Whole genome sequencing provides answer in PRRSV investigation

Whole genome sequencing had a deeper discriminatory power and provided more information when compared to classical ORF5 Sanger sequencing.


By Sunil Mor and Albert Rovira, University of Minnesota College of Veterinary Medicine Veterinary Diagnostic Laboratory

via National Hog Farmer - Feb 11, 2020


Porcine reproductive and respiratory syndrome continues to challenge the swine industry in many ways. As an RNA virus, it is well-documented that this virus has the ability to change constantly. As these changes accumulate through time, viral diversity increases which in turn becomes a challenge for the pig as the immune system does not recognize the virus and thus, previously generated immunity will only protect partially.


PRRS virus changes through either mutation (e.g. minor changes in its genome) or through recombination which occurs when two different viral strains are coinfecting the same pig, they exchange fragments of their genome and a whole new virus is then generated.


Currently, producers and practitioners work intensely to protect herds from new introduction of viruses as the cost of an outbreak continues to be significant due to throughput disruption, morbidity and interventions aimed at controlling the outbreak. Within the prevention measures adopted, biosecurity programs play an important role as they are a first line of defense in avoiding transmission.


However, in certain regions of the country the establishment of herd immunity as a mitigating factor also plays a role. Immunity can be established after an outbreak of PRRS virus, or through exposure to the virus by the use of live and killed vaccines. Presently, PRRSV vaccines are being used in different ways and on different animals (e.g. sows, gilts and growing pigs). In certain occasions, both the wildtype virus and the vaccine strain virus can be present in one pig which may increase the chances of new strain generation.


Recently, we developed the capability of sequencing the whole virus as opposed to small portions as it has been done for the last couple of decades. This breakthrough has allowed us to open a whole new chapter in describing the diversity of the virus and at the same time it has enabled practitioners to better understand field scenarios, such as outbreak investigations as it will be summarized in this article.


The case described here summarizes the recombination of two PRRSV vaccine strains. This case occurred in a...