Explainer

23 Feb 2021

Introducing Mutation Explorer: An open-access dashboard by COG-UK

The COG-UK Mutation Explorer (COG-UK-ME) is an interface that provides access to data on SARS-CoV-2 mutations and variants of interest in the COG-UK genome sequence data set.

COG-UK-ME draws UK genome data from the MRC-CLIMB database. We largely focus on spike gene mutations of potential or known importance based on epidemiological, clinical and/or experimental observations. We provide information on cumulative frequency, and data for the last 28 days to give an approximate assessment of recent changes. This data visualisation tool allows anyone to follow information over time on important changes in the SARS-CoV-2 genome.

 

 

How does COG-UK-ME work?

Selecting the ‘Mutational Explorer’ tab takes you to 3 tables. Table 1 lists mutations in the spike gene that have led to an amino acid change (called a substitution, which we concentrate on because it may change the way that the virus interacts with humans). Mutations are ranked by frequency in the MRC-CLIMB database (the most common mutations first). A search function allows individual mutations to be selected, and a file downloaded containing a list of COG-UK identifiers, dates and lineages. For example, selection of E484K provides links to information for each genome that carries this mutation, the date of the sample, and the lineage the isolate belongs to. Data can also be visualised for each mutation in a graph by clicking the “Visualiser” tab. This shows the number of times the selected mutation has been detected over time.

Table 2 shows mutations of possible or known biological importance, and Table 3 shows Variants of Concern as defined by Public Health England. Both tables include extra information derived from global sources. For example, the variant P1 first detected in Brazil has not been identified in the UK, but is included for completeness.

COG-UK-ME also displays mutations that could affect the way that the virus interacts with the human immune response based on laboratory studies (see ‘Antigenic information’ tab). Scientific evidence is graded. ‘High confidence’ is applied when a mutation is found by multiple independent studies using multiple different approaches, including  studies using polyclonal (convalescent or post-vaccine) antisera; ‘medium confidence’ means this has been found by multiple independent studies; and ‘lower confidence’ indicates this has been found by a single study only. Mutations with an antigenic role can also be filtered by domains of the Spike protein.

The Explorer will be updated with new functions over time, based on new scientific observations and ways of describing and thinking about variants.

 

COVID-19 Genomics UK (COG-UK)

The current COVID-19 pandemic, caused by 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 April 2020 supported by £20 million funding from the COVID-19 rapid-research-response “fighting fund” from Her Majesty’s Treasury (established by Professor Chris Whitty and Sir Patrick Vallance), and administered by the National Institute for Health Research (NIHR), UK Research and Innovation (UKRI), and the Wellcome Sanger Institute. The consortium was also backed by the Department of Health and Social Care’s Testing Innovation Fund on 16 November 2020 to facilitate the genome sequencing capacity needed to meet the increasing number of COVID-19 cases in the UK over the winter period.