Visualising SARS-CoV-2 Spike Protein Mutations: An Interactive Web-Based Application

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the virus behind the COVID-19 pandemic, has caused over 198 million infections and over 4.2 million deaths globally as of early August 2021 (World Health Organisation, 2021). The SARS-CoV-2 spike protein, responsible for viral infectivity and transmissibility, is mutating rapidly and with it, Variants of Concern (VOCs) are emerging as deleterious mutations are acquired. The COVID-19 Genomics UK consortium (COG-UK) analyse and share SARS-CoV-2 sequence data via their Mutation Explorer (ME) website, but this information is currently designed for an expert audience. There is a pressing public need to understand these topics, as they have direct relevance to control measures, restrictions to daily life, and to illness.

Introducing interactivity and visualisation techniques can be effective for teaching these topics, allowing for active learning and higher user engagement. Visualising 3D protein models can enhance user understanding of structure and function, and animations can convey dynamic protein properties. This project designed an educational and interactive 3D visual resource for the COG-UK/ME in the form of an online application. The final application contains 3D molecular animations, an interactive 3D spike protein model, and visual information on VOCs.

The COG-UK/ME and application were user-tested, assessing the usability and knowledge acquisition effectiveness of each resource. Participants were recruited from Twitter and tested remotely using a pre-test versus post-test experimental design. Between-groups and within-groups statistical analysis was performed for the control and test groups in order to compare both resources. The findings show that the application demonstrated better usability, and significantly improved both self-reported knowledge confidence and knowledge acquisition in comparison to the COG-UK/ME.

There were several limitations within this project, including limited participant turnout and diversity. Additional user-testing should be conducted to develop further insights into the potential of this project and generate more reliable statistical analysis. Despite this, the application demonstrates encouraging results and suggests significant improvements in educating the general public on SARS-CoV-2 spike protein mutations and VOCs compared to the COG-UK/ME website.

This project was conducted in association with The Glasgow School of Art, The University of Glasgow MRC-Centre for Virus Research, and the COVID-19 Genomics UK (COG-UK) Consortium.

SARS-CoV-2 Virions

Spike Protein & ACE-2 Binding

Spike Protein & Antibody Evasion

Spike Protein Glycosylation Movement

SARS-CoV-2 Mutations: How Mutations of the Receptor-Binding Domain (RBD) Impact Viral Properties

SARS-CoV-2 Mutations: How Mutations of the N-Terminal Domain (NTD) Impact Viral Properties

Dissertation Final Presentation