing trend^[17].

Omicron BA.2

The Omicron variant was first detected in Scotland on 29 November 2021^[18]. It had a growth advantage over the previously dominant Delta variant, but a lower clinical severity. The parent variant (Pango lineage B.1.1.529) can now be separated into three main groups: BA.1, BA.2 and BA.3. The BA.1 lineage of Omicron was originally dominant within Scotland, however, the first specimen date reported for BA.2 was 23 December 2021; BA.2 is now the dominant variant in Scotland and its incidence is increasing^[19]. The latest BA.2 risk assessment update issued on 23 March indicates that BA.2 has a growth advantage compared to BA.1; however, the clinical severity of BA.2 is similar to that of BA.1^[20]. The increasing prevalence of BA.2 has correlated to increasing Covid-19 prevalence in Scotland since mid-February.

According to estimates from the Covid-19 Infection Survey, the trend in the percentage of people with Covid-19 infections compatible with Omicron BA.2 in Scotland was uncertain in the most recent week to 26 March, while the percentage of people with infections compatible with the Omicron BA.1 decreased in the most recent week (Figure 4). The Covid Infection Survey estimated that 7.17% (95% credible interval: 6.54% to 7.84%) of the private residential population would test positive with a Covid-19 infection compatible with BA.2 on 23 March^[21].

Unlike Omicron BA.1, BA.2 does not contain the deletion that leads to S Gene Target Failure in a widely used PCR testing platform available at UKGov Pillar 2 Lighthouse Laboratories. This is used as a reasonable proxy to track BA.2 as opposed to BA.1. UKGov laboratories process the majority of PCR tests in Scotland. Of the new cases in Scotland that were notified on 28 March from UK Government laboratories, 95.1% were S gene positive. This is an increase from 90.1% of cases 10 days previously^[23].

Details of risk assessments for both BA.1 and BA.2 carried out by UKHSA can be found on the UK government's website^[24] and in the State of the Epidemic reports published on 4 February and 28 January 2022. For more information on vaccine effectiveness and Omicron BA.2, please see the Vaccine Effectiveness Against Omicron section.

Recently UKHSA has announced changes to their variant classification system which will take effect from 1 April 2022^[25]. In the new system, a Variant of Concern (VOC) category will be assigned to emerging or circulating variants which show a detrimental change in biological properties such as transmissibility, severity or immune evasion and growth rate potentially compatible with maintaining transmission and/or displacing the current dominant variant. New variants will receive a variant number (V-date-number) and will undergo routine assessment when sufficient number of cases will accrue. There will be no other variant categories, including no Variant Under Investigation (VUI) category. Previous variants of concern which no longer meet the criteria above will be redesignated.

Covid-19 Cases

Please note that from 5 January, the Covid-19 case definition includes cases confirmed by either a PCR or LFD test, or both. Comparisons over time need to be made with caution. For more information on the difference between reporting and specimen date, please see this earlier publication. Cases data by specimen date includes reinfections (where a person has a positive test 90 days or more since their last positive test) since the beginning of the pandemic, while cases data by reporting date includes reinfections starting from 1 March.

In previous reports there was an update on Covid-19 cases by reporting date to give readers an indication of the most recent data. However, due to the inclusion of reinfections on 1 March and technical issues experienced by PHS in the days to 15 March, cases by reporting date do not yet show a reliable trend and this analysis has therefore been excluded from the state of the epidemic report.

By specimen date, the seven-day combined PCR and LFD case rate (including reinfections) decreased in Scotland in the week leading up to 27 March. This follows a period of sharply increasing case rates from late February to mid-March. There were 1,311 weekly combined PCR and LFD cases per 100,000 population in the week to 27 March, which is a 15% decrease from 1,536 weekly cases per 100,000 on 20 March. This remains a very high case rate compared to previous phases of the pandemic in Scotland (Figure 5)^[26].

Comparisons with data from before 5 January 2022 must be made with caution as differences are likely to reflect changes in testing behaviour and policy rather than changing infection levels alone.

The week leading up to 27 March saw decreasing case rates in all age groups compared to the week ending 20 March. In the most recent week, the greatest decrease in case rates was 28% for those aged 0 to 19 year. There was a slight decrease for those aged 50 and older which ranged from 5% decrease among those aged 60 to 69, to 12% decrease among those aged 80 or older (Figure 6)^[28].

Rising numbers of weekly Covid-19 cases among care home residents throughout February and March were in line with the increasing case numbers among older age groups in the same period. In the week to 27 March, there were 593 reported cases among care home residents, which is a decrease of 25% from the previous week ending 20 March (793 cases). The number of care home cases in the most recent week is lower than previous peak of 833 weekly cases in the week to 9 January 2022 and has decreased to below the previous peak of 641 weekly cases in the week to 10 January 2021^[31].

Due to different case definitions across the UK, comparisons between countries cannot be made at this time. The four nations rely on different sets of Covid-19 tests for reporting cases. Cases data from Scotland includes PCR and LFD test results. Cases data from England includes PCR, LFD and LAMP (loop-mediated isothermal amplification) test results. For both Scotland and England, positive rapid lateral flow test results can be confirmed with PCR tests taken within 48 hours and if this PCR test result is negative, these are removed as cases. Cases data from Northern Ireland includes both PCR and LFD tests results, while cases data from Wales relies only on PCR test results. Cases from Scotland, Northern Ireland and England include reinfections based on a 90-day threshold, while cases data from Wales includes reinfections based on a 42-day threshold.

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 trends in estimated infection levels in private residential households across the UK, please see the previous section on the Covid Infection Survey.

Reinfections

A reinfection is 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 increase in the proportion of reinfections seen in late 2021 corresponds to the emergence of the Omicron BA.1 variant in the UK. The proportion of reinfections in Scotland when Omicron BA.1 was first detected on 29 November^[32] was 0.8% percent of total cases. These are cases in individuals for whom it has been 90 or more days since their last positive Covid-19 test.

The proportion of reinfections among the total weekly cases has increased in the most recent week. By specimen date, there was a total number of 7,514 reinfection cases confirmed by either a PCR or LFD test in the week leading up to 27 March. This represents 10.5% of reported cases and compares to 10.0% in the week leading up to 20 March. This is the highest level of reinfections seen in the pandemic (Figure 7).

LFD Testing

The weekly total of tests reported in the week to 27 March decreased by 21% from the previous week leading up to 20 March. There were 543,688 reported tests in the week to 27 March (Figure 8)^[34].

YouGov survey results have shown that on 15 to 16 March, 53% of respondents had taken a LFD/antigen test and 9% a PCR test in the past week^[35]. Of those who had taken a LFD/antigen test, 44% recorded the result of their last LFD/antigen test online and 54% did not record the results online^[36].

The Scottish Contact Survey asks whether people use LFD tests and if so how often. Approximately 80% of individuals had taken at least one lateral flow test within the last 7 days for the survey pertaining to the 17 March to 23 March^[37].

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^[38]. The SCS^[39] is based on a longitudinal survey with a larger sample of around 3,000, with the responses being modelled to represent the Scottish population.