Alpha variant spread via ‘super-seeding’ event: warning over COVID-19 variants

Alpha variant spread via ‘super-seeding’ event: warning over COVID-19 variants

The COVID-19 Alpha (or Kent) variant is not 80% more transmissible, as was originally thought, according to a new study published by researchers at universities including Oxford. But, they warn, the rapid spread of the variant around the UK last year has major implications for the treatment of other variant outbreaks, because it resulted from multiple ‘exports’. It was, in fact, a major ‘super-seeding’ event, with the variant ‘exported’ numerous times from the large outbreak in the Kent/London area.

There had been biological changes to the virus, to create the Alpha variant. But results of the largest phylogeographic analysis ever conducted, show its rapid spread was caused by it being exported on multiple occasions between November 2020 and January 2021.

Published last night in the journal Science, the research maps the spread of the variant (also known as lineage B.1.1.7), showing it went from its origins in Kent and Greater London to all but five counties in Wales, Scotland, Northern Ireland and England by 19 January.

Dr Moritz Kraemer, lead author on the study and Branco Weiss Research Fellow in Oxford’s Department of Zoology, says, ‘As people travelled from London and the South East to other areas of the UK they ‘seeded’ new transmission chains of the variant. This continued as a national ‘super-seeding’ event which did not start to slow until early January. Although travel restrictions were introduced on 20 December, the exponential growth in Alpha variant cases compensated for this.’

The study shows the scale of the outbreak and mobility were the significant factors affecting its spread and early growth rates. And, according to the researchers, this highlights the need for epidemiologists to work closely with virologists and geneticists rapidly to create accurate transmissibility estimates for new variants.

Dr Kraemer says, ‘As new variants emerge, we expect they will spread significantly before travel restrictions are put in place, as likely happened with the Delta variant. Given the scale of its current outbreak, it seems probably that the UK is now an important exporter of the Delta variant across Europe and some other parts of the world.

‘The UK has decided to ease its restrictions because of our high vaccination rates and a confidence that we have protected the most vulnerable people in society. But that is not the case in most other countries and the Delta variant could be starting this process again elsewhere, highlighting the urgent need for faster and equitable distribution of vaccines worldwide.’ 

Professor Oliver Pybus, lead researcher of the Oxford Martin Programme on Pandemic Genomics, explains, ‘The Alpha variant does contain genetic changes which makes it more transmissible. It is likely the Alpha variant was 30% to 40% more transmissible than the initial strain. And the early estimates were higher because we did not know how much its growth was exacerbated by human mobility and by how many contacts different groups of people have. Crucially, as more variants emerge and spread in other countries worldwide, we must be careful to account for these phenomena when evaluating the intrinsic transmissibility of new variants.’

Verity Hill, co-author and researcher from the University of Edinburgh, expands, ‘The Alpha variant began by spreading mostly within London and the South East, even during the November lockdown in England. Once this was lifted, it spread rapidly across the country, as human movement increased significantly. Our ability to be able to trace the origins of the Alpha back to a point source in the South East of England has important implications for how new variants arise and how they will spread across the UK.’

Dr Samuel V. Scarpino, lead researcher from the Network Science Institute at Northeastern University and External Faculty at the Santa Fe Institute, highlights the importance of integrative pathogen surveillance systems, says, ‘Uncovering the mechanisms of B.1.1.7 emergence allows governments to respond more effectively and advances our scientific understanding of epidemics. The challenge now is to build similar surveillance systems globally. Equitable, ethical data systems will be critical for ending this pandemic and preventing future ones.’