Detection and characterization of a novel genotype of porcine astrovirus 4 from nasal swabs from pigs with acute respiratory disease

Metagenomic sequencing of three nasal swabs collected from 10- to 21-day-old pigs exhibiting unexplained acute respiratory disease from two different commercial production facilities in Oklahoma identified a novel genotype of porcine astrovirus 4 (PAstV-4). The genomes had only similar to 75 % nucleotide sequence identity to previously characterized PAstV-4 isolates, while the capsid-encoding ORF2 had only similar to 53 % amino acid sequence identity to reference strains. A TaqMan assay targeting the novel ORF2 gene found 21 % and 19 % incidence in nasal and fecal swabs, respectively, submitted for unrelated diagnostic testing. PAstV-4 RNA levels were significantly higher (P = 0.04) in nasal swabs, suggesting a possible atypical respiratory tropism.