Sign up now!
Don't show this again
Download the report!Continue to Site >
or wait 7 secs

Thank you for confirming your subscription!

(And remember, if ever you want to change your email preferences or unsubscribe, just click on the links at the bottom of any email.)

We’re glad you’re enjoying Pig Health Today.
Access is free but you’ll need to register to view more content.
Already registered? Sign In
Tap to download the app


Collect articles and features into your own report to read later, print or share with others

Create a New Report


Read Later

Create a new report

Report title (required) Brief description (optional)
follow us

You must be logged in to edit your profile.

Favorites Read Later My Reports PHT Special Reports
Pig Health Today is equipped with some amazing (and free) tools for organizing and sharing content, as well as creating your own magazines and special reports. To access them, please register today.
Sponsored by Zoetis

Pig Health Today | Sponsored by Zoetis


Molecular diagnostic tools help distinguish wild-type and vaccine strains of PRRSV

Porcine reproductive and respiratory syndrome virus (PRRSV) continues to challenge the US swine industry. The virus has become more difficult to control despite aggressive biosecurity methods, multiple commercial vaccines, live-virus inoculation methods and the implementation of vaccination protocols, said Phillip Gauger, DVM, PhD, in a recent research paper.1

Fortunately, multiple molecular diagnostic assays are available for detecting, sequencing and characterizing PRRSV, said Gauger, who is a diagnostic pathologist with the Iowa State University Veterinary Diagnostic Laboratory and leader of the molecular diagnostics section.

Challenges with PRRSV

“One particular challenge facing the industry has evolved through the use of modified-live PRRSV (MLV-PRRSV) vaccines and the inability of diagnostic tests to distinguish between the detection of wild-type PRRSV (WT-PRRSV) and/or vaccine-like strains of the virus,” Gauger said.

“Vaccine-like MLV-PRRSV can replicate in vaccinated animals for long periods of time; is capable of transmission to unvaccinated pigs; can genetically evolve through point mutations in the genome; and may experience recombination with WT-PRRSV.”

These factors can complicate the overall epidemiology or genetic ecology of PRRSV, and multiple tests or sequencing assays may be needed to distinguish between the presence of MLV-PRRSV or WT-PRRSV when mixed infections are suspected, Gauger said.

New testing options available

New molecular testing methods have been developed to not only detect PRRSV in a specimen but also characterize the presence of different PRRSV strains in a production system. These methods attempt to distinguish between detection of a MLV-PRRSV, WT-PRRSV or multiple strains of the virus, Gauger explained.

PRRS CLAMP refers to a molecular diagnostic sequencing tool that can help distinguish between the presence of wild-type and vaccine strains of PRRSV.

“CLAMP is a term — not an acronym — to suggest what the assay will do during its performance,” Gauger said. “Thus, it clamps down on the homologous sequence of a MLV-PRRSV and prevents amplification and sequencing of that gene. CLAMP is the bridged nucleic acid designed to bind tightly to the homologous target, when present, and ultimately allows preferential sequencing of a WT-PRRSV.”

Numerous molecular diagnostic assays are presently available to detect PRRSV in swine diagnostic specimens, Gauger said, but each one has certain benefits and limitations (see box).

Future promising

Next-generation sequencing offers a range of processes that can provide the whole-genome sequence of a specific virus, Gauger explained. It can also detect the presence of novel viruses or allow for deep sequencing of the microbiome.

“For routine diagnostic purposes, PRRSV whole-genome sequencing may be an appropriate option to answer a diagnostic question or monitor the epidemiology of a PRRSV circulating in a production system,” he said.

“Although no molecular diagnostic test is perfect, these tests and combinations of different assays improve the probability of detecting and characterizing a strain or multiple strains of PRRSV present in a group of pigs,” Gauger added.

“They also help reduce the risks associated with moving pigs that are unknowingly infected with WT-PRRSV, especially when MLV-PRRSV is present in the same population.”

Existing Diagnostic Tools

PRRSV-screening real-time polymerase chain reaction (PCR) assay: These tests are highly sensitive and can detect low concentrations of PRRSV and all strains. They are highly specific and multiplexed for PRRSV type 1 or type 2 species but are not designed for further characterization of the virus nucleic acid and are not capable of differentiating different genetic strains of the virus, Gauger said. If a PRRSV-screening PCR assay is positive, additional testing may be needed.

PRRSV ORF5 gene sequencing: This test is a molecular diagnostic assay based on amplification of the ORF5 gene followed by the selective determination of the sequence of nucleotides within the gene. “Diagnostic reports with ORF5 sequence data will also include a comparison of nucleotide identity with the MLV-PRRSV vaccine strains,” Gauger said.

PRRSV vaccine-like reverse transcription real-time PCR: “This test can detect the presence of MLV-PRRSV and is suggested for use in PRRSV monitoring protocols in combination with other diagnostic tests (PRRSV-screen PCR and/or sequencing),” Gauger said. “Or, it may be used when the history, clinical impressions and vaccine use are well-known to justify the use of this assay,” Gauger said.

PRRSV CLAMP sequencing assays: This assay is used when both MLV-PRRSV and WT-PRRSV are suspected in a population of pigs. The CLAMP process utilizes a bridged nucleic acid as described earlier to prevent amplification and sequencing of MLV-PRRSV, allowing preferential sequencing and detection of WT-PRRSV, if present. It can detect WT-PRRSV sequences of lower concentration in vaccinated pigs and helps reduce the risk of transmitting a WT-PRRSV that could remain undetected without the more advanced molecular tools currently available, Gauger said.



1 Gauger P, Harmon K. Iowa State University Veterinary Diagnostic Laboratory, Department of Veterinary Diagnostic and Production Animal Medicine, Ames, Iowa. PRRS CLAMP: molecular diagnostic tools to distinguish wild-type and vaccine strains of PRRSV. Presented at Am Assoc Swine Vet annual meeting, March 2021.

Share It
Challenges associated with controlling porcine reproductive and respiratory syndrome virus (PRRSV) have resulted in the increased use of molecular diagnostic tests and sequencing, according to Phillip Gauger, DVM, PhD, Iowa State University.

Click an icon to share this information with your industry contacts.

Posted on September 16, 2021

tags: ,
  • Genetic diversity, changing clinical picture make IAV-S detection challenging

    By Phillip Gauger, DVM, MS, PhD Associate Professor Iowa State University   Influenza A virus in swine (IAV-S) remains among the top health challenges facing the US swine industry and, worse yet, it may be on the increase.1 Based on porcine respiratory samples...

  • Understanding swine flu’s diversity key to better control programs

    The number of swine influenza cases as well as the diversity of circulating flu viruses have increased in the past several years, based on experience at Iowa State’s Veterinary Diagnostic Laboratory, according to Phillip Gauger, DVM, associate professor at the...

You must be logged in to edit your profile.

Share It
When a sow doesn’t reach her full potential, the cost to the farm and the income stream of the sow herd is often “grossly underestimated,” said John Deen, DVM, PhD, a professor at the University of Minnesota.

Click an icon to share this information with your industry contacts.
Google Translate is provided on this website as a reference tool. However, Poultry Health Today and its sponsor and affiliates do not guarantee in any way the accuracy of the translated content and are not responsible for any event resulting from the use of the translation provided by Google. By choosing a language other than English from the Google Translate menu, the user agrees to withhold all liability and/or damage that may occur to the user by depending on or using the translation by Google.