This is our Friday rubric: every week a new Science Page from the Bob Morrison’s Swine Health Monitoring Project. The previous editions of the science page are available on our website.
In today’s Science Page Kim VanderWaal, Nakarin Pamornchainavakul, and Mariana Kikuti explore a new UMN VDL tool which allows people to upload their sequence and get their genetic variant classification but also know which PRRS variants are on the rise.
What are genetic variants? Genetic variants are groups of closely related sequences (on average, <2.5% different on ORF5) that provide a finer-scale level of classification within PRRSV-2 sub-lineages. These provide a label that can facilitate communication and monitoring of different PRRSV-2 viruses circulating in a farm, system, or region. Compared to RFLPs, variant classifications are more reliable for determining relatedness (i.e., whether virus A is the same or different than virus B), and are useful for epidemiological investigations, such as determining possible sources of introduction and tracking between-farm spread. The UMN and ISU Veterinary Diagnostic Labs, MSHMP, and SDRS already have capabilities to classify sequences by variant. The PRRS-Loom webtool (see below) was also developed for end-users to classify their own sequences and to report general epidemiological trends.
How common is each variant (“Variant list” tab on PRRS-Loom)? Also available on the webtool is a list of all currently identified variants in the U.S. The “percent.12.months” column shows the percentage of sequences from the past 12 months that belong to each variant. In the right column, you can find which variants are associated with commercial MLVs.
Which variants are on-the-rise? In the same tab (“Variant list” tab), the U.S. occurrence trend indicates whether the occurrence of a variant is accelerating (more than doubled in the past one year compared to two years ago), decelerating (decreased by one half in the past year compared to two years ago), or somewhere in between (stable incidence). In the future, we plan to provide an indicator of the predicted growth trajectory of a variant for the next year.
History of variant splits (“Splitting variants” tab)? A small percentage of sequences (~5%) are part of variants that arose from the splitting of an existing variant. Nearly three quarters of such sequences were part of the recent split of variant 1C.5. Variants are split when there is an offshoot that shows substantial genetic divergence from the original variant. A history of these splits can be found in the “Splitting variants” tab.
How can I classify my sequences? The PRRS-Loom webtool allows any user to upload their sequences (no data is retained by the webtool) for variant classification. In the webtool, sequences can be uploaded as a FASTA file or copy-pasted into the window. Sequences that cannot be assigned to any variant with >0.25 probability listed as “unclassified.”
Explore PRRS-Loom functionalities to uncover its value as a vital resource for both practitioners and researches for variant classification and tracking trends in PRRSV-2 molecular epidemiology.
See the paper: VanderWaal et al. 2025. PRRSV-2 variant classification: a dynamic nomenclature for enhanced monitoring and surveillance. mSphere 10:e00709-24. https://doi.org/10.1128/msphere.00709 -24