Rapid Increase of a SARS-CoV-2 Variant With Multiple Spike Protein Mutations Observed in the United Kingdom

December 23, 2020

By Denise Baez

A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant has been identified in the United Kingdom, and preliminary analysis suggests that the variant is significantly more transmissible than previously circulating variants, according to a Threat Assessment Brief issued by the European Centre for Disease Prevention and Control.

The new variant, referred to as SARS-CoV-2 VUI 202012/01 (Variant Under Investigation, year 2020, month 12, variant 01), shows an estimated potential to increase the reproductive number (R) by ≥0.4, with an estimated increased transmissibility of up to 70%, according to the report. There is no indication, as of now, of increased infection severity associated with the new variant.

SARS-CoV-2 VUI 202012/01 is defined by multiple spike protein mutations (deletion 69-70, deletion 144, N501Y, A570D, D614G, P681H, T716I, S982A, D1118H), as well as mutations in other genomic regions.

A rapid increase in coronavirus disease 2019 (COVID-19) cases in the United Kingdom prompted an epidemiological and virological investigation. The most affected region was in Kent/South East England, which saw an increase in the 14-day case notification rate from 100 cases per 100,000 population in week 41 of 2020 to over 400 per 100,000 in week 50 of 2020.

Analysis using viral genome sequence data identified a large proportion (>50%) of cases belonging to the novel variant. As of December 13, 2020, a total of 1,108 individuals had been identified with the novel variant in England, with the earliest case identified on September 20, 2020.

There are indications of a more widespread occurrence of cases across the United Kingdom, as well as small numbers of cases detected in other countries, including Denmark and the Netherlands.

Given that there is currently a lack of evidence to indicate the extent to which the new virus variant is spread outside the United Kingdom, the European Centre for Disease Prevention and Control is recommending 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.

The United Kingdom has an established SARS-CoV-2 genome sequencing consortium called COG-UK. It consists of the national public health institutes, National Health Service organisations, academic institutions, and the Wellcome Sanger Institute. They are working to keep sequencing coverage high and geographically representative and to keep turnaround times low. This initiative increases the likelihood that emerging variants are identified and can be assessed in a timely fashion.

Reference: https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-vari...

SOURCE: European Centre for Disease Prevention and Control