SARS-CoV-2 B.1.1.7 lineage

Summary of evidence from the U.K.

This document has been prepared by the European Molecular Biology Laboratory to provide a summary of epidemiological information for public health officials and governments. The lead author is Dr Moritz Gerstung, of EMBL’s European Bioinformatics Institute (EMBL-EBI) at the Wellcome Genome Campus in the United Kingdom. Other contributors include Deputy Director General and EMBL-EBI Director Dr Ewan Birney FRS and EMBL-EBI Director Dr Rolf Apweiler.

The B.1.1.7 lineage was first discovered on September 20 in Kent by the U.K.’s Coronavirus Genome consortium COG-UK, which has sequenced more than 170,000 SARS-CoV-2 genomes [1,2]. It has since spread to nearly every British local authority and 57 other countries [3]. While B.1.1.7 is not evidently causing more severe disease [4], it is approximately 30-50% more transmissible as evidenced by epidemiology [5,6] and contact tracing [7]. This higher transmissibility has led to a massive surge in cases in England, which has pushed the health care system to its limits and led to declaration of a third national strict lockdown [8] on January 4, 2021.

The availability of detailed genomic surveillance information enabled reconstruction of B.1.1.7’s spread in great detail. Of particular concern is its capability to proliferate (R>1) in nearly every English local authority during the second national lockdown from November 5 to December 2 throughout which B.1.1.7 cases increased three- to fourfold – even though mostly at low absolute numbers at the time and so not affecting the aggregate case levels [9]. It is important to note that the UK November lockdown did lead to suppression of other SARS-CoV-2 lineages (R9]. Following the end of the lockdown, the pattern of faster proliferation was sustained throughout December, leading to a tenfold increase in B.1.1.7 cases in London, while other SARS-CoV-2 cases only grew 40% as observed in population testing data from the Office of National Statistics [10].

While cases of B.1.1.7 exported to other countries will initially be in single numbers, B.1.1.7 cases can double weekly, as evidenced recently in Denmark, which does genomic surveillance of 10% of its SARS-CoV-2 samples [11]. Coincidentally, B.1.1.7 can be detected by commercial qPCR assays due to its Δ69-70 deletion, leading to dropout of 1/3 genomic regions tested in many laboratories as part of standard SARS-CoV-2 diagnostics [4,12]. The rate of Δ69-70 is low (0.5-5%) in other circulating SARS-CoV-2 lineages.

In summary, it is important to understand these new features of B.1.1.7:

  • The B.1.1.7 virus has different biological properties to previous strains. Importantly this includes 30-50% higher transmission rates, potentially leading to a six to eightfold increase in cases over a month. This raises major concerns about the speed at which the pandemic will progress. Currently there is no evidence of a change in disease gravity or progression.
  • B.1.1.7 transmission was not contained by the English “November Lockdown”, which reduced other SARS-CoV-2 case numbers two fold.
  • A prediction of B.1.1.7’s higher transmissibility is that a stricter lockdown, sufficient to reduce the incidence of previous SARS-CoV-2 by 90% within a month, may only reduce B.1.1.7 incidence by 20-40% over the same period.
  • There is a substantial time (~2 months) from initial seeding of B.1.1.7 to noticing its impact due to aggregate case numbers, in particular in the presence of other circulating variants of the virus.
  • B.1.1.7 can be detected using certain available qPCR tests via S-gene target failure
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