COG-UK preliminary analysis reveals the frequency and source of virus introductions into the UK
*** IMPORTANT: This ongoing research has not been peer-reviewed. ***
The latest analysis of the COVID-19 epidemic in the UK combines large-scale data and genomic sequencing to provide a detailed picture of the number and sources of SARS-CoV-2 introductions into the UK. The study by researchers at the University of Oxford, University of Edinburgh, and the COVID-19 Genomics UK Consortium (COG-UK), shows how and when the SARS-CoV-2 virus entered the UK, mostly from European countries during March. The rate of virus importation peaked around 15 March.
The study found that the UK epidemic was composed of a very large number transmission lineages. Each lineage was founded by a separate introduction event from inbound international travel, then grew through local transmission within the UK. The study detected 1356 independent transmission lineages, based on analysis of genome and travel data up to 22 May 2020. However, this is likely to be an underestimate of the actual number of virus introduction events that have resulted in onwards transmission, because we have generated virus genome sequences for only a small fraction of UK infections.
An estimate of the daily intensity of SARS-CoV-2 importation into the UK indicated that importation intensity to the UK rose rapidly in early March, peaked around 15th March, then quickly declined to a low level in April. This pattern is driven by the interplay between two trends throughout March: a substantial fall in the number of inbound travellers and a rapid growth in the number of infections in many European countries.
The study found that early importations from Italy were, by early March, surpassed in number by importations from inbound travellers from Spain and France. The diversity of source locations also increased in March, with importations attributed to a growing range of countries. The contribution of China and other Asian countries to the number of importations was very small.
Many UK transmission chains are no longer detected by genome sequencing and have likely been extinguished. In early March the epidemic mostly comprised chains that had been newly detected for the first time, whilst by late April most transmission chains had not been detected by genomic sampling for more than a week. This trend reflects the declining number of SARS-CoV-2 cases in the UK during April.
The report constitutes preliminary descriptive findings and has not been peer-reviewed. Work on these data is ongoing and findings may therefore change in the future. The analysis does not attempt to model or evaluate the effectiveness of public health interventions or travel restrictions.
“Due to our ability to track the genomes of the SARS-CoV-2 virus through the sequencing by the COG-UK consortium, we can now link that with other forms of data to truly understand how the pandemic moves through a country or region. This is a powerful tool that in future could be used to accurately inform public health policy on appropriate steps to take to limit the flow of such a virus and protect people.”
Dr Ewan Harrison, COG-UK and fellow at the Wellcome Sanger Institute
The COVID-19 Genomics UK Consortium (COG-UK) – comprised of the NHS, Public Health Agencies and numerous academic and research institutions – is delivering large scale, rapid sequencing of the SARS-CoV-2 virus from positive COVID-19 samples and sharing intelligence with hospitals, regional NHS centres and the Government.
“The COG-UK consortium has now sequenced more than 24,000 genomes. This is providing the foundation for a better understanding of this outbreak. It also helps us shape our future response, including the development of systems to predict the introduction of SARS-CoV-2 into the UK. This could inform policy decisions on travel, and may provide valuable information to other countries through international collaboration.”
Professor Sharon Peacock, Director of the COVID-19 Genomics UK Consortium (COG-UK)
Wellcome Sanger Institute/COG-UK
Cambridge, CB10 1SA
Phone: 01223 496851
Phone: 01865 287365
Notes to Editors:
It is important not to conflate “number of introductions to UK” with “number of infections in UK”. Almost all cases in the UK were the result of transmission that occurred within the UK. Further, transmission lineages vary in size, therefore it is not wrong to extrapolate “X% of lineages were imported from country Y” to “X% of UK cases resulted from importation from country Y”.
“Preliminary analysis of SARS-CoV-2 importation & establishment of UK transmission chains”. Pybus, Rambaut et al. https://virological.org/t/preliminary-analysis-of-sars-cov-2-importation-establishment-of-uk-transmission-lineages/507
COG-UK is 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.
The current COVID-19 pandemic, caused by the SARS-CoV-2 virus, 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.
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 over twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here: https://www.cogconsortium.uk/about/
COG-UK is 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. For more information, visit: https://www.cogconsortium.uk
COG-UK researchers make highly cited list
Eight COG-UK Consortium members and associates have been recognised by Clarivate as some of the most highly cited researchers of 2020.
COVID-19 in care homes — what have we learned from genome sequencing?
Read COG-UK partner Quadram Institute’s explainer blog on the latest findings of how the SARS-CoV-2 virus spreads within care homes.
The value of large-scale coordinated sequencing activities to understand a pandemic in real-time
In recent work from COG-UK consortium investigators, Erik Volz and colleagues investigated the D614G mutation in the population by using more than 25,000 viral genomes that have been sequenced in the UK over a period between February and June 2020 in order to understand the pandemic in real-time.