Use of new genomic tools in the fight against PRRS virus

Diseases are often perceived as having a single cause and in the case of infectious disease, we expect to identify a single infectious agent or microbe as the source. Yet this isn’t always the case, as our surrounding environment is more complex and often contains a larger diversity of microbes than those found in a laboratory setting. As a result, an infection may be caused by interactions between several pathogenic microbes. Thanks to the development of new biological analysis techniques over the last 15 years, it is now known that respiratory infections on pig farms are typically caused by more than one microbe (co-infection). For example, lung lesions in an individual pig might be caused by a viral species and a bacterial species or by two different types of viruses. We must keep co-infections in mind when identifying strategies to treat or prevent infectious diseases. Researchers must also understand the root cause of the morbidity observed during co-infections. For example, is the damage caused simultaneously by both infectious agents or does a single microbe cause the initial infection that weakens the pig’s defenses providing the opportunity for the second microbe to cause an infection. Depending on the scenario, it is possible that different prophylaxes or treatments will be selected.

Furthermore, the possibility of co-infections directly impacts diagnostic procedures. Typically, a veterinarian will select a diagnostic test that aims to identify a subset of microbes that are likely to cause the specific symptoms and lesions observed in the animal. These molecular tests are developed based on currently available biological data and technology to provide the fastest results at an affordable cost. However, like microbes, our knowledge and technology are constantly evolving. New sequencing technology (high throughput sequencing) that allows low cost whole genome sequencing of microbes is now part of the veterinarian’s diagnostic tool kit and is providing new interesting results.

Notably, the current gold standard used to diagnose porcine reproductive and respiratory syndrome (PRRS) virus is to detect a single gene that allows the discrimination between the non-pathogenic vaccine type and the pathogenic wild-type. Briefly, the diagnostic test is performed by using PCR to amplify a small fraction of the viral genome and does not involve whole viral genome sequencing. Although whole viral genome sequencing is now fast and affordable.

Earlier sequencing technologies were time consuming and expensive, as a result with these technologies sequencing the human genome (200 000 times larger that PRRS virus genome) required a concerted international effort, 2.7 billion dollars and 13 years (1990-2003). Nowadays, this great achievement would be accomplished in a few days in a single laboratory.

The team of Dr. Carl A. Gagnon, a CRIPA researcher at the Université de Montréal, asked PhD student, Christian Lalonde, to reanalyze the PRRSV-positive clinical samples stored in the freezer by the diagnostic service at the Faculty of Veterinary medicine. Surprisingly, this reanalysis revealed that in 5.5% of these samples, the pigs were actually infected with 2 different type of PRRS viruses: these pigs were co-infected. In some cases, vaccinal type and wild type viruses were found in the same pig. How do these co-infections impact on porcine health and treatment options? Researchers have yet to find out.

The most fascinating discovery that came from sequencing the entire genomes of these viruses was that previously identified vaccinal type viruses were not as they appeared. Based on the older diagnostic test that only test one gene, the herd was identified as vaccinated and this led the veterinarian to mistakenly exclude PRRS as a cause of the pulmonary problems. Yet, the pathogenic wild type virus had acquired a gene, specifically the gene used to differentiate the disease-causing virus from the vaccinal type. This isn’t unprecedented as biologists know that genomes can be modified under certain conditions. For example, viruses that infect the same host can swap some of their genes and the resulting virus, called a recombinant virus, has genes from both viral strains. In our re-analysis, newly identified recombinant PRRS viruses represented approximately 5.5% of the sequenced viruses. Based on the number of co-infections and recombinant viruses found in the freezer of the diagnostic service, this new sequencing method has the potential to dramatically improve the accuracy of a PRRS diagnosis in approximately 11% of cases.

The other interesting results arising from the whole genome sequencing analysis is that the PRRS viruses infecting Quebec herds have changed significantly from the vaccinal virus in recent years. These changes indicate convergent evolution of the pathogenic type that is divergent from the vaccinal virus. The impact of these genetic changes needs to be studied in greater detail.

In summary, the major findings of this reanalysis are that whole genome sequencing improves the accuracy of PRRS diagnosis by 11% compared to the current diagnostic test, decreases the rate of false identification of vaccinal types in a herd, and improves monitoring of genetic changes in the viral population.

Source: Presentation of March 12 2018, Café CRIPA, Génome complet du virus SRRP: surprises dans les échantillons cliniques, C. Lalonde, C. Provost and C.A. Gagnon.

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