Using genomic analysis to map the introduction of SARS-CoV-2 virus in the UK

The SARS-CoV-2 virus was introduced to the United Kingdom well over 1,000 times in early 2020, according to researchers who analyzed more than 50,000 viral sequences from the first wave of the COVID-19 pandemic in the UK.

The virus lineages introduced before the UK's national lockdown in March tended to be larger and more geographically dispersed. Infectious disease epidemics are composed of chains of transmission, yet little is known about how co-circulating transmission lineages vary in size, spatial distribution and persistence. Understanding these features could help target interventions, track variants with different impacts on their human hosts, and more.

The UK's COVID-19 epidemic during early 2020 was one of the world's largest. It was also well represented by virus genomic sampling, in large part because of efforts by the national COVID-19 Genomics UK (COG-UK) consortium. Through its consortium, the UK shares large volumes of virus genetic data publicly on a weekly basis. Here, researchers led by Louis du Plessis used data from this consortium and from other sources to reconstruct where and when COVID-19 was introduced to the UK during its first wave (March - June 2019).

They also used information on epidemiological factors and travel data. Before the March 23 lockdown, more than 1,000 identifiable UK transmission lineages - including all eight of the largest, longest-enduring lineages - were established and co-circulating in the UK, according to their results. Even as the largest and most widespread lineages persisted into the summer, the UK national lockdown coincided with limited importation and reduced regional lineage diversity, say du Plessis and colleagues. Their results suggest that earlier travel and quarantine interventions could have helped to reduce the acceleration and intensity of the UK's first wave of cases. They also show that highest number of transmission chains were introduced to the UK from Spain (33%), France (29%), and then Italy (12%) - with China accounting for only 0.4% of imports.

The results of the study show it's possible to use genomic tracking to trace individual virus transmission lineages accurately through time and space - an approach that could be adopted at regional, national, and international scales for future pandemics.