Leman: Porcine astrovirus 4
Porcine astrovirus 4 is evolving locally within production companies and sites
30 March 2026
1 minute read
By: [Excerpts of a poster presentation by Mariana Meneguzzi and colleagues at the University of Minnesota and the University of Florida, USA, during the 2025 Leman Swine Conference]
Astroviruses (AstVs) infect a wide range of mammals and birds and have been associated with gastrointestinal, neurological, and respiratory clinical presentations, as well as asymptomatic infections.
A major limitation in advancing the understanding of AstVs is the lack of widely available diagnostic tools. In pigs, five genotypes (PAstV1 through PAstV5) have been identified in both healthy and diarrheic pigs worldwide. In the United States, PAstV4 has been detected in nasal swabs, intestinal contents, and fecal samples of pigs. Recently, the ability of PAstV4 to cause clinical respiratory signs as a primary pathogen was confirmed. However, detection has primarily relied on RT-PCR–based methods and has been largely limited to individual samples with few reports addressing herd-level characterization.
Oral fluids (OF) are a composite sample type that have been frequently used in swine medicine as a practical tool for herd-level monitoring. The phylogenetic characterization of PAstVs in swine herds from the US, particularly using sequencing data from OF samples, has not yet been documented. In this study, probe-enriched long-read sequencing data was used to recover whole or partial genomes of PAstV4 from OF samples collected between 2017 and 2018 from wean-to-finish herds in the Midwestern United States.
Using this novel data, a phylogenetic analysis of PAstV4 genomes was conducted and their diversity was evaluated across 10 different production companies comprising 59 sites. A phylogenetic tree was constructed from the aligned sequences. Pairwise genomic distances of the samples were calculated excluding PAstV4 reference sequences from this analysis. PAstV4 was the most abundant virus recovered across most samples.
Most samples yielded a high genome fraction (ranging from 10.33% to 99.58%), and substantial coverage depth (ranging from 0.11 to 1848.51) was obtained for PAstV4. Genetic distance analysis revealed that PAstV4 sequences were more similar within sites than across different sites and production companies.
The observed similarity of within-site and across-company genetic diversity suggests that PAstV4 is evolving locally within production companies or sites. This study is the first to utilize OF samples with target-enrichment and long-read sequencing technology for the recovery of partial and whole PAstV4 genomes and to investigate their genetic diversity in US commercial swine herds.
