Putting DNA to Work
  INFECTIOUS DISEASE

Identify The Disease - Text Only Version

Every virus has its own DNA sequences. The goal is to probe them all.

In 2002, a number of people suddenly became ill with an unknown condition. The outbreak came to be known as Severe Acute Respiratory Syndrome, or SARS.

The identification of the cause of SARS provides an example of the great speed that modern DNA sequencing has brought to the detection of infectious diseases.

In this activity the user attempts to match an unknown virus with one of 11,000 sequences.

The user will see 11,000 DNA sequences taken from 1,000 viruses on the next screen.

When people became ill with SARS, the goal was to learn more about the SARS virus by comparing samples from sick patients to all of these sequences as quickly as possible.

Finding a match is extremely difficult.

Sequence Scanning

An unidentified virus sequence is shown in yellow letters on the black bar at the bottom. The user moves the scroll bar on the right to scan through the known virus sequences to place a match between the red lines, and identify the unknown virus. Then clicks "I found it", or lets the computer search for him/her by clicking "Find it for me".

The user may find a match; a sequence from human parainfluenza virus 3.

Streamlining the Process.

The "virus chip" is a new tool that uses the wealth of available DNA sequence information to identify disease agents quickly by comparing DNA sequences from all the known viruses with samples of the unknown virus.

Making a Virus Chip

The virus chip is an ordered arrangement of 11,000 specific 70-letter DNA sequences, which represent 1,000 different viruses. All of the sequences were shown in the previous activity.

To make and analyze a virus chip, a sample of each 70-letter sequences is prepared and arranged as a tiny dot on a small glass slide using a special robot. The virus chip can now be used to identify the cause of a disease.

Collecting DNA Samples

DNA samples are collected from an infected patient and an uninfected patient.

The DNA from the infected patient is tagged with a special marker to appear red.

The DNA from the uninfected, or control, patient is tagged with green.

Testing the Samples

The DNA samples from the two patients are then mixed together and injected under a glass cover slip on the virus chip. The strands of the tagged DNA will bind with matching strands of DNA on the virus chip.

The virus chip is then washed to remove any pieces DNA that did not bind with the DNA on the virus chip.

Visualizing the Results

Under a laser scanner the spots to which the tagged DNA matched will light up either green or yellow, if the tagged DNA is found in the control patient, or red, if the DNA is only found in the infected patient.

The red spots show the sequences that match the unknown virus, because they are only found in the infected patient.

Analyzing the Results

Sophisticated computer software is used to convert the information about the number, location, and intensity of the red spots into a bar code. Each line in the bar code corresponds to a red spot on the chip. The width of a line is determined by the intensity of the red color in that spot.

Scientists can look at these bar codes to quickly determine to what family a virus belongs and if it is a newly discovered virus. In the next activity, see if you can match up viral bar codes to known viruses to get a match.

Bar Code Scanning

In the activity a user is asked to choose one of three unidentified virus sequences; its bar code appears at the bottom on the right.

Then the user scrolls through the known virus sequences to find a place a match between the red lines, and identify the unknown virus. They click "I found it", or let the computer search for him/her by clicking "Find it for me".

The user may find 3 possible matches.

Match 1 is a sequence from human parainfluenza virus 3.

Match 2 is a sequence from human rhinovirus B.

In apparent match 3 the user correctly identifies the coronavirus family, but there is no perfect match. The sample is SARS, a coronavirus never seen before.


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