9 Dec 2020

Genomic analysis of epidemic waves of COVID-19 in Scotland and Wales


Two new reports submitted to the Scientific Advisory Group for Emergencies (SAGE) by members of the COG-UK Consortium that address the same question in different countries — what effect did the lockdown have on the SARS-CoV-2 lineages introduced into and then transmitted within Scotland and Wales since the start of the pandemic?

The two reports are available for download here: Scotland and Wales.

These reports provide a forensic level of detail on the movement of the virus over time, which can be plotted against the interventions that were used, including travel restrictions and lockdown.

This type of analysis relies on detecting mutations that are continually arising in the genome of the virus over time, as a result of ‘mistakes’ that are introduced into the genetic code and the action of anti-viral molecules. This results in a virus having a genetic sequence that can be likened to a barcode. SARS-CoV-2 variants with similar barcodes that are all descended from a unique introduction of SARS-CoV-2 to the UK are referred to as UK lineages and given numbers.

What is obvious on reading the two reports is the similarity in findings between the two countries. They tell a tale of repeated introductions of the virus confirming earlier COG-UK analyses (Filipe et al., 2020Plessis et al. 2020), after which some of the viruses undergo very extensive spread through the population. It is important to note that the viruses that were sequenced represent around a quarter of all diagnosed cases, and so the data generated is an under-representation.

In Scotland, the analysis confirmed about 300 independent introductions of the virus into the country, defined based on new lineages being seen for the first time. This under-calls introductions since the same ‘new’ lineage could be introduced many times, but this is only counted the first time it is detected. Only around a quarter of these ‘new’ lineages appeared to become established (defined as being detected more than five times). This is likely to relate to the opportunity for some lineages to maintain R0>1, e.g., linked to spread through superspreading events, when large numbers of people become infected during a single event.

A striking observation was that following the first lockdown, the majority of virus lineages that had been circulating in the population in Scotland appeared to become extinguished. Very few lineages persisted over the summer. This supports the idea that it is possible to eradicate the virus from a country when stringent public health measures are in place. What was then observed going into the second wave is that disease was caused by new lineages that has been introduced into the country, many of which could be traced to introductions from countries outside of the UK. Summer holidays and other travel abroad taken at a time when disease was under control in Scotland, but less so elsewhere, has had a predictable outcome.

In Wales, the analysis identified that the current population of circulating SARS-CoV-2 is also different to the lineages that were present in March and April 2020. Early on in the pandemic, a high proportion of cases could be linked to imports into Wales, with a drop in both the number of extant lineages and new introductions following the first lockdown. Like Scotland, Wales observed that the majority of lineages circulating in Wales appeared to become extinguished following the package of measures introduced in Wales as part of the first lockdown.

Wales also observed that after the easing of the first lockdown, the rise in cases forming the start of the second wave was driven by imports — from other parts of the UK and the wider world. The Welsh analysis also examined transmission on a more local level, identifying that cases in areas of high population density (cities) were more likely to result from local chains of transmission, whereas those in less urban areas were more likely to be associated with imports from elsewhere and rarely led to local onward transmission.

So, what can we conclude? Perhaps the obvious. The pandemic in Scotland and Wales has been driven by importations. This provides indisputable evidence for the importance of border controls, including effective screening and isolation policies. Once introduced, spread is driven by travel, and then onward spread by population density. Genomics data permits us to quantify the number of these introductions and better understand spread from one geographical region to another, providing invaluable information that can help shape policy and practice.



COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by the SARS-CoV-2, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.

COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation.

COVID-19 Genomics UK (COG-UK)

The COVID-19 Genomics UK (COG-UK) consortium works in partnership to harness the power of SARS-CoV-2 genomics in the fight against COVID-19.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative collaboration of NHS organisations, the four public health agencies of the UK, the Wellcome Sanger Institute and sixteen academic partners. A full list of collaborators can be found here.

The COVID-19 pandemic, caused by SARS-CoV-2, represents a major threat to health. The COG-UK consortium was formed in March 2020 to deliver SARS-CoV-2 genome sequencing and analysis to inform public health policy and to support the establishment of a national pathogen sequencing service, with sequence data now predominantly generated by the Wellcome Sanger Institute and the Public Health Agencies.

SARS-CoV-2 genome sequencing and analysis plays a key role in the COVID-19 public health response by enabling the identification, tracking and analysis of variants of concern, and by informing the design of vaccines and therapeutics. COG-UK works collaboratively to deliver world-class research on pathogen sequencing and analysis, maximise the value of genomic data by ensuring fair access and data linkage, and provide a training programme to enable equity in global sequencing.