Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine

Abstract

Feral swine are known reservoirs for various pathogens that can adversely affect domestic animals. To assess the viral ecology of feral swine in the USA, metagenomic sequencing was performed on 100 pooled nasal swabs. The virome was dominated by small, ssDNA viruses belonging to the families Circoviridae, Anelloviridae and Parvovirinae. Only four RNA viruses were identified: porcine kobuvirus, porcine sapelovirus, atypical porcine pestivirus and a novel Orthopneumovirus, provisionally named swine orthopneumovirus (SOV). SOV shared~90 % nucleotide identity to murine pneumonia virus (MPV) and canine pneumovirus. A modified, commercially available ELISA for MPV found that approximately 30 % of both feral and domestic swine sera were positive for antibodies cross-reactive with MPV. Quantitative reverse transcription-PCR identified two (2 %) and four (5.0 %) positive nasal swab pools from feral and domestic swine, respectively, confirming that SOV circulates in both herds.

The porcine virome and xenotransplantation

“…Torque teno virus (Anelloviridae) was the most commonly detected virus (73%), PCV2 was identified in 13% of the samples. Only four RNA viruses were identified: kobuvirus, sapelovirus, pestivirus and an orthopneumovirus [17]. This is in contrast to previous studies of the faecal virome which were dominated by RNA viruses [6,7].…”

“…When the virome of feral swine (wild boars) in the US was analysed, a total of 16 different viruses were identified [17]. Mainly single stranded DNA viruses were detected including Circoviridae, Anelloviridae and Parvovirinae.…”

ICTV Virus Taxonomy Profile: Pneumoviridae

“…Members of the Human orthopneumovirus species are divided into the co-circulating subgroups A1, A2, B1 and B2. Viruses closely related to murine orthopneumovirus have been isolated from dogs and pigs [6].…”

First demonstration of the circulation of a pneumovirus in French pigs by detection of anti-swine orthopneumovirus nucleoprotein antibodies

“…Seven different viruses have been identified in several animal species as belonging to this family: avian metapneumovirus (AMPV) and human metapneumovirus (HMPV) for the Metapneumovirus genus, bovine respiratory syncytial virus (BRSV), ovine respiratory syncytial virus (ORV), human respiratory syncytial virus (HRSV), pneumonia virus of mice (PVM), and canine pneumovirus (CPV) for the Orthopneumovirus genus. More recently, an eighth pneumovirus was identified by metagenomic sequencing of pooled nasal swabs in feral swine in the USA [ 4 ]. This newly identified Orthopneumovirus shows 93% and 91% protein identities with PVM and CPV, respectively, and was named swine Orthopneumovirus (SOV).…”

“…This newly identified Orthopneumovirus shows 93% and 91% protein identities with PVM and CPV, respectively, and was named swine Orthopneumovirus (SOV). Since no specific enzyme-linked immunosorbent assay (ELISA) is available for SOV, based on the close genetic relationship between PVM and SOV Hause et al used a commercial ELISA to detect antibodies to PVM and found that 31% of the analysed feral swine sera were antibody positive [ 4 ]. Finally, analyses by the same PVM ELISA of sera from different American farms revealed that sera were 33% to 93% positive, dependent on the farms, and confirmed that SOV is also present in domestic swine.…”