Why Sequence?

You have the diagnostics in hand. The results tie your stomach in knots, the sample is PRRS virus  PCR positive. If you are lucky, you have not experienced this before but if you are like the other 99% of the people in the swine industry, you have had this feeling. But what now? Do you have enough information with this result to take your next steps?

In brief, sequencing a PRRSV PCR positive sample, along with advanced diagnostic software and interpretation from your veterinarian can help identify where the PRRSV came from and possibly how it got there. The goal is to make better diagnostic decisions and implement preventative biosecurity measures in the future.payne_brian

PCR to the Sequence
A positive PCR result means that the lab found PRRS viral RNA in the sample sent to them. The RNA may be from vaccine virus or may be from a field strain of PRRSV. If it is the field strain, where did it come from? Fortunately, scientists have developed technology called nucleic acid sequencing to look further at a PRRSV PCR positive sample to identify the variant of PRRSV and allowing us to look at the genetic makeup of the virus.

The Power of a Database and Advanced Diagnostic Software
Sequence information from one variant, by itself, does not allow us to make many decisions as it only represents a small portion of the virus and does not provide information on which vaccine to use, whether the pig is protected against PRRSV, etc. Simply put: it is an epidemiological tool. We must have other sequences so we can compare them. It is like a jigsaw puzzle; having a single piece with no others surrounding it does not allow you to visualize the picture. With the entire sequence database, we can then start comparing your strain to others. We can see if they are genetically similar or different and to what degree they are related. The more numerous the jigsaw pieces (sequences) that are added to the database, the more interconnections that can be made and, therefore, the picture becomes more clear.

We use a software program called Disease Bioportal from University of California at Davis to visually investigate our PRRSV sequence database with mapping, charting, ‘family trees’ called dendograms, timeline animations, and reports. When there is a database of historic and recent PRRSV isolates (a multitude of puzzle pieces) from a region or from a flow or from a single company, we are often able to make strong correlations. And like a jigsaw puzzle, should there not be enough puzzle pieces fitting together, the image and solution to where the PRRS virus came from, may not be found.

Our Successful Jigsaw Puzzling, Examples
1.Improving Biosecurity: Use of Sequencing and Bioportal allowed us to track a PRRSV from one state to another and then through five different farms. Investigations allowed us to understand that the PRRSV was introduced via semen, was laterally shed between pigs, and transported mechanically via hared agricultural equipment. This allowed for discussions on which biosecurity and prevention practices to be implemented.

2. Utilizing Resources Wisely: Sequencing PRRSV positive PCR samples in three individual downstream finishers that 1) are sourced from a single sow farm and 2) all became PRRSV-positive within 3 weeks of one another showed that they shared a closely related variant”. But with thorough analysis, it was determined the three finisher farms could not have become infected at the same time from the sow farm. This allowed limited resources to be focused at the finisher farms and not at the sow herd.

3. Eliminating Panic: Generically, PRRSV variants are given a 3-digit ID called an RFLP (such as 1-7-4 or 1-3-2). These are based off the genetic pattern of the virus and where specific enzymes (endonucleases) can react with the genetic material. However, while helpful at times, it can also be confusing. For example, one farm’s gilt-iso site came back with an RFLP of 1-1-4, one-month after the sow herd was diagnosed with a 1-3-4 strain. Potential panic of having two strains involved was alleviated when we investigated further using Bioportal and determined that a minor mutation of the original strain caused the change in the RFLP; in other words, it was not a new virus.

We often recommend sequencing for PRRSV but not always. Talk with your consulting veterinarian to help determine if this advanced diagnostic technology is beneficial for you and your business.

For any questions or concerns regarding this topic please do not hesitate to contact our Pipestone team of veterinarians and swine specialist at 507-562-PIGS.

Brian Payne, DVM
Pipestone Veterinary Services