Today we are sharing a recent publication from the VanderWaal lab looking at PRRSV sequences from Canada. The full publication is available in open access on the journal Pathogens’ website.
Methods
- 3,573 PRRSV-2 ORF5 sequences from 2020-2024
- From Quebec, Ontario, Manitoba, Alberta, Saskatchewan
- Analysis also included sequences from GenBank and the Morrison Swine Health Monitoring Project (MSHMP)
- Classification of lineage was completed using the PRRS-Loom webtool
- A spatiotemporal stratified subsampling methodology was used to narrow down the US and worldwide datasets and to account for geography, time of sampling, and genetic diversity.
- Phylogenetic trees, recombination analysis, and phylogeographic analysis were then performed on the remaining sequences
Results
- Five lineages (1, 5, 7, 8 and 9), subdivided into 13 sub-lineages (1A, 1B, 1C, 1E, 1F, 1H, 1I, 1J, 5A, 7, 8A, 8C and 9A) were identified in the Canadian sequences.
- 26.7% of the Canadian sequences could not be categorized by the model due to the large genetic diversity.
- Almost 34% of the dataset was considered to be “vaccine-like”.
- Two recombination events were detected, one in sub-lineage 1L, and the other one in sub-lineage 1K.
- More sub-lineage diversity was seen in sequences from Quebec compared to other Canadian provinces.
- Some sub-lineages i.e. 1C, 1H, 1I, 1K, 1L originated in Quebec and then moved to the USA whereas sub-lineages 1A, 1B, and 1E originated in the USA Midwest and then made their way to Canada.
Abstract
PRRSV-2 represents a major threat to the swine industry. Canada is one of the world’s leading pork producers and a major trading partner of live pigs with the United States, yet PRRSV-2 evolutionary dynamics in these two countries are often studied independently, partly due to limited publicly available sequence data from Canada. We analyzed more than 3000 PRRSV-2 ORF5 sequences collected between 2000 and 2024 from five Canadian provinces. Thirteen previously described sub-lineages were detected in Canada, while approximately one-third of the sequences could not be assigned to any known sub-lineage. Phylogenetic analyses incorporating global reference sequences revealed that most unclassified sequences clustered into four distinct monophyletic clades, exhibiting genetic distances greater than 9.5% from recognized sub-lineages. We propose two new sub-lineages, 1K and 1L, corresponding to clades that were prevalent and persistent over time, whereas the remaining two clades were rare and last detected in 2021. We reconstructed cross-border transmission histories and found that sub-lineages 1C, 1H, 1I, 1K, and 1L originated in Canada, whereas 1A, 1B, 1E, and 1F originated in the United States. Transmission patterns varied across sub-lineages, ranging from unidirectional to bidirectional movement. Our findings refine PRRSV-2 classification and provide insights to inform targeted surveillance, particularly at national borders.