The porcine reproductive and respiratory syndrome virus (PRRSV-2) remains the most economically devastating swine pathogen in the US, with losses exceeding $1 billion dollars annually. The emergence and turnover of dominant PRRSV lineages are well documented, typically occurring on a 1 to 4-year cycle.
Since its emergence in 2020, sub lineage 1C.5 has spread rapidly, contributing to more than 45% of US detections. In 2023, an unprecedented clonal expansion within 1C.5, designated as variant 1C.5.32, was identified in Iowa. Within a year, 1C.5.32 accounted for over 38% of all PRRSV-2 sequences in the state. This study characterized the genetic and epidemiological factors underpinning the success of this variant.
PRRSV-2 open reading frame 5 (ORF5) sequences from the Iowa State University Veterinary Diagnostic Laboratory collected between January 1, 2023, and March 31, 2025, were classified using Nextclade, identifying 1,214 sequences with 1C.5.32 designation over the timespan of the study.
Compared to other major lineages, variant 1C.5.32 displays lower reverse transcription quantitative polymerase chain reaction (RT-qPCR) cycle threshold (Ct) values, suggesting higher viral loads. The clonal expansion was characterized by maximum-likelihood phylogenetic inference, with within and between-clade distances calculated for major lineages.
This variant demonstrated reduced genetic diversity relative to its parental sublineage 1C.5. Effective population size was inferred using BEAST to assess genetic diversity and evolutionary dynamics. The prior 1C.5 sublineage derived from a recombination event. The 1C.5.32 variant sequences were screened for further recombination with RDP5, but none were detected.
Phylogeographic spread was modeled using Markov jumps and log Bayes factor-supported transitions between Iowa quadrants and US states. Bayesian phylogeographic analysis revealed strong transition signals from the northeastern quadrant of Iowa to surrounding regions, illustrating the spatial dynamics of its rapid expansion.
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