The Power of a Test

Diagnostic Testing
For weeks, Marcus had been checking the Centers for Disease Control and Prevention (CDC) website in the evenings after work. The virus, referred to as SARS-CoV-2, was spreading across the globe and seemed to be taking hold in the United States, with cases of the associated respiratory disease COVID-19 increasing daily. The World Health Organization (WHO) had officially classified the outbreak as a pandemic, and large numbers of cases were being reported in the state where Marcus lived.

When he arrived for work this morning, the laboratory director, Dr. Elaine Cordozo, called an emergency staff meeting. When everyone had gathered in the conference room, she made an announcement. “Working with our state’s health department, we have been given the important job of serving as a sample processing and testing laboratory for COVID-19 infection. We will begin preparations for conducting this testing immediately and will commence testing of patient samples as soon as possible.”

The next several days were a blur for Marcus and his colleagues. They worked quickly to get the laboratory testing set up. Finally, the day arrived that they would commence with COVID-19 diagnostic testing.

How does COVID-19 testing work? How do healthcare professionals make a diagnosis of COVID-19 infection? Let’s follow Marcus through the process.

Read the following graphic article to learn about the SARS-CoV-2 virus and how it infects the human body:
• Corum, J. and C. Zimmer. 2020. How coronavirus hijacks your cells. The New York Times.
<https://www.nytimes.com/interactive/2020/03/11/science/how-coronavirus-hijacks-your-cells.html>

Watch this video to learn about the COVID-19 testing process:
• The Jackson Laboratory. 2020. COVID-19 testing process. Running time: 1:15 min.
<https://youtu.be/ORRLyCZpIus>

Carefully read the CDC test protocol outlined in Table 1 below to learn about how SARS-CoV-2 is detected after the sample is collected from the patient and received by the clinical lab:


Stage 3 Data analysis To generate diagnostic report
Analyze graphs of quantitative PCR results (fluorescence data and PCR cycle number) for each sample to determine if it is SARS-CoV-2 virus positive, negative, or ambiguous. The fewer cycles it takes to detect, the more abundant the viral genome is in the sample. Cycle number and level of fluorescence all contribute to interpreting results as strong positives, strong negatives, or ambiguous.

Questions
1. After reviewing the protocol above, what terms have you heard of before?
2. After reviewing the protocol above, what terms are unfamiliar to you?

Read the following graphic article to learn about the SARS- CoV-2 genome:
• Corum, J. and C. Zimmer. 2020. Bad news wrapped in

protein: inside the coronavirus genome. The New York Times.
<https://www.nytimes.com/interactive/2020/04/03/science/coronavirus-genome-bad-news-wrapped-in-protein.html>

Let’s take a closer look at the equipment used and at each stage of the protocol to better understand how a sample is processed and analyzed for COVID-19.

General Equipment Used for Sample Preparation
The essential molecular biology equipment used in a diagnostic lab is depicted in Figure 1. After individual patient samples arrive at the diagnostic lab, they are processed in small tubes stored on tube racks. Micropipettors are used to draw up liquid solutions used in the various steps of this protocol. Multiple samples can be handled in parallel together on microplates to save time. These plates can hold 96 different samples, and are loaded onto a special PCR machine used for the amplification and detection of the target sequence.

Questions
3. What samples are typically collected from patients suspected of coronavirus exposure?
4. Name three sources of nucleic acids you expect to find in a patient sample.