Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China

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.

contrasting

confidence: 55%

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

Hause

Padmanabhan

Pedersen

et al. 2016

“…PAs4 was previously shown to be commonly detected in swine diarrhoea samples in the USA (Xiao et al, 2013). PAs4 was also readily identified in both diarrhoeic and normal swine faeces in China (Zhang et al, 2014). An aetiological role for PAs4 in clinical disease has not been established.…”

mentioning

confidence: 92%

Widespread detection and characterization of porcine parainfluenza virus 1 in pigs in the USA

Palinski

Chen

Henningson

et al. 2016

Porcine parainfluenza virus 1 (PPIV1) was first identified in 2013 in slaughterhouse pigs in Hong Kong, China. Here, two near-complete genomes were assembled from swine exhibiting acute respiratory disease that were 90.0-95.3 % identical to Chinese PPIV1. Analysis of the HN gene from ten additional PPIV1-positive samples found 85.0-95.5 % identity, suggesting genetic diversity between strains. Molecular analysis identified 17 out of 279 (6.1 %) positive samples from pigs with respiratory disease. Eleven nursery pigs from a naturally infected herd were asymptomatic; however, nasal swabs from six pigs and the lungs of a single pig were quantitative reverse transcriptase (qRT)-PCR positive. Histopathology identified PPIV1 RNA in the nasal respiratory epithelium and trachea. Two serological assays demonstrated seroconversion of infected pigs and further analysis of 59 swine serum samples found 52.5 % and 66.1 % seropositivity, respectively. Taken together, the results confirm the widespread presence of PPIV1 in the US swine herd.

“…Phylogenetic analysis of the Pol and identification of two picornavirus capsid domains near the 3¢ terminus suggested inclusion of posavirus 3 in a new, unassigned family of Picornavirales (Hause et al, 2015a). Posavirus was also identified in faecal samples from pigs in China (Zhang et al, 2014).…”

mentioning

confidence: 93%

Highly diverse posaviruses in swine faeces are aquatic in origin

Hause

Palinski

Hesse

et al. 2016

Posaviruses are a group of highly divergent viruses identified in swine faeces that are distantly related to other members of the order Picornavirales. Eighteen posavirus genomes were assembled from 10 out of 25 (40 %) faecal-swab pools collected from healthy adult swine. Phylogenetic analysis of the conserved RNA-dependent RNA polymerase (Pol) domain found that posaviruses form a large, highly diverse, monophyletic clade, which includes similar viruses identified in human (husavirus) and fish (fisavirus) faeces or intestinal contents, respectively. Quantitative reverse transcription PCR analysis of water samples collected from commercial swine barns identified four out of 19 (21 %) samples were positive using a 5¢-nuclease assay targeting the Pol region of posavirus 1. ICPD (immunoprecipitation coupled to PCR detection) assays to explore serological evidence of posavirus infection found only a single positive sample, suggesting posaviruses do not commonly infect swine, and together these results suggests a likely aquatic host.