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The evolution of SARS-CoV-2 in the UK

The COVID-19 pandemic has constantly produced new variants, since SARS-CoV-2 adapts to humans by accumulating around 24 mutations per year. The first dominant mutation was D416G, which rendered this variant 20% more transmissible than the Wuhan ancestral strain. The B.1 lineage thus became established and spread rapidly throughout the world in April-May 2020. Since then, new strains have emerged, including the Alpha (UK), Beta (South African), Gamma (Brazilian) and Delta (Indian) variants.

So as to better understand their role in the pandemic’s course, UK and German scientists (at the European Bioinformatics Institute and Wellcome Sanger Institute, Hinxton and the German Cancer Research Centre, Heibelberg) evaluated the rates of growth and the geographical propagation of different variants in the UK. The study was based on genome data referenced by the COG-UK consortium between September 2020 and June 2021, which included 3 waves of the epidemic and 2 lockdowns. Researchers modelled the propagation dynamics of 71 lineages (amongst 281 178 genomes) in 315 regions with between 100 and 200 000 inhabitants.

The results show that a large diversity of lineages was in circulation up to November 2020, when the incidence of COVID-19 cases reached a second peak in the UK, causing a second lockdown. At the beginning of this wave, the B.1 lineage and its sub-lineage B.1.1 were predominant. But between September and October 2020, they were rapidly displaced by B.1.177, which had a higher rate of growth. The second lockdown (at the beginning of November) had led to a reduction in the overall number of cases and thereby hastened the disappearance of several lineages in all regions, to the advantage of Alpha/B.1.1.7 (UK) which continued to circulate.

During lockdown, the incidence of Alpha exploded, despite restrictive measures applied regionally, generating a third wave of the epidemic (December 2020 – February 2021). It is 1,5 times more infectious than B.1.1. By April, only 22 different lineages remained (the peak had been 137). Then new strains were introduced by foreign travel and, from May 2021, the Beta and Gamma variants replaced Alpha little by little. However, Beta and Gamma seemed to spread in a different way, since they appeared in several places at the same time, with a lower growth rate than Alpha. Introduced in March 2021, the Delta or Indian variant became dominant by the end of June with a growth rate of 58%. It had greater transmissibility and more capacity to escape immune responses, but did not carry the N501Y and E484K mutations like Alpha, Beta and Gamma.

The arrival of these variants increased the overall rate of growth of SARS-CoV-2 by a factor of 2,4 over the 10 months of the study. Restrictive sanitary measures, which had been effective against the first strains, now showed their limits. Due to a lack of genomic monitoring in India in 2020, the transmissibility of Delta had not been anticipated. 

This study shows that when a strain is dominant, insufficient surveillance conceals the emergence of new variants. We need to urgently model the effects of immunity on the dynamics of SARS-CoV-2 progression, since when it becomes endemic and herd immunity is attained, it is very possible that new variants with escape potential will emerge. It is therefore indispensable to fund constant, effective and global genomic monitoring so as to be prepared for this eventuality.

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