Genomics traces COVID-19 transmission chains in the UK

18 January 2021

Genomic epidemiological analysis of the initial UK COVID-19 outbreak has allowed a team of researchers to accurately characterise the early chains of transmission throughout the country.

A collaboration between the Universities of Oxford and Edinburgh has produced the most extensive genomic analysis of any known epidemic by studying over 50,000 SARS-CoV-2 genomes. This genomic data, the majority of which was sourced from the COVID-19 Genomics UK consortium, was used in conjunction with travel data to retrospectively trace and map individual virus transmission lineages from the first wave.

‘By reconstructing where and when COVID-19 was introduced to the UK we can see that earlier travel and quarantine interventions could have helped to reduce the acceleration and intensity of the UK’s first wave of cases’ said lead author Professor Oliver Pybus, from the University of Oxford’s Department of Zoology.

The full study, published in Science, revealed that the virus was imported into the UK over 1000 times prior to the March 2020 lockdown. Results also showed that the origin and rate of introduction evolved rapidly over time. During the early months of last year, the highest sources of importation were from Spain (33 percent), France (29 percent), and Italy (12 percent). Only 0.4 percent of such cases were imported directly from China.

It appears that more than 1000 identifiable transmission lineages were already established and co-circulating in the UK prior to the first lockdown, including the eight most wide-spread and persistent lineages. While the introduction of the national lockdown coincided with a reduction in new lineage importation, extinction of lineages was only seen in areas of low prevalence. Earlier lineages, which were larger and more widely dispersed, survived national restrictions and continued to persist once measures were eased.

The research team, which contributed to the identification of the rapidly spreading ‘new variant’ B.1.1.7, is currently investigating the extent to which earlier persistent lineages are contributing to the more recent waves of COVID-19. This genomic surveillance of the ongoing epidemic provides crucial information to guide future public health actions.

‘This kind of continuous, nationally coordinated genomic sequencing not only allows the high-resolution analysis we present, but also helps other countries to place their genomic data into context and assists the global pandemic response,’ said co-author Verity Hill from the University of Edinburgh.

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