10 Jun 2020

COG-UK preliminary analysis reveals the frequency and source of virus introductions into the UK

News release

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*** IMPORTANT: This ongoing research has not been peer-reviewed.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 OxfordUniversity 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.

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.