The U.K. has led the effort in sequencing SARS-CoV-2 viral genomes. Indeed, half of the more than 100,000 SARS-CoV-2 genomes shared online by October had been contributed by the U.K. This is largely due to the work of the national COVID-19 Genomics UK (COG-UK) consortium. Now, a group has studied the 50,887 SARS-CoV-2 genomes, producing an analysis of the genetic lineage structure and importation dynamics of the first wave of the COVID-19 epidemic in the U.K. The results of the study show that 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.
This work is published in Science in the paper titled, “Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the U.K.”
The U.K.’s COVID-19 epidemic during early 2020 was one of the world’s largest. Through the COG-UK consortium, the U.K. shares large volumes of virus genetic data publicly on a weekly basis. Louis du Plessis, PhD, a postdoctoral fellow in the department of zoology at the University of Oxford, and his collaborators used data from this consortium and other sources to reconstruct where and when COVID-19 was introduced to the U.K. during its first wave (March–June 2020). They also used information on epidemiological factors and travel data.
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 research found that there were more than 1,000 independent introductions of the SARS-CoV-2 virus to the United Kingdom in early 2020. However, du Plessis tweeted that they “expect this number to be an underestimate.”
The team of researchers from different regions around the U.K. found that virus lineages introduced before the U.K.’s national lockdown in March tended to be larger and more geographically dispersed.
Before the March 23 lockdown, more than 1,000 identifiable U.K. transmission lineages—including all eight of the largest, longest-enduring lineages—were established and co-circulating in the U.K., according to their results. Even as the largest and most widespread lineages persisted into the summer, the U.K. national lockdown coincided with limited importation and reduced regional lineage diversity, according to du Plessis and colleagues.
The team generated a value called an estimated importation intensity (EII) to measure the intensity of the importation of SARS-CoV-2 into the U.K. That value was highest, they found, in mid-March, prior to the national lockdown.
Their results suggest that earlier travel and quarantine interventions could have helped to reduce the acceleration and intensity of the U.K.’s first wave of cases.
Comparing the EEI (in addition to genomics data and modeling) from the U.K. to other countries in Europe, they show that the highest number of transmission chains were introduced to the U.K. from Spain (33%), France (29%), and then Italy (12%)—with China accounting for only 0.4% of imports.
Not surprisingly, the importation rate fell post-lockdown. But the authors noted that, “earlier lineages were larger, more dispersed, and harder to eliminate, highlighting the importance of rapid or pre-emptive interventions in reducing transmissions.”
The authors added that they are currently investigating the degree to which the surviving lineages contributed to the U.K.’s ongoing second epidemic, including the effect of specific mutations on lineage growth rates.