Rapid increase of a SARS-CoV-2 variant with multiple spike protein mutations observed in the United Kingdom 20 December 2020

Summary
Over the last few weeks, the United Kingdom (UK) has faced a rapid increase in COVID-19 cases in South East England, leading to enhanced epidemiological and virological investigations. Analysis of viral genome sequence data identified a large proportion of cases belonged to a new single phylogenetic cluster. The new variant is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H) present as well as mutations in other genomic regions. While it is known and expected that viruses constantly change through mutation leading to the emergence of new variants, preliminary analysis in the UK suggests that this variant is significantly more transmissible than previously circulating variants, with an estimated potential to increase the reproductive number (R) by 0.4 or greater with an estimated increased transmissibility of up to 70%. This new variant has emerged at a time of the year when there has traditionally been increased family and social mixing. There is no indication at this point of increased infection severity associated with the new variant. A few cases with the new variant have to date been reported by Denmark and the Netherlands and, according to media reports, in Belgium.
Given that there is currently a lack of evidence to indicate the extent to which the new virus variant is spread outside the UK, timely efforts to prevent and control its spread are needed, and include the following:
− Public health authorities and laboratories are urged to analyse and sequence virus isolates in a timely manner to identify cases of the new variant. People with an epidemiological link to cases with the new variant or travel history to areas known to be affected should be identified immediately to test, isolate and follow up their contacts in order to stop the spread of the new variant.
− If cases infected with this new SARS-CoV-2 variant or other new SARS-CoV-2 variants of potential concern are identified, countries should notify through the Early Warning and Response System of the European Union.
− The importance of strict adherence to non-pharmaceutical interventions according to national policies needs to be communicated to the public, and in particular guidance on the avoidance of non-essential travel and social activities should be stressed.
− Laboratories should review the PCR performance and drop-out of the S-gene. PCR could be used as an indicator for cases with the new variant for further sequencing and investigation.
− Suspected cases of COVID-19 reinfection should be followed up, closely accompanied by sequencing respective virus isolates from these cases. Similarly, cases with treatment failures using convalescent plasma or monoclonal antibodies should be further studied.
− With the implementation of vaccination, close monitoring of COVID-19-vaccinated individuals needs to be ensured to identify possible vaccination failure and breakthrough infections. Virus isolates from these cases should be sequenced and characterised genetically and antigenically.

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