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PRRSView helps classify, track the PRRSV circulating in your farm

Tools help swine veterinarians, producers assess their own sequences, translate the received sequence into useful PRRSV epidemiological information.

January 3, 2023

5 Min Read
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National Pork Board

Porcine reproductive and respiratory syndrome virus is the preeminent viral swine disease in the United States. In 2014, PRRSV was estimated to cause production losses of $664 million annually in the United States (1). As this study is now a decade old and the emergence of newly aggressive PRRSV strains has occurred since then, it is likely the cost has increased in proportion to the complexity of the PRRSV challenges that still occur in the United States.

Current methods of PRRS control involve a mixture of strict biosecurity practices in conjunction with immunological solutions including the use of modified live vaccines or live virus inoculation, in addition to routine sample submission for testing to veterinary diagnostic labs  when PRRSV is suspected on a farm.

When a client (veterinarian or producer) receives a PRRSV diagnosis containing an ORF5 sequence from their VDL, there are two primary questions that will likely follow; what genetic group is this sequence, and where did it originate? The first question was historically answered by providing a restriction fragment length polymorphism pattern (2), and the primary use was to determine if the PRRSV strain was the same one currently circulating on the farm, or if a new strain had been introduced. Currently, the method of classifying PRRSV ORF5 sequences is changing as VDLs transition towards an ORF5 genetic lineage classification-based nomenclatures (3, 4). The genetic lineage system is more applicable to the vast genetic diversity observed in PRRSV circulating in swine and is more appropriate to use for tracking the genetic similarities between sequences.

As the PRRSV situation has grown more complex in the US, the frequency of the aforementioned client questions to the Iowa State VDL has increased. The adoption of the ORF5 lineage system has also created a need to develop tools that can support rapid classification of clients' sequences.

To meet the growing demand of these requests and provide user-friendly supportive infrastructure in place, the ISU VDL designed PRRSView. This analytical PRRSV ORF5 sequence web-based portal allows clients to investigate and explore these questions independently.

Currently three tools are available:

  1. An ORF5 lineage identification tool

  2. An ORF5 BLAST tool

  3. An ORF5 RFLP tool for clients still interested in the historic RFLP classification scheme

Each tool is designed to help the client answer a specific diagnostic question.

ORF5 lineage tool
Designed to classify ORF5 sequences into a specific genetic lineage, addressing the question of which genetic group their PRRSV ORF5 sequence is most related to, this tool assesses the genetic lineage of an ORF5 sequence by building a phylogenetic tree based on a curated set of reference sequences from each lineage (Figure 1). In addition, this tool will calculate the similarity of the entered ORF5 sequence with five vaccine strains; Ingelvac ATP, Ingelvac MLV, Primepac, Fostera and Prevacent as well as calculate the similarity to the PRRSV-1 Lelystad strain and provides the RFLP pattern of the sequence. This tool produces an ORF5 dendrogram for the client to inspect with regards to the classification of their sequence, and the vaccine similarities are provided in a table.

ISU Fig 1 010323.png

ORF5 BLAST tool:
Designed to assess the question of where in the USA has a specific PRRSV ORF5 strain been observed and circulating in swine, the tool approaches this question by comparing the producer's PRRSV ORF5 sequence with prior sequences collected by the ISU VDL. Up to 10 similar strains are provided after completing the BLAST function, with information about the date the sequence was generated, the state of origin, the lineage classification, RFLP pattern and the percent homology to the query sequence provided. This information is neatly summarized in a table, with the addition of a pie chart displaying the breakdown of states where the PRRSV sequence has been detected.

ORF5 RFLP Tool:
This tool calculates the RFLP pattern of a producer's PRRSV ORF5 sequence that is submitted to the tool by the producer.

Video tutorials regarding the use of each tool have been created and are provided in a "Tutorials" section. An example FASTA file is also provided for the tutorial.

The focus of PRRSView is to provide analytical support, allowing veterinarians and producers to assess their own sequences and translate the received sequence into useful PRRSV epidemiological information. This web-based portal was designed with the client as the focus, and provides intuitive and visual output. Veterinarians and swine producers are encouraged to give the website a try and provide feedback for further development.

References:
1. Holtkamp DJ, Kliebenstein JB, Neumann EJ, Zimmerman JJ, Rotto HF, Yoder TK, et al. Assessment of the economic impact of porcine reproductive and respiratory syndrome virus on United States pork producers. Journal of Swine Health and Production. 2013;21(2):72-84.

2. Wesley RD, Mengeling WL, Lager KM, Clouser DF, Landgraf JG, Frey ML. Differentiation of a porcine reproductive and respiratory syndrome virus vaccine strain from North American field strains by restriction fragment length polymorphism analysis of ORF 5. J Vet Diagn Invest. 1998;10(2):140-4.

3. Shi M, Lam TT, Hon CC, Murtaugh MP, Davies PR, Hui RK, et al. Phylogeny-based evolutionary, demographical, and geographical dissection of North American type 2 porcine reproductive and respiratory syndrome viruses. J Virol. 2010;84(17):8700-11.

4. Paploski IAD, Pamornchainavakul N, Makau DN, Rovira A, Corzo CA, Schroeder DC, et al. Phylogenetic Structure and Sequential Dominance of Sub-Lineages of PRRSV Type-2 Lineage 1 in the United States. Vaccines (Basel). 2021;9(6).

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