PRRSV sequencing surveillance for the pathogenic 1-4-4 lineage 1C variant at the AHL

Jim Fairles and Davor Ojkic

Animal Health Laboratory, University of Guelph, Guelph, ON

AHL Newsletter 2021;25(3):17.

Restriction fragment length polymorphism (RFLP) analysis is been one of the tools used to study the molecular epidemiology of porcine reproductive and respiratory syndrome virus (PRRSV).  Currently, PRRSV ORF5 sequencing is the major method of PRRSV sequencing whereby homology tables and phylogenetic trees are generated and used to compare viruses.

The current sequencing software also automatically provides the traditional RFLP “number”.  This number is used to help name and categorize similar PRRSV viruses.  There are some concerns regarding this methodology however, as RFLP only analyzes very specific areas of the PRRSV ORF5 sequence and can produce results that are open to misconception.  For example, two 144 RFLP viruses can be quite different.

However, this nomenclature is still commonly used in the industry, therefore, AHL continues to report RFLP results to clients when sequence comparisons are performed.  Recently, a highly pathogenic PRRSV 1-4-4 lineage 1C variant in the USA has been associated with high rates of sow and piglet mortality, abortions and slow growth in finishers: https://farmscape.ca/f2ShowScript.aspx?i=27596.  AHL has obtained a copy of this sequence and added it to the standard list of sequences that are used to compare new sequences.  Historical data have been reviewed and 1-4-4 sequences have been compared with this new 1-4-4 lineage 1C variant, as seen in Table 1.

Recent Ontario sequences (2019-2021) have a maximum of only 87.9% homology to the US 1-4-4 variant.  To be considered “similar”, greater than 98% homology is required.  It is hoped that current biosecurity standards in the swine industry prevent this virulent variant from surfacing in Ontario.  AHL will continue to provide surveillance around this threat by monitoring sequence homology closely.  An incursion of this US PRRSV strain into Ontario would be considered a new and unusual event under the OMAFRA Animal Health Act, and as such, would be immediately notifiable.  AHL

Table 1.  Percentage homology of PRRSV 1-4-4 sequences identified at the AHL since 2019 compared to the pathogenic US 1-4-4 lineage 1C variant.