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Fatally Flawed?

Early Genetic Testing for the COVID-19 Virus


Amy C. Groth
Department of Biology
Eastern Connecticut State University


The novel coronavirus (SARS-CoV-2), which causes the respiratory illness COVID-19, was first detected in China in late 2019 and rapidly spread throughout the globe in the first few months of 2020.  Efforts to slow the spread of the virus in the United States were hampered by a lack of testing, due in part to defects in the initial test kits sent to labs across the country from the Centers for Disease Control and Prevention (CDC). In this directed case study, students will explore the different classes of viruses, the various types of possible pathogen tests and the importance of controls and assay design in designing diagnostic tests. Students will also utilize online databases and programs to identify the regions targeted in the CDC test, analyze the similarity between the coronaviruses that cause SARS and COVID-19, estimate the mutation rate of SARS-CoV-2 and apply that knowledge to generate hypotheses about the efficacy of testing methods for SARS-CoV-2. The case is designed for upper-level biology classes in molecular biology, genetics, biotechnology, virology and potentially cell biology, microbiology, or bioinformatics.


  • Describe viruses and classify the three different types based on their genomes.
  • Describe the possible methods of testing for pathogens and the controls and reagents required for proper testing.
  • Compare and contrast potential testing methods for a novel, rapidly spreading RNA virus, such as a coronavirus.
  • Utilize genetic databases to identify genetic sequences and compare viral genomes.
  • Calculate an estimated mutation frequency of SARS-CoV-2 based on available sequence data.


COVID-19; SARS-CoV-2; coronavirus; virus; pandemic; SARS; BLAST; BLAT; GenBank; mutation; PCR; qPCR; TaqMan; alignment; positive control; negative control; genetic test;

Topical Areas


Educational Level

Undergraduate lower division, Undergraduate upper division


PDF, Word

Type / Methods

Directed, Laboratory



Subject Headings

Biology (General)  |   Bioinformatics  |   Biotechnology  |   Cell Biology  |   Forensic Science  |   Genetics / Heredity  |   Microbiology  |   Molecular Biology  |   Science (General)  |  

Date Posted


Teaching Notes

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Supplemental Materials

For the convenience of students, a worksheet repeating the questions and tasks from Part II of the case is provided below in an editable format.


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