Oxford researchers 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.
Researchers from the Oxford Martin Programme on Pandemic Genomics 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 the continued exponential growth of introductions. They also call for rapid and coordinated pathogen genomic sequencing to ensure future pandemic preparedness and warn that the emergence of new COVID-19 variants continues to pose a threat requiring continued monitoring.
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.
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.
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, with the earliest importation into the UK likely occurring before the variant was even identified on 15th November 2021.
Around 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. The number and distribution of these chains 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 did little to curb the rate of importations of Omicron, as it was now arriving from countries not on the list, and despite ‘Plan B’ restrictions Omicron spread rapidly throughout England.
“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.
Genomic surveillance is an essential part of tracking infections
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, Professor of Evolution and Infectious Disease at Oxford University 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.”