New Parvoviruses and Picornavirus in Tissues and Feces of Foals with Interstitial Pneumonia

Abstract

Six foals with interstitial pneumonia of undetermined etiology from Southern California were analyzed by viral metagenomics. Spleen, lung, and colon content samples obtained during necropsy from each animal were pooled, and nucleic acids from virus-like particles enriched for deep sequencing. The recently described equine copiparvovirus named eqcopivirus, as well as three previously uncharacterized viruses, were identified. The complete ORFs genomes of two closely related protoparvoviruses, and of a bocaparvovirus, plus the partial genome of a picornavirus were assembled. The parvoviruses were classified as members of new ungulate protoparvovirus and bocaparvovirus species in the Parvoviridae family. The picornavirus was classified as a new species in the Salivirus genus of the Picornaviridae family. Spleen, lung, and colon content samples from each foal were then tested for these viral genomes by nested PCR and RT-PCR. When present, parvoviruses were detected in both feces and spleen. The picornavirus, protoparvovirus, and eqcopivirus genomes were detected in the lungs of one animal each. Three foals were co-infected with the picornavirus and either a protoparvovirus, bocaparvovirus, or eqcopivirus. Two other foals were infected with a protoparvovirus only. No viral infection was detected in one animal. The complete ORFs of the first equine protoparvoviruses and bocaparvovirus, the partial ORF of the third equine picornavirus, and their detection in tissues of foals with interstitial pneumonia are described here. Testing the involvement of these viruses in fatal interstitial pneumonia or other equine diseases will require larger epidemiological and/or inoculation studies.

Keywords: Equus caballus; cabavirus; foal; metagenomics; parvovirus; picornavirus.

Figure 1

(A) Phylogenetic analysis of equine parvoviruses NS1. (B) Phylogenetic analysis of equine parvoviruses VP1. The scale indicates amino acid substitutions per position. The amino acid (aa) pairwise alignments were performed with Geneious R10 software using the in-built MAFFT algorithm. The phylogenetic trees were constructed using the maximum likelihood method with substitution model: Le Gascuel 2008 based model with gamma-distributed (G+) for NS1 and VP1 in MEGA software version X. Viral taxa from this study are highlighted with triangles.

Figure 2

Phylogenetic analysis of RdRp (3CDpol) protein region of novel equine cabavirus picornavirus. The amino acid phylogenetic tree was constructed using the maximum likelihood method with two substitution models: Le Gascuel 2008 model based with gamma distributed, invariant sites (G + I) for 3CD in MEGA software version X. Viral taxon from this study is highlighted with triangle.