The SARS-CoV-2 Spike Protein Mutation Explorer: using an interactive application to improve the public understanding of SARS-CoV-2 variants of concern

Figures & data

Table 1. The protein visualisation and 3D modelling software used in the development of the SSPME.

Software	Use	Developer
Autodesk Maya	3D modelling and animation	Autodesk, Inc. (https://www.autodesk.com/)
Molecular Maya (mMaya)	Importing, modelling, rigging and animating molecular structures within Autodesk Maya	Digizyme, Inc. (https://www.digizyme.com/)
PyMOL	Molecular visualisation and 3D model generation	Shrödinger, Inc. (https://pymol.org/)
UCSF Chimaera	Molecular visualisation and 3D model generation	Resource for Biocomputing, Visualisation, and Informatics (RBVI), UCSF (https://www.cgl.ucsf.edu/chimaera/)

Table 2. The experimentally resolved data used in generating the 3D models of proteins during the development of the SSPME.

Protein	PDB/file identifier	Reference
Angiotensin-Converting Enzyme 2 (ACE-2)	6M17 chains B, E	(Yan et al., 2020)
Full-length glycosylated spike protein, 1 RBD open	6VSB_1_1_1	(Woo et al., 2020)
Full-length glycosylated spike protein, all RBDs closed	6VXX_1_1_1	(Woo et al., 2020)
Membrane protein	M_dimer_new_1	(Heo & Feig, 2020)
Envelope protein	E_protein_1	(Heo & Feig, 2020)
Lysosome-Associated Membrane Protein 1 (LAMP-1)	5GV0	(Terasawa et al., 2016)
V-ATPase	5VOX	(Zhao et al., 2017)
Transient Receptor Potential Mucolipin 1 (TRPML1)	5WJ5	(Schmiege et al., 2017)
Solution structure of human secretory IgA1	3CHN	(Bonner et al., 2009)
Crystal structure of pembrolizumab, a full length IgG4 antibody	5DK3	(Scapin et al., 2015)

Figure 1. The 3D SARS-CoV-2 spike protein scene of the SARS-CoV-2 Spike Protein Mutation Explorer. Screenshots show the 3D SARS-CoV-2 spike protein embedded in the viral membrane (A) and the same scene when the user has rotated the model and is hovering their mouse over the NTD (B).

Figure 2. Accessing additional information through the SARS-CoV-2 Spike Protein Mutation Explorer. Screenshots show (A) the VOC menu, which is accessed via the right-hand side button which is labelled ‘VOC’ and contains an image of two simple viruses and (B) the Glossary panel, which is accessed from the bottom right-hand side button containing an image of books.

Figure 3. Information about Regions of Interest (ROI) in the SARS-CoV-2 Spike Protein Mutation Explorer. Screenshot shows the NTD-specific ROI page, one of the four ROI-specific pages, which is accessed by clicking the button labelled ‘NTD’ on the interactive 3D spike protein (see Figure 2). Going from top to bottom, the buttons along the right-hand side allow the user to hear the narrated text, alter the text size, access the animation and access the Glossary panel.

Figure 4. Explanatory animations in the SARS-CoV-2 Spike Protein Mutation Explorer. Screenshots show 3D molecular animations, which are contained within the RBD- and NTD-specific ROI pages of the SARS-CoV-2 Spike Protein Mutation Explorer, showing (A) SARS-CoV-2 virus particles and (B) a close-up SARS-CoV-2 spike protein avoiding host antibodies, with the antibody binding sites highlighted with a dashed line. Mucin proteins present in the nasal mucus are visible as background detail.

Table 3. The demographics collected from all participants within this study.

	Control group	Test group
Female participants	5	6
Male participants	4	8
Age range (mean ± SD)	21–64 (42.78 ± 12.88)	20–66 (41.14 ± 14.88)
Level of attained education	Range from secondary school (14%) to a Master’s degree (57%)	Range from secondary school (7%) to a PhD or higher (50%)
Computer use	Use a computer every day or almost every day	Use a computer every day or almost every day
Self-reported experience with interactive applications	67% experienced	64% experienced
	22% with some experience	7% with some experience
	11% with no experience	29% with no experience
Self-reported general virology knowledge	14% knowledgeable	65% expert or knowledgeable
	57% with a basic knowledge	21% with a basic knowledge
	29% with no knowledge	14% with no knowledge
Self-reported SARS-CoV-2 knowledge	29% knowledgeable	64% expert or knowledgeable
	57% with a basic knowledge	36% with a basic knowledge
	14% with no knowledge	0% with no knowledge
Self-reported understanding of SARS-CoV-2 VOCs	29% well-informed	50% well-informed
	28% moderately informed	21% moderately informed
	43% slightly informed	29% slightly informed

Figure 5. The flow of the seven stages of the experimental questionnaire.

Figure 6. Knowledge acquisition with the CG (n = 9) and TG (n = 14). The number of correct answers out of 11 questions between the pre-and post-experiment quiz questions is shown for both the CG and TG, with individual responses plotted along with box and whisker plots. Differences between pre-and post-experiment were tested for significance with a Wilcoxon Signed Rank Test. *p < .005; n.s. p > .05.

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