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How to detect a virus

Today on Health Talk, we’re talking virus detection: how scientists come to suspect a new virus and the steps they take to develop a test to confirm their suspicions.

Developing the first test for a new virus is a laborious process, one with which University of Minnesota assistant scientists Sunny Sonnabend and Lindsey Raymond in the U of M’s Veterinary Diagnostic Laboratory are intimately familiar. These two scientists are part of the U of M College of Veterinary Medicine (CVM) team behind the nation’s first porcine epidemic diarrhea virus (PEDV) rapid detection test, unveiled earlier this year.

Here’s what it takes to develop a test like no other:

Step 1: Suspect there’s a new virus in town.

Prior to this year, the coronavirus behind PEDV had only been observed in countries outside the United States. Somehow the virus managed to jump the Atlantic (or Pacific, as we still don’t know where the virus came from) and cause extreme diarrhea, vomiting and dehydration — often leading to mortality — in pigs across the nation. PEDV’s arrival didn’t just make for an unpleasant experience all around, but it also led to extreme concern over the hardiness of existing U.S. biosecurity measures intended to keep oversees viruses like PEDV from spreading to North America.

Step 2: Investigate ways to combat the virus.

Once a farmer suspected his pig might be infected, he turned to veterinarians to find out if the suspected illness was, in fact, PEDV. Veterinarians turned to the nation’s scientists and experts for help, realizing there was no test to detect whether an illness could be attributed with certainty to this new strain of PEDV.

How To Detect A Virus

Step 3: Start working on a test.

This is where the CVM team including Sonnabend and Raymond comes in. The lab began creating a test to detect PEDV. They started by investigating how the new virus was similar to existing viruses. They learned that PEDV was a 99 percent match for the PEDV strain previously seen in Asia and Europe. Test development began from there.

The aim was to be able to routinely detect one particular section of ribonucleic acid (RNA), the carrier of a virus’ genetic information in many cases, with a high level of accuracy.

To do that, scientists extracted RNA from pig tissues found in the feces or intestines of animals presumably dead because of PEDV. Tissue samples were mashed up and spun down, in a repeated process that broke the cells open, added liquid and removed unwanted, additional bacteria. The end result was a few milliliters of purified and testable material.

To improve researchers’ ability to detect a hard-to-see section of RNA indicative of PEDV, the “clean” solution was then mixed with virus-detecting “primers” to amplify any trace of the virus to a detectable level.

The primers enabled the virus to replicate to a level that researchers could see with their Agarose gelbare eyes—or, in cases where the virus wasn’t present, not see at all. A peak in the test results graph was a confirmation of PEDV. A flat graph meant no PEDV in the sample at all.

“Probes” were later added to the test to allow computer-detection of the virus in lieu of having a researcher read each test result manually.

With the probes, primers, tissue sample and fully developed test in hand; the Veterinary Diagnostic Lab is now able to assess around 300 samples per hour for signs of PEDV. Within 24 hours, pig farmers and producers can learn if PEDV is at the root of the problem and begin taking steps to avoid spreading the virus further, if need be. Virus detection test completed, the CVM can proudly check the first step in prevention – early detection – off the list.