Blog

8 May 2020

Commentary: COG-UK Report 5, 7th May 2020

Commentary

Commentary: COG-UK Report 5, 7th May 2020

The 5th report from COG-UK includes analysis of a total of 10,483 SARS-CoV-2 genomes, sequenced before 7th May 2020.

The report also includes analysis of viral genomes sequenced from five care homes in London. The samples were taken from staff and residents between 13th and 15th of April 2020. Of the 210 samples assessed, 91 were positive for SARS-CoV-2. 55 of these samples were of high enough quality for analysis. These data were used for phylogenetic studies within each care home, and for comparison with 277 non-care home viral genomes originating in London.

Analysis of the data suggests that in one care home, there were at least four separate introductions of the virus. A similar pattern of multiple introductions of the virus was observed in two other care homes, although less data were available for these sites. There was also some evidence that following an introduction of the virus, in some cases, there was transmission within a care home.

No common pattern or direction was seen for transmission, either between staff and residents or between symptomatic and asymptomatic people.

Further analysis identified a putative cluster of viral sequences, containing samples from multiple care homes. The presence of similar sequences across different care homes could suggest either transmission of SARS-CoV-2 between care homes, or separate introductions of the same viral lineage to different care homes from the community or other healthcare settings. Since the completion of this report, additional sequence data have been analysed. This analysis indicated that the sequences from care homes are part of a widespread viral lineage and consequently it is not possible to determine which of these scenarios is the case.

The findings highlight the importance of ongoing, larger studies, with additional metadata. Such studies will be vital to study transmission in care settings and inform control strategies.

The researchers anticipate that as the number of genomes sequenced increases, they will be able to provide a high resolution view of viral lineage diversity in the UK. This will make it possible to distinguish dominant local lineages and track viral spread from one part of the UK to another.

In such a fast-moving situation, the consortium members note it is important to consider the limitations of phylogenetic analysis, and the importance of caveats when interpreting data.

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9 Sep 2021

An app for understanding SARS-CoV-2 spike protein mutations

An interactive web-based application has been developed to help explain reports on SARS-CoV-2 mutations and variants generated by COG-UK for a non-expert audience.

An interactive web-based application, the SARS-CoV-2 Spike Protein Mutation Explorer, has been developed to help explain reports on SARS-CoV-2 mutations and variants generated by COG-UK for a non-expert audience.

The app is designed to provide additional context for the COG-UK Mutation Explorer (COG-UK/ME), an interface that provides access to data on SARS-CoV-2 mutations, variants of interest and variants of concern in the COG-UK genome sequence dataset, particularly those in the viral spike protein.

COG-UK/ME is targeted at an expert audience, but given the emergence of new variants, the general public and media are increasingly interested in understanding how the mutations it reports affect the properties of SARS-CoV-2 and the effectiveness of vaccines.

With this in mind, Sarah Iannucci, a biomedical artist, created an interactive web application  as part of her MSc in Medical Visualisation and Human Anatomy at the Glasgow School of Art and University of Glasgow. The SARS-CoV-2 Spike Protein Mutation Explorer allows non-expert users to visualise and better understand mutations reported through the COG-UK/ME interface.

The application features an interactive 3D model of the SARS-CoV-2 spike protein, in which regions of interest (such as the receptor-binding domain, shown below) can be highlighted, with associated information panels explaining what they do and why mutations at these locations can affect the behaviour of the virus.

Users can also view images of variants of concern and their characteristic mutations, as well as detailed animations showing how the spike protein of SARS-CoV-2 binds to new host cells, is neutralised by antibodies, and why mutations in particular parts of the spike can alter the spread of the virus and the effectiveness of vaccines.

 

Try the app for yourself HERE on the University of Glasgow’s Centre for Virus Research (CVR) website.

 

Acknowledgements

This application was developed by Sarah Iannucci using data from the COG-UK/Mutation Explorer team (Derek W. Wright, Joseph Hughes, William Harvey, MacGregor Cox, Rachel Colquhoun, Ben Jackson, Andrew Rambaut, Thomas Peacock, David L. Robertson and Alessandro M. Carabelli), with virology advice from the MRC-University of Glasgow Centre for Virus Research (Ed Hutchinson, Joseph Hughes, William Harvey and David L. Robertson) and technical advice from the School of Simulation and Visualisation at the Glasgow School of Art (Matthieu Poyade).

 

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