SARS-CoV-2 Macromolecular Model

How we created a Three-dimensional molecular model of the virus behind Covid-19. 

Covid-19 Home Introduction Background Method Downloads Models

Our Covid-19 Models

3D Printed Virion

Like all our SARS-CoV-2 models the Chapel Prints Covid-19 Virion Model is based on our in-house PDB render of the virion, which contains over 7 million atoms. This model is one of the largest on the market with the viral envelope measuring 15cm in diameter. All four of the main Spike protein conformations are depicted as well as partially visible M and E proteins set into the lipid bilayer surface.

3D Printed Proteins

Beyond the complete Virion, we also offer more detailed models of the key viral proteins. Our Covid-19 Arch sculpture includes the four conformations of the Spike protein and examples of the M and E proteins. These are all standalone models which magnetically attach to the lipid bilayer - showing how these proteins are placed in the viral envelope.

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Origami Virion

Because of the thousands of hours of research time and 70 or so hours of print time required to create the 3D printed virion model our items although competitively priced are expensive. Given we want to bring the learning advantages of a physical model to students of all backgrounds we’ve designed a cheap origami version of our model. This is still loosely based on our original digital model - depicting the surface features and four conformational types of Spike protein.

Abstract

Know your enemy.

As we all know too well, in late 2019 a novel coronavirus started circulating among the citizens of Wuhan in the Hubei province of China. By April 2021 around 141 million confirmed cases and more than 3 million registered deaths had been attributed to the coronavirus across the globe (1). The worldwide average case fatality rate appears to present at round 0.5-1% with vulnerable groups seeing a higher death rate (2). Cases of long-covid, affecting as much as 10% of the infected, can be debilitating and are characterised by fatigue and a myriad of symptoms extending beyond 12 weeks (3). All of us know someone badly affected by the disease and sadly many of us know someone who has been claimed by it.

By late-April 2021 around 928 million people had received at least one dose of a vaccination against Covid-19 (4). Lockdowns and measures to mitigate the spread of Covid-19 have negatively affected a majority of people globally for the past year. Here in the UK, we have recently come out of a 4-month lockdown which saw nonessential trade and travel restrictons – until a few weeks ago national school closures were still in place (5).

The lockdown measures and the Pfizer and AstraZeneca vaccines are now successfully supressing mortality, hospital admissions, and infection rates in those countries lucky enough to have substantial immunisation programs and associated mitigation measures (6-7). Covid-19 variants resistant to these vaccines are and will continue to arise and spread – notably the South African variant (8). However, given the growing arsenal of medical interventions (9), and an ever-increasing body of scientific information characterising the virus (10), it seems likely the worst is behind us for some privileged countries such as the UK and Israel. Sadly, the same cannot be said of some larger, poorer nations such as Brazil and India (11).

It is critical easing of Covid-19 restrictions does not breed complacency or forgetfulness. Further, as the vaccination programs gain pace over the months and years ahead, vaccination uptake must still be encouraged, misinformation countered (12). Beyond Covid-19, there will be further pandemics. Understanding how and why this pandemic occurred can save lives and reduce further suffering in the future.

Towards this end we have spent several months collection data and constructing a ditigal three-dimensional model of the SARS-CoV-2 virion. To the best of our knowledge, this is one of the most up-to-date and accurate of the handful of virion models available (13-16). This intended as an educational tool and reminder of the pandemic. We have rendered our model as a 3D-printable sculpture and have physical sturctures of the Covid-19 virus for sale.

At the heart of the misinformation and conspiracy theories surrounding this pandemic is uncertainty, subjective opinion, and the intangibility of an invisible enemy. Our model gives a face to the opponent, shows the cogs and ratches behind the biological machinery of the Covid-19 infection, and importantly helps imagine the analogous medicinal spanners and wrenches that can combat the disease. Education and systematic understanding can offer solid reasoning and a clearer insight, in the face of what at times seems a biblical global health crisis. Holding in your hands, a highly accurate model of the now infamous Covid-19 virus is perhaps the most effective way to spread awareness on how to fight the pandemic, and make this nanoscopic enemy tangable.

Site Contents:

The Microbiology of Infection

An introduction to the cellular biology of infection.

The SARS-CoV-2 Proteins. 

A review of macromolecular components of SARS-CoV-2

Assembling our Virion Model

The method we used to assemble the Virion model. 

Virion model - STL render

Virion model - STL render

Download the Model

The conclusion of our efforts and where to download the Virion model.

Virion digital model - PDB render

Virion digital model - PDB render

References:

  1. Dong E, Du H, Gardner L 2020 ‘An interactive web-based dashboard to track COVID-19 in real time.’ Lancet Inf Dis., vol. 20, no. 5, pp. 533-534. doi: 10.1016/S1473-3099(20)30120-1

  2. WHO 2020, Estimating mortality from COVID-19, WHO, viewed 20 April 2021, <https://www.who.int/publications/i/item/WHO-2019-nCoV-Sci-Brief-Mortality-2020.1>.

  3. Sivan M, Taylor S 2020 ‘NICE guideline on long covid.', BMJ 2020, vol. 371, no. m4938. doi:10.1136/bmj.m4938.

  4. Holder J 2021, Tracking Coronavirus Vaccinations Around the World, New York Times, viewed 20 April 2012, <https://www.nytimes.com/interactive/2021/world/covid-vaccinations-tracker.html>.

  5. Wikipeadia 2021, Timeline of the COVID-19 pandemic in the United Kingdom (2021), Wikipeadia, viewed 20 April 2021, <https://en.wikipedia.org/wiki/Timeline_of_the_COVID-19_pandemic_in_the_United_Kingdom_(2021)>.

  6. Rekha R Rapaka, R R, Hammershaimb, E A, Neuzil, K M 2021 ‘Are some COVID vaccines better than others? Interpreting and comparing estimates of efficacy in trials of COVID-19 vaccines.’, Clinical Infectious Diseases, vol. ciab213, https://doi.org/10.1093/cid/ciab213.

  7. GOV.UK Coronavirus (Covid-19) in the UK 2021, Interactive Map [Covid-19 cases], GOV.UK, viewed 20 April 2021, <https://coronavirus.data.gov.uk/details/interactive-map>.

  8. Edara, V V, Norwood C, Floyd, K, et al. 2021 ‘Reduced binding and neutralization of infection- and vaccine-induced antibodies to the B.1.351 (South African) SARS-CoV-2 variant.’, [preprint] bioRxiv 2021.02.20.432046; doi: https://doi.org/10.1101/2021.02.20.432046.

  9. David Erskine 2020, Summary of COVID-19 medicines guidance: Critical care, Specialist Pharmacy Service, viewed 20 April 2021, <https://www.sps.nhs.uk/articles/summary-of-covid-19-medicines-guidance-critical-care/>.

  10. Else H 2021, How a torrent of COVID science changed research publishing — in seven charts, Nature [news], viewed 20 April 2021, <https://www.nature.com/articles/d41586-020-03564-y>.

  11. Ventura D 2021, Covid-19 in Brazil: the government has failed to prevent the spread of the virus, The BMJ Opinion, viewed 20 April 2021, < https://blogs.bmj.com/bmj/2021/03/05/covid-19-in-brazil-the-government-has-failed-to-prevent-the-spread-of-covid-19/>.

  12. Brennen, JS, Simon, FM, Howard, PM, Nielsen, RK 2021, Types, Sources, and Claims of COVID-19 Misinformation, The Reuters Institute, viewed 20 April 2021, <https://reutersinstitute.politics.ox.ac.uk/types-sources-and-claims-covid-19-misinformation>.

  13. Kbrowne 2020, SARS CoV-2 Virion (NIAID), NID 3D Print Exchange, viewed 20 April 2021, <https://3dprint.nih.gov/discover/3dpx-013323>.

  14. Coronavirus Structural Task Force, Sars-CoV-2 – The Coronavirus (For the Public), Coronavirus Structural Task Force, viewed 20 April 2021, <https://insidecorona.net/for-the-public/>.

  15.  Biologic 2021, SARS-CoV-2 Virion, Biological Models, viewed 20 April 2021, <https://biologicmodels.com/viruses/sars-cov-2-virion/>.

  16. Hays VF 2020, How I Built a 3-D Model of the Coronavirus for Scientific American, Scientific America, viewed 20 April 2021, <https://www.scientificamerican.com/article/how-i-built-a-3-d-model-of-the-coronavirus-for-scientific-american/>.

 

About the Author - Declaration of Interests

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The research outlined here was produced and written by Samuel A. McKie, for the author's other scientific work seeing references (1a, 2a, 3a). The associated SARS-CoV-2 virion macromolecular model was researched and assembled towards creating a 3D printed model to be sold commercially. The PDB and dsv model structures and the research presented here is released under the Attribution-NonCommercial 4.0 International license.

  • 1a McKie, SA 2016, 'Antibiotics: where to throw the spanner in the ribosomal machinery?', Future Medicinal Chemistry, vol. 8, no.16, pp.1981-2002.

  • 2a McKie, SA 2016, ‘Polypharmacology: in silico methods of ligand design and development.’, Future Medicinal Chemistry, vol. 8, no. 5, pp. 579-602.

  • 3a McKie JH, McKie SA 2017, ‘Synonymous codon bias as a basis for novel antibiotic design: from nucleotide wobble constraint to ribosomal garrotte.’, Future Medicinal Chemistry, vol. 9, no. 12, pp. 1377-1400.