SARS-CoV-2 Introduced Into UK More Than 1,000 Times Early in Pandemic, Study Finds

NEW YORK – SARS-CoV-2 was introduced into the UK more than a thousand times at the start of the COVID-19 pandemic, according to a new analysis.

By analyzing more than 50,000 SARS-CoV-2 genomes, about half of which were collected in the UK, in conjunction with travel and epidemiological data, a University of Oxford-led team of researchers examined the origins and spread of SARS-CoV-2 in the UK. The initial wave of the pandemic peaked there in April 2020, and by late June nearly 40,500 COVID-19-related deaths were reported in the UK. 

As they reported on Friday in Science, the researchers found that more than 1,000 viral lineages were imported into the UK before June 2020, mostly from Italy, France, and Spain, and began to circulate. But the national lockdown implemented March 23 then limited the further importation of the virus and reduced the diversity of lineages still in the UK.

"The transmission structure and dynamics measured here provide a new context in which future public health actions at regional, national, and international scales should be planned and evaluated," Oliver Pybus, a professor of evolution and infectious disease at Oxford, and his colleagues wrote in their paper.

Through its national COVID-19 Genomics UK (COG-UK) consortium, the UK has generated thousands of SARS-CoV-2 genome sequences, which Pybus and his colleagues analyzed in conjunction with viral genomes from other sources. In all, they analyzed 50,887 SARS-CoV-2 genomes, 26,181 of which were from the UK and collected before June 26, 2020. The UK samples represent 9.29 percent of the confirmed UK COVID-19 cases by that time.

Using a large-scale molecular clock phylogenetic pipeline they developed, the researchers identified 1,179 viral lineages that took hold in the UK from outside the country. Because of how the samples were collected, the researchers noted that this number is likely an underestimate. Additionally, by combining their phylogenetic data with epidemiological and travel data, the researchers teased out the origins of the viral lineages, estimating that about a third of UK transmission lineages originated from Spain, 29 percent from France, and 12 percent from Italy.  

Similarly, a team led by MRC-University of Glasgow Centre for Virus Research reported last month there were hundreds of introductions of SARS-CoV-2 into Scotland from continental Europe early in the pandemic, and community spread was already occurring by the time viral control measures were put into place. 

This new UK-wide analysis likewise noted that the lineages they identified were established and circulating prior to the national lockdown. The lockdown, however, affected the diversity and importation of SARS-CoV-2 lineages. 

Prior to the lockdown, most of the transmission lineages were small and included fewer than 10 genomes, but the eight largest lineages included more than a quarter of the sampled genomes. These larger lineages also tended to be more geographically widespread.

Additionally, some regions of the UK tended to have higher levels of viral genetic diversity. For instance, the Greater London area, as well as Hertfordshire and Essex, had high levels of viral diversity, which the researchers attributed to commuter travel to and from London and the nearness of international airports.

But, following the national lockdown, the number of imported lineages fell, as did the diversity of lineages in the UK, and some smaller lineages may have been eliminated. The large lineages persisted longer than the others, with some potentially circulating through the summer.

The researchers noted that the extent to which the surviving lineages are contributing to the ongoing COVID-19 wave in the UK is unclear but is under investigation.