Story of the UK’s COVID-19 Delta variant epidemic revealed by genome tracing

In a paper in the journal Nature, the international team - co-led by Moritz Kraemer and Oliver Pybus from the Department of Biology - used extensive data across virus genomics, human mobility and contact tracing to show how Delta expanded out of India, and how relaxing social restrictions in the UK facilitated its spread.

The study describes in detail the rise of the Delta variant in March 2021, including several sub-lineages, which drove a rising number of overall COVID-19 cases across India. The variant was then imported into the UK a minimum of 1,458 times, with around 90% of those introductions from India happening before the country was added to the UK’s travel ‘Red List’ on 23rd April.

Dr Verity Hill, co-lead on the paper, researcher at the University of Edinburgh Institute of Evolutionary Biology, and Department of Biology alumnus (2013 - 16) says:

“We have been able to use the extensive virus genomic dataset collected by COG-UK and scientists around the globe to explore the impact of international travel restrictions, hotel quarantine and local movement restrictions on variant spread.”

At the same time, the UK was gradually removing its social restrictions, with mobility increasing to 70% of pre-pandemic levels by June 2021, up from 20% in January that year. In contrast to the spread of the previous COVID-19 variant Alpha across the UK, London played a lesser role in the emergence of Delta with transmission clusters expanding from Bedfordshire and urban areas across the North West. The majority of UK Delta cases belong to a single transmission chain sampled mostly in Greater Manchester and Lancashire.

Sumali Bajaj, co-lead author of the paper from the University of Oxford’s Department of Biology, notes that:


“After testing for various factors, relaxing social restrictions after 21st May in England increased the spread of the virus, particularly among young people and unvaccinated populations. There was a high crossover between those two groups, with people under the age of 30 ineligible for vaccines until 26th May."


A group of people smile and cheers glasses of beer. All are lowering their face masks

By June 2021, the UK was one of the four main exporters of the Delta variant alongside the USA, Russia, and Mexico.

Genomic testing was performed on around 40 to 60% of all positive COVID-19 tests in England between March and May 2021, enabling a detailed understanding of the rise of Delta and its transmission across the country. Although data from Scotland, Wales and Northern Ireland was not included, case count data suggests England was the main source of the UK’s Delta epidemic.

The study found that once travel restrictions were introduced they were effective at reducing the onward transmission of imported Delta variant cases from India, but community transmission and importations from other countries not on the ‘Red List’ were already occurring. As a result, Delta became the dominant variant in the UK by mid-May, responsible for more than 90% of COVID-19 cases in that summer’s spike.

Dr Moritz Kraemer, author and director of the Oxford Martin Programme on Pandemic Genomics and Associate Professor of Computational and Genomic Epidemiology, says:

“The results of this study tell us a lot about what non-pharmaceutical measures to control disease spread can and can’t do because Delta’s import to and transmission within the UK occurred across periods of open and restricted international travel from the main import location, and through different stages of social restrictions easing. We also see the beginnings of the impact of the vaccine rollout.

"By understanding how the Delta epidemic played out we hope public health officials and policymakers can better respond to future COVID-19 variants, communicable disease outbreaks and pandemics.”

To read more about this research, published in Nature, please visit: