COVID-19 Mapping

Our Mission

Create a comprehensive model demonstrating the internal impacts of the SARS-CoV-2 virus on the human body. We are interested in how the different systems of the body react and interact with the virus; how the workings of these internal systems can lead to possible treatments for infected patients and in developing protective vaccines.

Project Instructions

Our project can be viewed on a Thinglink page. You can navigate through the page clicking on the icons located on various parts of the body to learn more.

  • Thinglinks: Arrow icons will take you to other more specific Thinglinks, and you can use the home icons on the top rights of the Thinglinks to return to the main page. Book icons represent articles, photo icons lead to visuals, and magnifying glasses are models related to the SARS-CoV-2 virus that we have created.

  • Loopy models: To use click on the up or down arrows located on any of the nodes and watch its "contents" travel to and interact with other nodes. The + and - signs on the edges indicate positive and negative relationships between edges. Feel free to explore the indirect impacts which changing one node has on all the others within the systems.

  • SageModeler: To run a model, make sure to that the simulate arrow in the top left corner of the screen is open. Once open, to run the model press on the "record" button. Feel free to adjust the steps.

Feel free to reference our Tools page for a visuals of the different types of models and to see how we used them.

Now that you know the basics on how to use our project, have fun and feel free to explore!


Please use this glossary to better understand the terms used within our models.

  • ACE2 (angiotensin-converting enzyme 2): a membrane protein that is present in many cells of the human body. SARS-CoV-2 viruses often enter cells via this pathway.

  • AKI (Acute Kidney Injury): a sudden episode of kidney failure or kidney damage that happens within a few hours or a few days.

  • Alveolus: any of the many tiny air sacs of the lungs which allow for rapid gaseous exchange.

  • Anosmia: the partial or complete loss of the sense of smell. It is considered to be one of the symptoms of COVID-19.

  • ARDS (acute respiratory distress syndrome): An acute lung condition where organs have inadequate oxygen supply due to fluid buildup in the lungs. It has been commonly observed in patients being hospitalized for COVID-19.

  • B Cell: A type of white blood cell that makes antibodies. Also known as B lymphocytes.

  • Cytokine: small signaling molecules produced typically by immune cells.

  • Cytokine storm: in which cells release too many cytokines. This can lead to an overreaction of the immune system, eventually cause organ failure and/ or death. It has been commonly observed in people who develop severe cases of COVID-19.

  • ELISpot (Enzyme-linked immunosorbent spot assay): a laboratory procedure to detect antibody-secreting B cells.

  • Epithelium: one of the four types of body tissues, it is the thin tissue forming the outer layer of a body's surface and lining the alimentary canal and other hollow structures.

  • ER (Endoplasmic reticulum): a large organelle made of membranous sheets and tubules, it is the transportation system of a cell.

  • ERGIC (ER–Golgi intermediate compartment): a complex membrane system between the rough endoplasmic reticulum (ER) and the Golgi apparatus.

  • Golgi Apparatus: the cell organelle responsible for transporting, modifying, and packaging proteins and lipids into vesicles for delivery to targeted destinations.

  • Hypoxia: a condition in which the body, or parts of it, is deprived of oxygen.

  • IFN-gamma (Interferon gamma): a cytokine critical to both innate and adaptive immunity, and functions as the primary activator of macrophages, in addition to stimulating natural killer cells and neutrophils.

  • Keratinocytes: the most common type of skin cells.

  • Macrophage: specialized cells involved in the detection, phagocytosis, and destruction of bacteria and other harmful organisms.

  • MERS (Middle East Respiratory Syndrome): an illness caused by a coronavirus first discovered in Saudi Arabia in 2012.

  • Natural Killer Cells: a white blood cell, a type of immune cell that has small particles with enzymes that can kill tumor cells or cells infected with a virus.

  • Neutrophil: a type of white blood cell that protects you from infections.

  • Olfaction: the sensation or action of smelling

  • Polyproteins: a large protein that is split into smaller proteins with different biological functions

  • Phagocytosis: a process by which certain living cells called phagocytes ingest or engulf other cells or particles.

  • Pulmonary scarring: the scarring of the lungs causing the lung tissue to be thick and still

  • Pulse Oximetry: a noninvasive test that measures the oxygen level in your blood

  • Regulatory T cells: a specialized subpopulation of T cells that act to suppress the immune response

Tools Used


In order to create an interactive graphic which viewers may use to navigate our model we used thinglink. We embedded links to our models, graphics and informational resources


Our loopy simulations demonstrate feedback loops in simple and interactive ways.

Sage Modeler:

To allow for more quantitative and observable changes to occur within our models we used the Sage Modeler. When viewing the models, users can manipulate the amounts of different variables and view the results. Tables and graphs can also be used to view the loops.


For simple animations, we created gifs to illustrate how various systems look like when they are functioning.

Our Project


While we strive to provide you with the most up-to-date information about the internal impacts of the SARS-CoV-2 virus on the human body, our site is by no means meant to provide medical advice. To view the most recent research and guidance on the novel coronavirus, please refer to the CDC as well as your state and local health departments.

Works Cited

Here is the complete list of works we consulted to create our project.

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The content of these pages was created by students for students with the help of educators, modelers, and scientists. The views expressed herein are those of the authors and do not necessarily reflect the views of NSF or ISB.