Quick Quiz: Outbreak Scenario

What to know

This page guides you through an activity to learn how genomic sequencing can help identify infectious diseases, determine their severity, track their source, and inform treatment and prevention actions.

Letters in four colors indicating the four types of nucleotide bases in a DNA strand say "Sequence the Source"

Sequence the Source

In this activity, there is an outbreak of Pathogen X in your community.

As a scientist in a local public health department, you and your team must extract genomic data from patient samples collected in the community. This detailed data holds the key to how the pathogen functions.

The genomic data will be connected to information from the patient, such as what foods they ate or if they had contact with certain animals. Using the combined data, you will determine which strain of the pathogen is causing people to get sick and how it is spreading.

Step 1: Sequence the data

Patient samples are sent to public health labs. Scientists extract the pathogen's genetic material—it's DNA or RNA—and read the genomic data.

Here is one of the samples your team is analyzing:

A strand of DNA with one fragment labeled with "CGATCGAAGAT."
Pathogen DNA is extracted from the sample. The genomic data can help scientists identify the strain infecting the patient.

Step 2: Analyze the data

Bioinformaticians use powerful computers to analyze the pathogen’s genomic data. The data are often visualized in phylogenetic trees. Phylogenetic trees are diagrams that help us visualize how organisms are related to each other.

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A simplified phylogenetic tree with 4 strains. Each has a distinct gene fragment and a short list of characteristics.
Match the sequence of the letters in the patient sample to the strains shown here. Which strain does this patient have?

Step 3: Link the data

By combining the genomic data with public health data, epidemiologists can learn the source of the disease, how it is spreading, and how to stop it.

The patient's public health data. "This patient ate tacos with lettuce. They also recently adopted a puppy."
By integrating patient data with the genomic data, public health officials can investigate potential sources of the outbreak.

Review what you know

At this point, you and your team have collected 30 samples, sequenced them, analyzed them, and integrated the public health data for those patients. In this activity, researchers found six potential sources for the pathogen:

  • Lettuce
  • New Puppy
  • Backyard Poultry
  • Cheese
  • Deli Meat
  • Pet Turtles
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A phylogenetic tree shows colored dots for each sample collected. Next to the tree is patient data for each patient.
This collected data from 30 patients shows what we know at this stage of the outbreak.

Guess the source!

Based on your analysis, make your decision regarding the strain and the potential source of the outbreak. Use the information above to guide your choice.

  • Can you tell which strain is behind the current outbreak?
  • What do you think is the likely source?

Submit your answers here: Sequence the Source

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Content Source:
National Center for Emerging and Zoonotic Infectious Diseases (NCEZID)