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 . While B.1.1.7 is not evidently causing more severe disease , it is approximately 30-50% more transmissible as evidenced by epidemiology [5,6] and contact tracing . 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  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 . 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 .
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 . 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