By Kim VanderWaal, Nakarin Pamornchainavakul, Cesar A. Corzo, Mariana Kikuti, Albert Rovira and Igor Paploski, University of Minnesota

When talking to practitioners, they will tell you that porcine reproductive and respiratory syndrome control feels like a moving target. Despite ever-growing investments aimed at preventing between-farm spread, PRRS incidence at the national scale remains relatively steady year-over-year. However, underneath this apparent steady-state, epidemic-like spread events occur every few years with the emergence of novel genetic variants (Figure 1). For instance, the Lineage 1A 1-7-4 virus (blue line) emerged in ~2014 and rapidly spread throughout the country.

UMN. Figure 1. The black line shows the overall population size of the PRRSV-2 lineage responsible for most outbreaks in in U.S. for the past decade (Lineage 1). Colored lines represent different sub-lineages within Lineage 1; the most common RFLP-type in each lineage is shown in parentheses.

PRRS is one of the most rapidly evolving viruses in the world. Even compared to other RNA viruses, the rate of change is exceptionally high for PRRSV, with close to 1% of the genome experiencing point mutations per year (Figure 2A). Not all mutations have an equal impact, but one can expect a general trend where viral attributes (immunological or virulence attributes, for example) shift gradually through time as mutations accrue. 

UMN. Figure 2 A/B.

Another evolutionary mechanism of viruses is recombination. In hosts that are co-infected with two variants, portions of the viral genomes from each variant may be interchanged or “re-combined” during replication, resulting in offspring that are a genetic mosaic of the two parental variants. In contrast to point mutations, recombination results in a sudden shift in the genome composition of a virus (Figure 2B).

Recombination sometimes translates into changes in the attributes or behavior of the virus, but that’s not always true. The impact of recombination on viral attributes depends on which portions of the genome are exchanged (Figure 2B). Compared to the parental variants, recombinant offspring may or may not differ in their production impacts or their ability to spread in pig populations.

We think that recombination is likely a common phenomenon that occurs in herds co-infected by multiple PRRSV variants, but recombination may go undetected in the absence of intensive whole genome sampling.  However, many recombination events may result in viruses that never establish themselves in the herd nor become widespread.  While it is clear that recombination plays a role in PRRSV evolution and that some emerging variants are recombinants, our current understanding of the genetic determinants of viral characteristics, such as virulence or cross-immunity, does not allow us predict the impact of recombination. 

We have two basic tools for understanding PRRSV evolution: sequencing of the ORF5 gene, and whole genome sequencing. Both tools can help answer questions about the evolution and the epidemiology of a particular PRRSV variant, and the choice of tool will depend on the question (Figure 3). In contrast to ORF5 sequencing, obtaining a high-quality field sample (i.e., low CT) is more important for generating a whole genome. Additionally, the analysis of WGS data is complex and often requires expert consultation, whereas ORF5 sequences are much more straight-forward to analyze and interpret.

UMN. Figure 3.

Of course, if our aim is to understand the genetic basis of viral attributes or to describe the evolutionary origin of novel variants, a whole genome perspective is critical and ORF5 will reveal only an incomplete picture. That being said, we don’t have good historical WGS data, which makes tracking evolutionary history with whole genomes more challenging. We also don’t have a deep enough understanding of the genetic basis of viral attributes to be able to glean those insights from whole genome data.

The most common reasons that practitioners submit samples for sequencing are to a) distinguish between a resident and new variant on the farm and attempt to determine the possible source of introduction, and b) track the spread of novel PRRS variants. For these questions, ORF5 often will provide a sufficient answer and WGS may not add a great deal of additional insight. However, this will not always be the case and a whole genome perspective may be needed for atypical cases. So, the choice of tool depends on the question and aims of the practitioner.

As one example of this, the emerging L1C-1-4-4 variant is a recombinant virus, which is apparent from examining whole genomes. However, this group of viruses still appears as a distinct divergent clade on phylogenetic trees based on the ORF5 gene. So a whole genome is not needed to identify whether a particular sequence is part of this group of viruses. However, you cannot fully understand the evolutionary origins of this variant without whole genome data. And, while we know that these L1C-1-4-4 viruses all descended from a recombination event sometime in the past, we do not understand enough about PRRS whole genomes to determine if the recombination event played a role in this variant’s highly transmissible and virulent characteristics observed in the field. 

The information presented in this article was summarized from a keynote presentation at the 2023 Allen D. Leman Swine Conference, “Chasing a moving target: Rapid evolution and spread of PRRSV in the U.S.”

This work was funded by the joint US-UK NIFA-NSF-NIH-BBSRC Ecology and Evolution of Infectious Disease award, the University of Minnesota College of Veterinary Medicine Signature Programs, and the USDA Critical Agricultural Research and Extension Program.  The Morrison Swine Health Monitoring Project is supported by the Swine Health Information Center.

References

Pamornchainavakul, N., Paploski, I. A. D., Makau, D. N., Kikuti, M., Rovira, A., Lycett, S., . . . VanderWaal, K. (2023). Mapping the Dynamics of Contemporary PRRSV-2 Evolution and Its Emergence and Spreading Hotspots in the U.S. Using Phylogeography. Pathogens, 12(5). doi:10.3390/pathogens12050740.

Pamornchainavakul, Nakarin, Mariana Kikuti, Igor A. D. Paploski, Dennis N. Makau, Pamornchainavakul, N., Kikuti, M., Paploski, I. A. D., Makau, D. N., Rovira, A., Corzo, C. A., & VanderWaal, K. (2022). Measuring How Recombination Re-shapes the Evolutionary History of PRRSV-2: A Genome-Based Phylodynamic Analysis of the Emergence of a Novel PRRSV-2 Variant. Frontiers in Veterinary Science, 9. doi:10.3389/fvets.2022.846904

Paploski, I. A., Pamornchainavakul, N., Makau, D. N., Rovira, A., Corzo, C. A., Schroeder, D. C., . . . VanderWaal, K. (2021). Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States. Vaccines, 9(6), 608.