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.
Highlights
Over the last century, numerous equine viruses have been isolated and described [1,2,3,4] including equid alphaherpesviruses one and four (EHV-1 and EHV-4), associated with respiratory and neurological disease [5,6,7]
The equine viruses most commonly associated with respiratory disease are EHV-1, EHV-4, and equine influenza [5,35,36,37,38]
The six foals with fatal interstitial pneumonia analyzed here tested negative for equid influenza viral RNA, and EHV-1 and EHV-4 DNA, and no significant bacteria were isolated (Table 3)
Summary
Numerous equine viruses have been isolated and described [1,2,3,4] including equid alphaherpesviruses one and four (EHV-1 and EHV-4), associated with respiratory and neurological disease [5,6,7]. A flavivirus in the pegivirus genus named Theiler’s disease-associated virus (TDAV) was characterized using metatranscriptomics and was initially thought to cause equine serum hepatitis [16] Another pegivirus was detected by consensus PCR in horse plasma [17]. A flavivirus in the hepacivirus genus, initially identified in dog plasma, was subsequently shown to be a common but asymptomatic infection in horses [18] None of these 3 RNA viruses was reproducibly associated with equine serum hepatitis [19,20]. A study of sterile and non-sterile (e.g., feces) samples from horses revealed the presence of several circular DNA viral genomes of unknown tropism, as well as a second equine copiparvovirus named EqPV-CSF, in a horse with neurological problems [23]. Circovirus DNA was recently identified by viral metagenomics in the plasma of a horse with hepatitis [25]
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