19 Jan 2021

New SARS-CoV-2 variant & other mutations under review


A brief summary of the latest COG-UK mutational surveillance report, which explores SARS-CoV-2 spike gene mutations of potential or known importance.

On the 15th January 2021, a research report was released by the COVID-19 Genomics UK (COG-UK) consortium. This provides information on mutations and associated variants of interest in the gene encoding the SARS-CoV-2 spike protein that have been identified from sequence data generated by the consortium. We focus on SARS-CoV-2 spike gene mutations of potential or known importance based on epidemiological, clinical and/or experimental observations.

We also include information on several variants first identified elsewhere that are of current concern in the UK, but not all of these are in the UK dataset at the time of writing (as in the case of the lineage P.1 recently detected in Brazil). Frequency numbers are as of the 29th December 2020, but for the global variants of interest, updated numbers and reports of the geographic distribution can be found here.

The report is structured in four parts:

1) a list of high frequency individual mutations, a subset of which may be important;

2) highlighted mutations of potential or known clinical and public health importance based on current evidence;

3) a list of mutations known to lead to weaker neutralisation of the virus by convalescent plasma from people who have been infected with SARS-CoV-2, and/or some monoclonal antibodies (mAbs) that may be given to patients with COVID-19;

4) structural analyses of mutations and variants described in 2) above.

At the time of writing, we are not aware of any evidence that the mutations or combination of mutations detected to date will reduce vaccine efficacy.

We also highlight open access websites that provide updated information on circulating lineagesvariants of special interest, and amino acid replacement, insertion and deletion counts for all SARS-CoV-2 genes

Read the full report here.


COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by the SARS-CoV-2, represents a major threat to health. The COVID-19 Genomics UK (COG-UK) consortium has been created to deliver large-scale and rapid whole-genome virus sequencing to local NHS centres and the UK government.

Led by Professor Sharon Peacock of the University of Cambridge, COG-UK is made up of an innovative partnership of NHS organisations, the four Public Health Agencies of the UK, the Wellcome Sanger Institute and twelve academic partners providing sequencing and analysis capacity. A full list of collaborators can be found here. Professor Peacock is also on a part-time secondment to PHE as Director of Science, where she focuses on the development of pathogen sequencing through COG-UK.

COG-UK was established in March 2020 supported by £20 million funding from the UK Department of Health and Social Care (DHSC), UK Research and Innovation (UKRI) and the Wellcome Sanger Institute, administered by UK Research and Innovation.