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

11 August 2022

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A team of researchers led by Oxford and Edinburgh have today revealed how the Delta variant of COVID-19 became the dominant variant across the UK in 2021.

In a paper in the journal Nature, the international team 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.

90% of introductions from India were before the country was added to the ‘Red List’

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.

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

Dr Verity Hill, co-lead on the paper and researcher at the University of Edinburgh Institute of Evolutionary Biology, 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.”

We found that many of the cases in the Delta wave were due to transmission chains which were introduced before travel restrictions were enacted, and that relaxing movement restrictions within England was more important for increased case growth than additional international introductions. While this study was conducted on the Delta variant and using UK-specific data, we are optimistic that it provides evidence for designing successful and balanced packages of control measures for other variants and other countries.”

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.

Dr JT McCrone, co-lead on the paper and researcher at the University of Edinburgh Institute of Evolutionary Biology, says “Multiple imports followed by local spread is now an established model for the spread of COVID-19 variants. But the most exciting thing about this work is how the team combined insights from a collection of different datasets to get a very detailed picture of how international restrictions and local factors influenced the Delta wave in the UK. We were able to use the huge UK sequencing effort to show that travel restrictions work, and at the same time highlight how ineffective they are if implemented too late and not supported by local public health measures.”

People under the age of 30 were ineligible for vaccines until 26th May

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.

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.

Dr Moritz Kraemer, author and director of the Oxford Martin Programme on Pandemic Genomics, 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.”