The Definitive COVID-19 Cheat Sheet

Kyle Tretina, Ph.D.

Kyle Tretina, Ph.D., Genomics Application Scientist
Posted on July 7th, 2020

Introduction

If you’ve ever struggled with understanding the technical, specialized jargon that is often used when talking about COVID-19, you’re not alone. Fortunately, we’ve collected a team of clinicians and scientists to break down the meaning of the COVID-19-isms in a way that is understandable and memorable and includes the scientific data to back it up. We’ve interspersed figures with core ideas connecting the terms for the visual learners and to help you connect the dots.

Think of this as a pandemic cheat sheet that everyone should know in order to understand the wave of pandemic-related news reports and articles.

Biology Terms

BIG IDEA. SARS-CoV-2 is one example of a coronavirus and is the virus that causes the disease called COVID-19 (note: images not to scale)(1).

Coronavirus: a family of viruses named for the crown-like array of spikes on their surfaces. Including SARS-CoV-2, other viruses in this family are known to originate in bats, spill over to infect an intermediate host, and eventually cause widespread severe disease in humans (see SARS and MERS). It also includes other less dangerous viruses such as those that cause the common cold(2,3).

SARS-CoV-2: the name of the virus that causes COVID-19, also known as Severe Acute Respiratory Syndrome CoronaVirus 2). This virus is believed to have come from bats and possibly another animal before infecting humans(4).

COVID-19: the name of the disease caused by SARS-CoV-2, named by the World Health Organization (WHO) because it is a coronavirus-caused disease discovered in 2019(5).

ARDS (Acute Respiratory Distress Syndrome): is a serious condition where fluid builds up inside the tiny air sacs of the lungs, which leads to low blood oxygen levels and is one possible complication of COVID-19(6).

Ventilator: a medical device that helps hospital patients breathe(6,7).

Virus mutation: changes to the nucleic acid sequence (the nucleic acid of COVID- 19 is RNA) of the virus during an infection. Most scientists agree that there is only one strain of SARS-CoV-2 at the moment (8), so don’t worry about mutations right now(6–8).

Disease terms

BIG IDEA. An infected person with no symptoms (pre-symptomatic) can still spread COVID-19(9).

Incubation period: the amount of time between when a person becomes infected to when they get symptoms from that infection. For COVID-19 it is estimated to be 2 days(10).

Diagnosis: the identification of an illness by a medical doctor by examining symptoms and test results(11)

Asymptomatic infection: infected people who seem healthy throughout the whole infection (12)

Pre-symptomatic infection: infected before who haven’t had any symptoms, yet!(13)

Symptomatic infection: infected people who show signs of infection(11,14).

Super spreaders: an infected individual that spreads a disease to much more people than other infected individuals(15).

Immunity terms

Antibody: a protein made by immune cells in the body that can recognize an infectious agent and inactivate it(17)

Antigen: a protein or other substance that generates an immune response, especially antibodies

Immunity: any detectable immune response to an infection, possibly providing protection, but not always.

Immune protection: the development of an immune response that can protect an individual against a disease when the person is again in contact with the same bug(18).

Herd immunity: A few people that have not had the disease yet are protected by those surrounding them that have already had it.The critical number of people with immune protection required in order to provide indirect protection to non-immune people ranges typically between 70–90% (19).

Testing Terms

Big idea. There are three types of tests for COVID-19 in common use.

Viral test

  1. RT-PCR test: a test to detect the presence of the SARS-CoV-2 genetic material in a respiratory sample(21).
  2. Antigen test: a test to detect the presence of the SARS-CoV-2 particles in a respiratory sample.

Serological test (Antibody test): a test to detect the presence of antibodies that recognize a specific protein (such as a protein from SARS-CoV-2) in a blood sample(22).

There are three types of antibodies used in testing(22,23):

IgM antibody: the predominant antibody in the early primary immune response.

IgG antibody: the most abundant type of antibody in blood and the major antibody of the secondary immune response.

IgA antibody: the predominant antibody in mucous secretions such as saliva, tears, milk and intestinal juice.

Different types of samples can be used for COVID-19 testing(24):

Whole blood: unprocessed blood drawn directly from a body

Blood Plasma: the yellowish liquid part of the blood that carries cells and proteins throughout the body

Serum: plasma minus the clotting proteins (but including antibodies)

Nasopharyngeal swab/oropharyngeal swab: the use of an absorbent material (similar to a Q-tip) to swipe fluids from the back of the nose and/or mouth.

Sputum: the juicy mixture of saliva and mucus coughed up by sick people.

How good are the tests?

BIG IDEA: Scientists use sensitivity and specificity to measure the quality of their COVID-19 tests (25).

Test Sensitivity: also known as the true positive rate, is the proportion of people with the disease that also have a positive test result. That is: They are sick and the test is positive.

Test Specificity: also known as the true negative rate, is the proportion of people without the disease that also have a negative test result. That is: They are healthy and the test is negative.

False negative: a person with the disease who tests negative.

False positive: a person that does not have the disease who tests positive.

Personal protective equipment

PPE (personal protective equipment): the things people use to prevent infection like masks, face shields, gowns and gloves(26).

N95 mask: a specialized mask that is specifically designed to filter 95% of the air, and is now being used for the health personnel to provide protection against SARS-CoV-2(26,27).

Disease Control

Epidemiology: the study of disease spread and control(28)

Epidemic: a widespread disease

Pandemic: a disease that is affecting the whole world

Social Distancing : a set of practices that maintains a physical distance between people and reduces close interpersonal contact with the goal of preventing the transmission of a contagious disease. The CDC suggests 6 feet (about 2 arms’ length)(29).

Quarantine: It has been estimated that it can take up to 14 days for a person to show symptoms of the disease since the day the person is infected. It is why the term quarantine has been established for the days a person should stay at home when moving from one state to another or when it has been in contact with a possible COVID-19 infected person(10).

Flattening the curve: a public health strategy to slow the spread of a disease and keep the number of sick people below the capacity limits of the healthcare system. That way we are sure there are enough beds in general and intensive care beds and respirators in particular, for those that are very sick (29,30).

Ro (pronounced “R naught” or the reproduction number): for an infected person, the number of people that will acquire the infection from that person. It relates to how infective a person is(10,31).

Contact tracing: once an infection is detected, this is the detective work of finding people who may have come in contact with that person and collecting more information about those contacts, to prevent further spread(10).

New norm: All the new guidelines and rules to go back to work and socialize in the era of COVID-19.

Potential COVID-19 Treatments

BIG IDEA: biology, science, business and bureaucracy all contribute to how long it takes for a vaccine or other drug to be approved(2).

Vaccine: a substance (piece of the virus) given to a person to stimulate immune protection against a disease. It is the only treatment to prevent the infection. It is still under development(32).

Once infected, other treatments are being studied:

Hydroxychloroquine: a drug used to treat malaria, lupus, and rheumatoid arthritis. Early scientific evidence has not yet confirmed its usefulness for COVID-19.

Remdesivir: an antiviral drug used for HIV treatment. Early scientific evidence suggests that it may improve COVID-19 recovery time by a few days in certain cases, although it is not clear how broadly useful this drug will be (33).

Convalescent plasma: an experimental treatment for severe COVID-19 where patients receive plasma (containing antibodies) from other patients that have recovered from the disease(34). Early evidence suggests that it may work well in this setting, and further studies are investigating this treatment (34,35).

Clinical trial: a formal research experiment on human participants to test how safe a treatment is and how well it works. For instance, both hydroxychloroquine and Remdesivir are undergoing multiple clinical trials.


References

1. WHO. Naming the coronavirus disease (COVID-19) and the virus that causes it. who.int https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it.

2. Thompson, S. A. Opinion | How Long Will a Vaccine Really Take? https://www.nytimes.com/interactive/2020/04/30/opinion/coronavirus-covid-vaccine.html (2020).

3. NIH. Coronaviruses. niaid.nih.giv http://www.niaid.nih.gov/diseases-conditions/coronaviruses.

4. Boni, M. F. et al. Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic. bioRxiv 2020.03.30.015008 (2020) doi:10.1101/2020.03.30.015008.

5. WHO. Naming the coronavirus disease (COVID-19) and the virus that causes it. The World Health Organization https://www.who.int/emergencies/diseases/novel-coronavirus-2019/technical-guidance/naming-the-coronavirus-disease-(covid-2019)-and-the-virus-that-causes-it.

6. Staff. ARDS — Symptoms and causes. mayoclinic.org https://www.mayoclinic.org/diseases-conditions/ards/symptoms-causes/syc-20355576 (2018).

7. Hamilton, J. New Evidence Suggests COVID-19 Patients On Ventilators Usually Survive. NPR.org https://www.npr.org/sections/health-shots/2020/05/15/856768020/new-evidence-suggests-covid-19-patients-on-ventilators-usually-survive (2020).

8. Yong, E. There’s no clear evidence that the pandemic virus has evolved into significantly different forms — and there probably won’t be for months. The Atlantic https://www.theatlantic.com/health/archive/2020/05/coronavirus-strains-transmissible/611239/ (2020).

9. He, X. et al. Temporal dynamics in viral shedding and transmissibility of COVID-19. Nat. Med. 26, 672–675 (2020).

10. CDC. Coronavirus Disease 2019 (COVID-19). Centers for Disease Control and Prevention https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guidance-management-patients.html#:~:text=The%20incubation%20period%20for%20COVID,CoV%2D2%20infection. (2020).

11. Staff. Coronavirus disease 2019 (COVID-19) — Diagnosis and treatment. mayoclinic.org https://www.mayoclinic.org/diseases-conditions/coronavirus/diagnosis-treatment/drc-20479976 (2020).

12. Huang, P. WHO Creates ‘Confusion’ About Asymptomatic Spread. Here’s What We Know. NPR.org https://www.npr.org/sections/goatsandsoda/2020/06/09/873166418/who-creates-confusion-about-asymptomatic-spread-here-s-what-we-know (2020).

13. Furukawa, N. W., Brooks, J. T. & Sobel, J. Early Release — Evidence Supporting Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 While Presymptomatic or Asymptomatic. Emerging Infectious Diseases 26,.

14. CDC. Coronavirus Disease 2019 (COVID-19) — Symptoms. Centers for Disease Control and Prevention https://www.cdc.gov/coronavirus/2019-ncov/symptoms-testing/symptoms.html (2020).

15. Kupferschmidt, K. Why do some COVID-19 patients infect many others, whereas most don’t spread the virus at all? Science https://www.sciencemag.org/news/2020/05/why-do-some-covid-19-patients-infect-many-others-whereas-most-don-t-spread-virus-all (2020).

16. CDC. Vaccines: Vac-Gen/Immunity Types. CDC.gov https://www.cdc.gov/vaccines/vac-gen/immunity-types.htm (2019).

17. HHMI. Immunity and Tolerance. HHMI.org https://www.hhmi.org/research/immunity-and-tolerance.

18. HHMI. Cells of the Immune System. HHMI BioInteractive https://www.biointeractive.org/classroom-resources/cells-immune-system.

19. Rogers, L. S. & JH Bloomberg School of Public Health. What is Herd Immunity and How Can We Achieve It With COVID-19? Johns Hopkins Bloomberg School of Public Health https://www.jhsph.edu/covid-19/articles/achieving-herd-immunity-with-covid19.html (2020).

20. Office of the Commissioner. Coronavirus Testing Basics. U.S. Food and Drug Administration https://www.fda.gov/consumers/consumer-updates/coronavirus-testing-basics (2020).

21. Jawerth, N. How is the COVID-19 Virus Detected using Real Time RT-PCR? IAEA https://www.iaea.org/newscenter/news/how-is-the-covid-19-virus-detected-using-real-time-rt-pcr.

22. HHMI. Immunology Virtual Lab. HHMI BioInteractive https://www.biointeractive.org/classroom-resources/immunology-virtual-lab.

23. Nussenzweig, M. C. Immunity and Tolerance. HHMI.org https://www.hhmi.org/research/immunity-and-tolerance.

24. Staff. Blood Components. redcrossblood.org https://www.redcrossblood.org/donate-blood/how-to-donate/types-of-blood-donations/blood-components.html.

25. CDC. Principles of Epidemiology: Lesson 5, Appendix A|Self-Study Course SS1978|CDC. CDC.gov https://www.cdc.gov/csels/dsepd/ss1978/lesson5/appendixa.html (2020).

26. CDC. Respiratory Protection During Outbreaks: Respirators versus Surgical Masks. CDC.gov https://blogs.cdc.gov/niosh-science-blog/2020/04/09/masks-v-respirators/.

27. CDC. Respiratory Protection During Outbreaks: Respirators versus Surgical Masks. CDC.gov https://blogs.cdc.gov/niosh-science-blog/2020/04/09/masks-v-respirators/.

28. CDC. Epidemiology Glossary | Data and Statistics | Reproductive Health | CDC. CDC.gov https://www.cdc.gov/reproductivehealth/data_stats/glossary.html (2019).

29. CDC. Coronavirus Disease 2019 (COVID-19) — Checklist for Individuals and Families. CDC.gov https://www.cdc.gov/coronavirus/2019-ncov/daily-life-coping/checklist-household-ready.html (2020).

30. CDC. Principles of Epidemiology | Lesson 1 — Section 11. CDC.gov https://www.cdc.gov/csels/dsepd/ss1978/lesson1/section11.html (2020).

31. Roberts, S. Flattening the Coronavirus Curve. NY Times https://www.nytimes.com/article/flatten-curve-coronavirus.html (2020).

32. CDC. Don’t Wait. Vaccinate to help protect yourself and your loved ones. CDC.gov https://www.cdc.gov/vaccines/adults/index.html (2019).

33. Beigel, J. H. et al. Remdesivir for the Treatment of Covid-19 — Preliminary Report. N. Engl. J. Med. (2020) doi:10.1056/NEJMoa2007764.

34. Cohut, M. Convalescent plasma therapy for COVID-19: Why is it promising? Medical News Today https://www.medicalnewstoday.com/articles/using-convalescent-blood-to-treat-covid-19-is-it-possible (2020).

35. Casadevall, A., Joyner, M. J. & Pirofski, L.-A. A Randomized Trial of Convalescent Plasma for COVID-19 — Potentially Hopeful Signals. JAMA (2020) doi:10.1001/jama.2020.10218.



Kyle Tretina, Ph.D.

Kyle Tretina, Ph.D.

Kyle has extensive research expertise and interest in the area of genomics, microbiology and immunology. He received his Ph.D. from the University of Maryland, Baltimore working at the Institute for Genome Sciences and came to Meenta from a postdoc at Yale University.

Scientific responses to 3 common myths about COVID-19
July 7th, 2020
Kyle Tretina, Ph.D. Genomics Application Scientist