COG-UK / Mutation Explorer

The COG-UK / Mutation Explorer (COG-UK/ME) provides information and structural context on mutations and associated variants in the genes encoding SARS-COV-2 proteins that have been identified from sequence data generated by the COVID-19 Genomics (COG-UK) Consortium by Tuesday 11 May 2021. We focus on SARS-CoV-2 spike gene mutations of potential or known importance based on epidemiological, clinical and/or experimental observations.

The Mutation Explorer comprises of:

  1. high frequency individual amino acid replacements (Table 1), a subset of which may be important
  2. mutations of potential or known clinical and public health importance based on current evidence (Table 2)
  3. the designated global variants of concern and their structural context (Table 3)
  4. frequency plots for mutations at specific residue in SARS-CoV-2 ORFs (Visualiser)
  5. mutations of potential antigenic significance as indicated by experimental studies: shown to lead to weaker neutralisation of the virus by convalescent plasma from people who have been infected with SARS-CoV-2 and/or demonstrated escape from some monoclonal antibodies (mAbs) that may be given to patients with COVID-19 (Antigenic Information: Antibody Sites)
  6. mutations in T cell epitopes as indicated by experimental studies (Antigenic Information: T Cell Epitopes).

Notes provides an explanation of scientific terms and a few limitations.

Disclaimer

Dashboard reports are not advice. They capture research findings which are always necessarily provisional. They are for research use only. Commercial use/resale is not permitted.

Credits

COG-UK/ME is developed within and funded by the COVID-19 Genomics UK Consortium by Derek W. Wright, Joseph Hughes, William Harvey, Rachel Colquhoun, Ben Jackson, Andrew Rambaut, Thomas Peacock, David L. Roberson, Alessandro M. Carabelli. COG-UK/ME is based on the CLIMB framework, and maintained by the MRC-University of Glasgow Centre for Virus Research. Follow COG-UK to be notified of updates.

COG-UK / Mutation Explorer

Latest UK sequence: Friday 07 May 2021

Mutational Frequencies

Antigenic Information

Spike protein gene mutations of potential immunogenic significance detected in the UK

The table lists those mutations in the spike gene identified in the UK dataset that have been associated with weaker neutralisation of the virus by convalescent plasma from people who have been infected with SARS-CoV-2, and/or some mAbs that may be given to patients with COVID-19 (referred to below as "escape").

There is no evidence at the time of writing for this impacting on the efficacy of current vaccines or the immune response to natural SARS-CoV-2 infection.


Download Data

Download a CSV file containing COG-UK sequence name, sample date, epidemic week and global lineage. Cumulative UK sequences are filtered by the selected amino acid replacement.

Download

Spike protein gene mutations in T cell epitopes detected in the UK

Table 2

T-cell epitope data have been compiled by Dhruv Shah and Thushan de Silva, University of Sheffield.

Predicted binding percentile rank values have been calculated by Morten Nielsen, The Technical University of Denmark.

T Cell Epitopes

Download Table 2

Download a CSV file comprising complete table 2 data.

Table 1

Table key

Confidence
  • High: Antigenic role of mutation is supported by multiple studies including at least one that reports an effect observed with (post-infection serum) convalescent plasma.
  • Medium: Antigenic role of mutation is supported by multiple studies.
  • Lower: Mutation is supported by a single study.
Spike protein domain definitions
  • SP, signal protein (residues 1-13)
  • NTD, N-terminal domain (14-303)
  • RBD, receptor-binding domain (331-527) which includes the RBM, receptor-binding motif (437-508)
  • FP, fusion peptide (815-834)
  • Residues outside of these specific domains are labelled by subunit, S1 (residues 1-685) or S2 (residues 686-1173)

Table 2

Table Key

  • WT Percentile Rank Value and Mut Percentile Rank Value: predicted IC50 nM for the corresponding reported restricting allele. Predictions were performed using the NetMHCpan BA 4.1 algorithm, hosted by the IEDB.
  • Fold difference indicates Increase/decrease in affinity defined by a two-fold difference in predicted IC50 nM.
  • Binding is reported as a percentile rank value (as described here), the lower the value the stronger the binding.
    • For HLA-I, values less then 2 are binders and values less than 0.5 strong binders.
    • For HLA-II, values less then 5 are binders and values less than 1 strong binders.