Coronavirus (COVID-19) - testing strategy: update - March 2021

3. How we test

Context – A Range of Rechnologies for a Range of Purposes

Scotland's testing strategy has deliberately developed and used a range of testing technologies in complementary ways to meet the overall strategic purpose for testing of contributing to suppressing the virus to the lowest possible levels, while mitigating wider harms. Each of these technologies has inherent attributes; advantages and disadvantages which inform the most appropriate deployment under the overarching strategy. 

These varying attributes include:

• how sensitive the test is – the proportion of true positive cases identified; 
• how specific the test is – the proportion of true negative cases identified; 
• the speed of result;
• logistics required, including laboratory infrastructure and workforce;
• whether the test is designed to diagnose active infection or evidence of prior infection;
• the test's suitability for whole population surveillance and monitoring;
• the test's ability to detect new variants of COVID-19, including those which may be problematic at this stage of the pandemic due to selective advantages such as increased transmissibility, increased severity, or reduction of pre-existing immune response and/or vaccine effectiveness.

The range of technologies available has increased since the last review of the strategy in October, with rapid antigen tests (Lateral Flow Devices or LFD) now enabling larger-scale routine testing, and targeted community testing, including the provision of asymptomatic testing at community level.

PCR (Polymerase Chain Reaction) testing remains the core technology for symptomatic testing. Since the October review, there have been three main focuses of development for PCR testing: increasing laboratory capacity; improving turnaround times; and increasing population access to sampling provision. 

Also core has been balancing the relative contribution of the UK Government Testing Programme and NHS Scotland laboratories to PCR processing capacity. The remainder of this section sets out developments in capacity; access; and investments to secure a lasting legacy of improved preparedness for future health threats. 

Capacity

The October review of the Testing Strategy set out the Scottish Government aim to increase overall PCR processing capacity to 65,000 tests per day by winter 2020. This was achieved through a combination of increased capacity via the UK Government Lighthouse network, and the building of three new NHS Scotland Regional Laboratories, with a combined capacity of 22,000 tests per day.

This has meant that testing capacity has been sufficient to meet symptomatic demand over the whole of autumn and winter in Scotland. Turnaround times have also improved across all testing routes. In the most recent weeks, turnaround times have remained consistently below 24 hours across all regional test sites, Local Test Sites (walk-through sites) and Mobile Test Units. Turnaround times for NHS Scotland laboratories and Regional Hubs are also within 24 hours for the vast majority of cases.

Over the next period, our aim is to maintain this performance in turnaround times by ensuring capacity across the network can remain within a daily operational maximum limit of approximately 70%. This is to ensure our symptomatic PCR testing has the maximum possible public health impact in terms of rapidly isolating positive cases, and ensuring their contacts can be traced as quickly as possible to enable them to isolate and prevent onward transmission. 

Figures published by Public Health Scotland show the overall Test and Protect system performs well in terms of timeliness of intervention to support the public health intention of isolating potentially infectious contacts to prevent further transmission. The WHO criteria for effective performance of a contact tracing system for COVID-19 is that at least 80% of new cases have their close contacts traced and in quarantine within 72 hours of case confirmation. 

The closest proxy to this in Scotland measures the time between a confirmed positive case being entered into the Test and Protect Contact Management System and the completion of the final close contact interview, advising the contact to self-isolate. In the reporting week 01 to 07 March 2021, statistics show that 98.3% of the contact tracing for all positive cases was completed within 72 hours and 93.9% completed within 48 hours. Since its launch the Test and Protect system has consistently performed strongly in terms of timeliness, including during the sustained increase in cases during autumn and winter 2020. 

Point-of-Care testing capacity has also increased over this period, through deployment of Lumira DX and other point-of-care testing in hospital settings. NHS Scotland now has capacity of 3,000 point-of-care tests per day, which are supporting the testing of patients on admission to hospital. The faster turnaround times of point-of-care tests compared to PCR has supported better patient flow in emergency departments over the particularly pressured winter months. 

The most significant change to capacity of new technology available has been the increase across the UK in LFD capacity since the end of 2020. Significant volumes of LFD devices have been procured under the UK National Testing Programme, with all four nations now having LFD capacity sufficient to expand routine asymptomatic and targeted community testing.

Finally, Scotland has invested in newer technologies to support surveillance testing, including wastewater testing and surveillance of variants of concern through whole genome sequencing. These developments are set out in the legacy section below.

Access

Daily case numbers through the testing system are published each day on the Scottish Government website and form a key ongoing indicator of national and local incidence of COVID-19. We know, though, that not everyone with COVID-19 displays symptoms, and not all who have symptoms are tested. So the daily case numbers consistently represent a significant underestimate of the actual number of daily new infections in Scotland.

Given our overall strategic intent of suppressing the virus to as close to elimination as possible, our aim in our testing strategy is make sure population access to symptomatic PCR testing is as comprehensive and accessible as possible (an updated Equalities Impact Assessment on Test and Protect is published alongside this Strategy Update). 

In addition to national accessible provision of PCR testing for symptomatic people, we have further developed a comprehensive programme of local targeted community testing – both symptomatic and asymptomatic – where prevalence is stubbornly high, or where communities have specific transmission risks they wish to address.

Improving Access to Symptomatic Testing

Our approach to improving access to symptomatic testing is to consider the full range of sampling routes available, engage with local partners to deploy all sampling channels holistically and flexibly to best reflect population need, and innovate where necessary; for example, to extend accessibility in more remote communities through small-scale test sites in rural areas of NHS Highland in partnership with the Scottish Fire and Rescue Service. 

Our symptomatic testing expansion will increase the proportion of the population within a thirty-minute drive of testing to beyond 95% of the population. We are also supporting access to testing for those without cars and in areas of higher deprivation, and we will double the proportion of the population within walking distance of walk-through local test sites to 36% – meaning an increase from 1 million people within walking distance of a Local Test Site to 2 million people. 

Scotland currently has 34 walk-through local test sites, 8 drive-through regional test sites, 21 small-scale or pick-up test sites in NHS Highland, and 42 mobile testing units, roughly half of which are deployed to do symptomatic testing. We have also worked with the UK Government and the Royal Mail to expand home test kit coverage to all of mainland Scotland.

Targeted Community Testing

In addition to addressing key barriers to accessing testing through our expansion of symptomatic test sites, we have continued to develop a national Targeted Community Testing programme which supports both symptomatic and asymptomatic testing. We have piloted innovative ways to engage with local communities and groups such as the set-up of testing sites in local community halls and places of worship. 

Scotland piloted Community Testing in December 2020. This included both the deployment of mobile units to boost symptomatic and asymptomatic whole community testing at early signs of rising prevalence, and the operation of fully Asymptomatic Test Sites using LFDs.

During the pilot, 22,133 tests were carried out with 850 positive cases found.

Since these pilots, we have worked closely with local partners and now have developed a comprehensive programme of locally led targeted community testing, with wrap-around support for isolation built in; supported by regular ongoing intelligence and data from a variety of sources. 

This has involved the allocation of over £5 million in additional funding this financial year to NHS Ayrshire & Arran, Borders, Dumfries & Galloway, Fife, Greater Glasgow & Clyde, Grampian, Lanarkshire and Forth Valley, and the 20 local authority areas they cover. Discussions are underway with the remaining health board areas and their local authorities with the aim of agreeing community testing proposals in the coming weeks. This includes discussions with island authorities where there may be specific transmission risks that island communities would wish to address using targeted community testing. 

Targeted Community Testing is being delivered through an expanded Mobile Testing Unit fleet and the deployment of community Asymptomatic Testing Sites. As of 15 March, 27 sites were operating across Scotland.

Working in partnership with territorial health boards and local authorities to target testing through this programme has, up to 15 March, identified over 1,700 positive cases that may otherwise have been missed, breaking chains of transmission in those communities. 351 of these came from asymptomatic individuals who might otherwise have risked transmitting to transmit COVID-19 to their family, friends or colleagues. 

The ability to identify and effectively respond to community transmission will become even more important as we start to relax restrictions. Therefore, we intend to write to all territorial health boards and local authorities shortly with a view to agreeing the additional funding needed to continue this programme into 2021-22.

Surveillance Testing – adapting to the next phase and building a world-class public health legacy

Scotland already has comprehensive surveillance testing in place both at a population level through the Office for National Statistics (ONS) Coronavirus (COVID-19) Infection Survey, and in key sectors such as schools in partnership with Public Health Scotland, and healthcare settings in partnership with NHS Boards.

This surveillance testing uses PCR testing to identify current infection and antibody testing to detect evidence of prior infection, and provide estimates of the proportion of the population, or certain workforces, who may have developed some degree of natural immunity.

The ONS COVID-19 Infection Survey uses PCR testing to estimate the number and proportion of people in Scotland that would have tested positive for the COVID-19 in the community, regardless of whether they report symptoms. The study also estimates the number and proportion of people aged 16 and over who would have tested positive for COVID-19 antibodies from a blood sample, suggesting they had the infection in the past or have been vaccinated. 

The study will play a key role in monitoring antibodies in the community population in Scotland which will help to indicate the extent to which the vaccination programme is building resistance to COVID-19 as its roll-out continues. ONS is currently considering plans for widening antibody testing to monitor vaccine effectiveness, and it is likely that testing to monitor will grow in importance as we move to future phases where more of the population are vaccinated. 

Wastewater Testing

Wastewater testing offers the potential to monitor prevalence and detect outbreaks of SARS-CoV-2. The Scottish Environment Protection Agency (SEPA), working in conjunction with Scottish Water and Public Health Scotland, has formed a monitoring network across Scotland for the purpose of analysing wastewater samples to determine the level of COVID-19 infection markers present. As of 2 February 2021, the monitoring network encompasses 70 sites covering 3.5 million people. Samples from these locations are tested at least weekly, which can be increased when local outbreaks are apparent.

Further to Scottish Government funding of £1.1 million in December 2020, SEPA has significantly expanded its lab capacity to support the programme with capacity now for 200 samples per week. This has allowed for the continuation of national monitoring at wastewater treatment works, and has also enabled wastewater sampling to begin at local sites within the Scottish Water network. This data is contributing to our knowledge of prevalence across Scotland, thereby aiding the direction of Community Testing resources, with national mobile resources able to be deployed where there is evidence that prevalence is rising.

The wastewater monitoring approach is a reliable indicator of low viral prevalence and a good early or lead indicator or signal of virus detection. It provides a complementary, unbiased data stream to prevalence detected from human testing, and is flexible in scale, with it possible, for example, to sample an entire city or just one building. 

Importantly for the challenges likely to be posed in the next phases of the pandemic in Scotland, it is also possible to detect viral mutations by sequencing wastewater samples. 

Wastewater testing can also be used to monitor other viruses and markers of public health, and so represents a significant post-COVID legacy benefit. These broader and longer-term use cases could include the monitoring of other viruses, such as influenza, rotavirus, norovirus, enterovirus, and the monitoring of antibiotic-resistance in bacterial pathogens. To this end, we are investing £2.3 million in the further development of Scotland's wastewater testing capability in 2021‑22.

Whole Genome Sequencing 

The next phases of the pandemic in Scotland will have two critical challenges – effectively and promptly stopping outbreaks before they build to sustained community transmission, and managing the risk of new strains of the virus emerging either from imports of from mutations occurring within Scotland. These risk our considerable progress in reducing prevalence levels. 

Whole genome sequencing is critical to all of these challenges. In outbreak management, sequencing can support analysis of whether an outbreak has its roots in single or multiple introductions. In managing import risk, sequencing of all positive cases found in our quarantine testing is supporting the detection of new variants of concern. Similarly, moving towards sequencing all identified positive cases within Scotland will allow detection of 'home-grown' mutations.

The increase in sequencing capacity will be complemented by the development of allele‑specific PCR tests. These are high throughput tests which can be used for rapid screening of known mutations within a variant of concern, which will facilitate early public health assessment and more rapid interventions to minimise spread in the community. Optimal service delivery options are currently being evaluated. 

While this allele-specific PCR testing is suitable for rapid follow-up PCR testing for known variants of concern (once developed), it is not capable of detecting yet to be identified mutations or new variants of concern VOCs. Therefore for comprehensive surveillance to detect the emergence of VOC, both allele-specific PCR testing and Whole Genome Sequencing will be required. 

Building on the experience and expertise of our world-class scientists, we expect to invest a further £13 million in 2021-22 to build a Whole Genome Sequencing Service for Scotland. This will both support our ability to maintain progress in the coming months – by better managing outbreaks and detecting imported variants of concern – and build a legacy of a genuine world-class public health system, better prepared in the event of any future pandemic. It will be capable of sequencing up to a thousand cases per day when fully built, and support not just protecting our progress against COVID, but our resilience to a range of threats, including antibiotic resistance. Our ambition is to be able to sequence all positive cases found in Scotland; and to build a legacy that can contribute globally as well as in Scotland. 

KEY:

• PCR – Polymerase Chain Reaction Testing
• LFD – Lateral Flow Device
• ePCR – endpoint PCR testing
• Point-of-Care testing – near-patient test
• Allele-Specific PCR – amplifies specific genetic variants – can be used to detect VoC