Animation of the SARS-CoV-2 coronavirus
Date:
12.05.2020
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Biomedical visualization studio Visual Science has created the most detailed and scientifically accurate 3D model of the SARS-CoV-2 virus at atomic resolution. The model is based on the latest scientific research into the structure of coronaviruses, as well as input from expert virologists involved in the research. This is the most accurate model of the SARS-CoV-2 viral particle currently available. To produce it, Visual Science employed the same techniques of structural bioinformatics used in basic research and drug development.

The SARS-CoV-2 virus model is a part of Visual Science’s non-commercial Viral Park project. Viral Park’s past successes include models of HIV, influenza A/H1N1, Ebola, papilloma, and Zika virions.

We use the same color scheme throughout the whole Viral Park project. Bright colors show the proteins encoded by the viral genome. Shades of gray correspond to the structures taken by virus from the host cell. Thus we emphasize the parasitic and non-autonomous nature of the viruses.

Models and visualizations created for the Viral Park have received prizes from Science magazine and the National Science Foundation, and have been featured in leading media outlets such as Science, Nature Medicine, The New York Times, The Washington Post, Scientific American, Wired UK, Der Spiegel, Stern, National Geographic, GEO, and more.

In their usual stunning style, the talented illustrators at Visual Science have created a model of the SARS-CoV-2 virus particle. It shows, in great detail, the intact particle with its spike glycoproteins embedded in the membrane. A cutaway view reveals the viral nuclecapsid inside the particle. These gorgeous images will enhance our understanding of the virus particle and for the non-scientist will make even more palpaple the virus that is infecting millions of people.

— Vincent Racaniello, Ph.D. Higgins Professor Department of Microbiology and Immunology Columbia University, New York

Great work on the spike and the images! Really well done. The spikes are about as accurate as they can be given our current knowledge. The images are striking.

— Dr. Jason S. McLellan, Associate Professor, Molecular Biosciences Department at the University of Texas at Austin

Wow, that’s really neat — I love the model where it is open and you can see the RNP — new favorite SARS-CoV-2 model.

— Dr. Benjamin Neuman, Professor and Chair of Biological Sciences, Texas A-M University-Texarkana

The model was built based on assumptions derived from all available experimental data. It is a good model. Nonetheless, one should keep in mind that the original crystal structure of CTD was obtained in the absence of RNA. Binding of RNA is likely to compact the structure due to strong protein-RNA interaction.

— Prof. Dr. Tai-huang Huang, Distinguished Research Fellow, Division of Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei

SARS-CoV-2 virus

At the end of December 2019, the World Health Organization (WHO)’s branch in China registered an outbreak of pneumonia of unknown origin. At the beginning of January 2020, the causative agent of the disease was determined — it was a novel coronavirus related to the viruses that cause Severe Acute Respiratory Syndrome (SARS) and Middle-East Respiratory Syndrome (MERS). The virus was later named SARS-CoV-2, and the disease it caused was termed COVID-19 (Corona Virus Disease 2019). On 11 March 2020, the WHO officially declared the outbreak of the new disease to be a pandemic [1].

What are coronaviruses?

In 1965, British virologists Tyrell and Bynoe, who were studying the common cold, cultivated a new virus, B814 [2]. Later, Tyrell and colleagues conducted microscopy studies and discovered similarities between this virus and several animal viruses, such as infectious bronchitis virus, mouse hepatitis virus and transmissible gastroenteritis virus of swine [3]. The viruses were predominantly of a roughly spherical shape with long surface projections, resembling the corona which appears around the solar disc during eclipses. This led the researchers to adopt the name “coronavirus” [4,5].

Viruses are an extremely diverse group of agents. Some are made up entirely of proteins and genetic material (for example common cold viruses or papillomaviruses), while others, like influenza or HIV, include a membrane envelope taken from the host cell. This envelope consists of a double layer of lipids and viral proteins embedded into it. Coronaviruses have this kind of envelope.

Unlike bacteria or higher organisms, viral genomes may be composed either of DNA or RNA. Coronaviruses use RNA, and their genomes are the largest among similar viruses. The coronavirus genome contains about 30,000 nucleotides — small molecules whose sequence encodes information about the structure of viral proteins [6]. For comparison, influenza’s genome is half this length [7]. Usually, a longer genome enables a virus to produce more types of proteins and therefore have more complex interactions with host cells during infection.

Scientists have described four distinct groups of coronaviruses, named in the letters of the Greek alphabet from alpha to delta. Alpha and betacoronaviruses infect mammals, while gamma and delta mostly infect birds and fish [8,9].

Animal coronaviruses can cause severe economic damage. In 2016, the coronavirus that causes fatal swine acute diarrhoea syndrome killed more than 24,000 piglets [10].

Before 2019, scientists were aware of six coronaviruses able to infect humans. Four of them (HCoV‐229E, HCoV‐OC43, HCoV‐NL63, and HKU1) cause symptoms similar to the common cold. The other two, SARS-CoV and MERS-CoV, infect the lower respiratory tract, with a high probability of severe illness and even death [11].

Atypical pneumonia and Middle-East respiratory syndrome

In the 20th century, human coronaviruses were not considered a major threat. However, in 2002, an outbreak of SARS caused by the previously undescribed coronavirus SARS-CoV occurred in the southern provinces of China [12]. During the outbreak, more than 8000 people were infected, of whom around 1000 died [13]. In 2012, the spread of another related virus, MERS-CoV, triggered an outbreak of MERS, which infected 2066 people and killed 720. This outbreak predominantly affected Saudi Arabia, but cases were registered in 27 different countries [14].

Both MERS-CoV and SARS-CoV were of zoonotic origin, first transmitted to humans from civets (small predatory mammals) and camels respectively. However, in both cases, the viruses had been transmitted to the intermediate hosts by bats [8,15].

SARS-CoV-2 — the causative agent of COVID-19

Like SARS, COVID-19, caused by the similar SARS-CoV-2 virus, is dangerous because of its potential to infect the lower respiratory tract, where both viruses attach to the ACE2 receptors on the cellular surfaces.

Characteristics of the virus

Many details on the symptoms, epidemiology and transmission of SARS-CoV-2 have yet to be studied in detail. The virus is known to be transmitted through coughs and sneezes, but whether it is fully airborne remains unknown [19]. One common transmission route is surfaces, upon which the virus can survive for several days, so frequent handwashing is an important preventive measure, as well as avoiding touching the face. It is likely that even people with no symptoms can transmit the virus [19].

The European Center for Disease Control analyzed the spread of the novel coronavirus in Italy and concluded that the basic reproductive number (number of people infected by a typical carrier) lies between 2,76 and 3,25 [20]

The incubation period of SARS-CoV-2 varies from 2 to 14 days, but it has been recorded at 4 days for most cases [21]. Most of those infected with SARS-CoV-2 show no symptoms, so it is difficult to estimate the number of such cases. Among patients with symptoms, 80% experience only a mild illness. Severe symptoms with hypoxia have been observed in 14% of cases, and 5% of cases are critical, involving respiratory failure [19].

The case fatality rate of Covid-19 is estimated to be between 0.9% and 1.4%, which is roughly 10 times higher than common influenza [22].

Origin of the virus

The sequence of the SARS-CoV-2 genome is most similar to that of a bat coronavirus named BatCoV RaTG13. With a similarity of 96.2%, scientists assume that these viruses are close relatives [16]. However, a 91.02% similarity with Pangolin-CoV has also been demonstrated. Interestingly, despite SARS-CoV-2’s greater similarity to Bat-CoV, the structure of its spike proteins, which play a key role in infection, is closer to those in pangolin coronavirus [17].

SARS-CoV-2 and its closest relatives might have been transmitted to humans from animals. One of the possibilities is transmission in the animal market of Wuhan, where the first cases were registered.. The possibility of SARS-CoV-2 being the offspring of laboratory coronavirus strains studied in Wuhan cannot be entirely excluded. However, this would have required prior isolation of a progenitor virus with very high genetic similarity, and no such virus has been described [18].

Read more about the structure of the virus and the modeling process in the section about the О строении вируса и процессе моделирования подробнее читайте в разделе о model of the SARS-CoV-2 coronavirus.

Show references
  • Head of the project, Look Dev:
    Ivan Konstantinov
  • Project coordinator, scientific consultant:
    Yury Stefanov, Ph.D.
  • Literature review
    Anna Zyrina, Ph.D., Yury Stefanov, Ph.D.
  • Molecular modeling:
    Dmitrii Shcherbinin, Ph.D., Anastasia Bakulina, Ph.D., Marina Pak
  • 3D-modeling and animation:
    Maxim Kulemza
  • Animation:
    Yury Stefanov
  • Animation superviser:
    Sergey Ivanchuk
  • Design:
    Elizaveta Oreshkina
  • Sound:
    Bad Zu, Sounds like a plan Studio
  • Project managers:
    Ivan Konstantinov, Yury Stefanov

We would like to thank Dr. Benjamin Neuman, Professor and Chair of Biological Sciences, Texas A&M University-Texarkana; Dr. Tai-huang Huang, Distinguished Research Fellow, Division of Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Nankang, Taipei; and Dr. Jason S. McLellan, Associate Professor, Molecular Biosciences Department at the University of Texas at Austin; authors of multiple research papers on the structure of coronaviruses or viral proteins, for their recommendations and helpful discussion of various aspects of the organization and genome packing of the SARS-CoV-2 virion.