Published: 21 Jul 2023 | Last Updated: 21 Jul 2023 15:55:39

Researchers from the Royal Veterinary College (RVC) and the University of Oxford responsible for tracking COVID-19 Alpha and Delta variant transmission across the UK have published their genomic tracing of the Omicron variant concluding that:

• The earliest importation of Omicron into the UK was likely before the variant was identified on 15th November 2021.
• 400 transmission chains responsible for an estimated 80% of Omicron infections were imported to the UK before 15th December 2021, when travel restrictions were introduced.
• Importations of Omicron into the UK grew exponentially from mid-December 2021 as Omicron epidemics were occurring in non-‘red list’ countries.
• Emergence of new COVID-19 variants continues to pose a threat requiring continued monitoring and coordinated genome sequencing programmes worldwide.

As the UK COVID-19 Inquiry continues, researchers from the Oxford Martin Programme on Pandemic Genomics at the University of Oxford, together with the RVC’s Professor Oliver Pybus and Dr Jayna Raghwani, have published their latest paper tracing the spread of COVID-19 variants throughout England. Studying the importation and transmission of Omicron from November 2021 to January 2022 they conclude that ‘red list’ travel restrictions did not stop continued exponential growth of introductions, and call for rapid and coordinated pathogen genomic sequencing to ensure future pandemic preparedness.

Published in the journal Science, the paper uses analysis of virus genomes and human mobility data to map in detail how Omicron was introduced and spread around the UK, triggering the Government’s ‘Plan B’ response in December 2021, comprising face coverings, work-from-home guidance and the use of NHS COVID passes.

It shows a very different pattern to the Alpha variant, which was first discovered in England and transmitted across the UK and worldwide by a ‘super-seeding’ event during December 2020 as people travelled for the Christmas and New Year holiday period. It was also different from the Delta variant, which was first imported to the North West and Bedfordshire, and had its early transmission supressed by local restrictions on human movements.

By contrast, the earliest Omicron transmission chains were more evenly distributed across the country, with ~20% starting in Greater London, ~15% in the South East and ~13% in the North West. This reflects the greater number of people travelling both internationally and within England compared to earlier COVID-19 variant outbreaks.

The study also shows that the UK Government’s ‘red list’ travel restrictions and ‘Plan B’ response did little to either curb the importation of Omicron, as it was now arriving from countries not on the list, or stop its local transmission.

“This does not mean that travel restrictions cannot be useful tools to contain or delay the spread of emerging infections,” says Joseph Tsui, DPhil student at the University of Oxford.

Dr Moritz Kraemer, Associate Professor of Computational and Genomic Epidemiology and leader of the study says

"Through the detailed study of three COVID-19 variants we can see that different transmission patterns require nuanced approaches. However, in all cases it is essential to act rapidly when new variants and new pathogens are discovered.

“Genomic surveillance is an essential part of tracking infections, especially when syndromic surveillance and contact tracing becomes more limited. It must become an integral part of our pandemic preparedness efforts both in the UK and internationally.”

The study identifies an urgent need for further work to improve and inform rapid decision-making during public health emergencies, including the development of robust and fast pipelines for large-scale genomic and epidemiological analysis. Earlier work by the team revealed the rapid dispersal of variants of concern through the airline network with implications for coordinated genomic surveillance.

Professor Oliver Pybus, Vice-Principal (Research and Innovation) at the RVC and co-senior author of the paper said,

"To ensure we are better prepared for the next pandemic we need to be able to identify new pathogens and variants rapidly so that effective measures to control them can be taken. We need to design genomic surveillance systems around how people travel and interact worldwide. This is a challenging task that can be achieved only through global cooperation and coordination.”

The study also warns that although the international public health emergency has ended and the public health burden of COVID-19 has greatly lessened as a result of reduced average disease severity and increased population immunity, the continued evolution of the SARS CoV-2 virus responsible for COVID-19 means that future variants of unknown virulence remain possible.

Dr Moritz Kraemer concludes that

“with what is now a huge bank of empirical evidence on what works and what doesn’t, the timelines decisions need to be made on, and what information we need to make those decisions we hope these analyses become an integral part of governments decision making in future disease outbreaks and pandemics.”

Information for Editors

The paper, Genomic assessment of invasion dynamics of SARS-CoV-2 Omicron BA.1 is published in the journal Science and is available online at http://www.science.org/doi/10.1126/science.adg6605 from 14:00 U.S. Eastern Time Thursday, 20 July 2023 (19:00 BST).

More information about the team’s previous study tracing the Alpha variant is available at https://www.oxfordmartin.ox.ac.uk/news/alpha-variant-super-seeding-uk/

More information about the team’s previous study tracing the Delta variant is available at https://www.oxfordmartin.ox.ac.uk/news/story-of-the-uks-covid-19-delta-epidemic/

For media enquiries, please contact:

• Jasmin De Vivo devivo@plmr.co.uk or rvc@plmr.co.uk
• Press Line: 0800 368 9520

About the RVC

• The Royal Veterinary College (RVC) is the UK's largest and longest established independent veterinary school and is a Member Institution of the University of London.
• It is one of the few veterinary schools in the world that hold accreditations from the RCVS in the UK (with reciprocal recognition from the AVBC for Australasia, the VCI for Ireland and the SAVC for South Africa), the EAEVE in the EU, and the AVMA in the USA and Canada.
• The RVC is ranked as the top veterinary school in the world in the QS World University Rankings by subject, 2023.
• The RVC offers undergraduate and postgraduate programmes in veterinary medicine, veterinary nursing and biological sciences.
• The RVC is a research led institution with 88% of its research rated as internationally excellent or world class in the Research Excellence Framework 2021.
• The RVC provides animal owners and the veterinary profession with access to expert veterinary care and advice through its teaching hospitals and first opinion practices in London and Hertfordshire.

About the Oxford Martin School

• The Oxford Martin School is a world-leading research department of the University of Oxford. Its 200 academics, work across more than 30 pioneering research programmes to find solutions to the world's most urgent challenges. It supports novel and high-risk projects that often do not fit within conventional funding channels, with the belief that breaking boundaries and fostering innovative collaborations can dramatically improve the wellbeing of this and future generations. Underpinning all our research is the need to translate academic excellence into impact – from innovations in science, medicine and technology, through to providing expert advice and policy recommendations.

For More Information Contact

• Kate O’Connor, Communications and Media Manager, Oxford Martin School ·       
• kate.oconnor@oxfordmartin.ox.ac.uk
• 01865 287365