1887

Journal of General Virology header logo

Volume 97, Issue 9

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

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 , and . Only four RNA viruses were identified: porcine kobuvirus, porcine sapelovirus, atypical porcine pestivirus and a novel , 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): feral swine , metagenomic sequencing , pig , pneumovirus , virome and virus
© Microbiology Society
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.000554
2016-09-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/jgv/97/9/2090.html?itemId=/content/journal/jgv/10.1099/jgv.0.000554&mimeType=html&fmt=ahah

References

  1. Afonso C. L., Amarasinghe G. K., Bányai K., Bào Y., Basler C. F., Bavari S., Bejerman N., Blasdell K. R., Briand F. X. et al. 2016; Taxonomy of the order Mononegavirales: update 2016. Arch Virol 161:2351–2360 [View Article][PubMed]
     [Google Scholar]
  2. Allan G. M., McNeilly F., Walker I. W., Young J. A., Fee S., Douglas A. J., Adair B. M. 1998; Serological evidence for pneumovirus infections in pigs. Vet Rec 142:8–12 [View Article][PubMed]
     [Google Scholar]
  3. Baroch J. A., Gagnon C. A., Lacouture S., Gottschalk M. 2015; Exposure of feral swine (Sus scrofa) in the United States to selected pathogens. Can J Vet Res 79:74–78
     [Google Scholar]
  4. Brock L. G., Karron R. A., Krempl C. D., Collins P. L., Buchholz U. J. 2012; Evaluation of pneumonia virus of mice as a possible human pathogen. J Virol 86:5829–5843 [View Article][PubMed]
     [Google Scholar]
  5. Clavijo A., Nikooienejad A., Esfahani M. S., Metz R. P., Schwartz S., Atashpaz-Gargari E., Deliberto T. J., Lutman M. W., Pedersen K. et al. 2013; Identification and analysis of the first 2009 pandemic H1N1 influenza virus from U.S. feral swine. Zoonoses Public Health 60:327–335 [View Article][PubMed]
     [Google Scholar]
  6. Corn J. L., Cumbee J. C., Barfoot R., Erickson G. A. 2009; Pathogen exposure in feral swine populations geographically associated with high densities of transitional swine premises and commercial swine production. J Wildl Dis 45:713–721 [View Article][PubMed]
     [Google Scholar]
  7. Cramer S. D., Campbell G. A., Njaa B. L., Morgan S. E., Smith S. K., McLin W. R., Brodersen B. W., Wise A. G., Scherba G. et al. 2011; Pseudorabies virus infection in Oklahoma hunting dogs. J Vet Diagn Invest 23:915–923 [View Article][PubMed]
     [Google Scholar]
  8. Decaro N., Pinto P., Mari V., Elia G., Larocca V., Camero M., Terio V., Losurdo M., Martella V., Buonavoglia C. 2014; Full-genome analysis of a canine pneumovirus causing acute respiratory disease in dogs, Italy. PLoS One 9:e85220 [View Article][PubMed]
     [Google Scholar]
  9. Drexler J. F., Corman V. M., Müller M. A., Maganga G. D., Vallo P., Binger T., Gloza-Rausch F., Cottontail V. M., Rasche A. et al. 2012; Bats host major mammalian paramyxoviruses. Nat Commun 3:796 [View Article][PubMed]
     [Google Scholar]
  10. Fabisiak M., Szczotka A., Podgórska K., Stadejek T. 2012; Prevalence of infection and genetic diversity of porcine circovirus type 2 (PCV2) in wild boar (Sus scrofa) in Poland. J Wildl Dis 48:612–618 [View Article][PubMed]
     [Google Scholar]
  11. Feng Z., Baroch J. A., Long L.-P., Xu Y., Cunningham F. L., Pedersen K., Lutman M. W., Schmit B. S., Bowman A. S. et al. 2014; Influenza A subtype H3 viruses in feral swine, United States, 2011–2012. Emerg Infect Dis 20:839–842 [View Article]
     [Google Scholar]
  12. Fishaut M., Schwartzman J. D., McIntosh K., Mostow S. R. 1978; Behaviour of respiratory syncytial virus in piglet tracheal organ culture. J Infect Dis 138:644–649 [View Article][PubMed]
     [Google Scholar]
  13. Franzo G., Cortey M., de Castro A. M., Piovezan U., Szabo M. P., Drigo M., Segalés J., Richtzenhain L. J. 2015; Genetic characterisation of porcine circovirus type 2 (PCV2) strains from feral pigs in the Brazilian Pantanal: an opportunity to reconstruct the history of PCV2 evolution. Vet Microbiol 178:158–162 [View Article][PubMed]
     [Google Scholar]
  14. Gaskamp J. A., Gee K. L., Campbell T. A., Silvy N. J., Webb S. L. 2016; Pseudorabies virus and Brucella abortus from an expanding wild pig (Sus scrofa) population in Southern Oklahoma, USA. J Wildl Dis 52:383–386 [View Article][PubMed]
     [Google Scholar]
  15. Glineur S. F., Renshaw R. W., Percopo C. M., Dyer K. D., Dubovi E. J., Domachowske J. B., Rosenberg H. F. 2013; Novel pneumoviruses (PnVs): evolution and inflammatory pathology. Virology 443:257–264 [View Article][PubMed]
     [Google Scholar]
  16. Hause B. M., Collin E. A., Peddireddi L., Yuan F., Chen Z., Hesse R. A., Gauger P. C., Clement T., Fang Y., Anderson G. 2015; Discovery of a novel putative atypical porcine pestivirus in pigs in the USA. J Gen Virol 96:2994–2998 [View Article][PubMed]
     [Google Scholar]
  17. Hause B. M., Duff J. W., Scheidt A., Anderson G. 2016; Virus detection using metagenomic sequencing of swine nasal and rectal swabs. J Swine Health Prod (in press)
    [Google Scholar]
  18. Krempl C. D., Lamirande E. W., Collins P. L. 2005; Complete sequence of the RNA genome of pneumonia virus of mice (PVM). Virus Genes 30:237–249 [View Article][PubMed]
     [Google Scholar]
  19. Madarame H., Ogihara K., Kimura M., Nagai M., Omatsu T., Ochiai H., Mizutani T. 2014; Detection of a pneumonia virus of mice (PVM) in an African hedgehog (Atelerix arbiventris) with suspected wobbly hedgehog syndrome (WHS). Vet Microbiol 173:136–140 [View Article][PubMed]
     [Google Scholar]
  20. McGregor G. F., Gottschalk M., Godson D. L., Wilkins W., Bollinger T. K. 2015; Disease risks associated with free-ranging wild boar in Saskatchewan. Can Vet J 56:839–844
     [Google Scholar]
  21. Mitchell J. A., Cardwell J. M., Renshaw R. W., Dubovi E. J., Brownlie J. 2013; Detection of canine pneumovirus in dogs with canine infectious respiratory disease. J Clin Microbiol 51:4112–4119 [View Article][PubMed]
     [Google Scholar]
  22. Mitra N., Cernicchiaro N., Torres S., Li F., Hause B. M. 2016; Metagenomic characterization of the virome associated with bovine respiratory disease in feedlot cattle identified novel viruses and suggests an etiologic role for influenza D virus. J Gen Virol 97:1771–1784 [View Article][PubMed]
     [Google Scholar]
  23. Müller T., Hahn E. C., Tottewitz F., Kramer M., Klupp B. G., Mettenleiter T. C., Freuling C. 2011; Pseudorabies virus in wild swine: a global perspective. Arch Virol 156:1691–1705 [View Article][PubMed]
     [Google Scholar]
  24. Pedersen K., Bevins S. N., Baroch J. A., Cumbee J. C Jr, Chandler S. C., Woodruff B. S., Bigelow T. T., Deliberto T. J. 2013; Pseudorabies in feral swine in the United States 2009–2012. J Wildl Dis 49:709–713 [CrossRef]
     [Google Scholar]
  25. Percopo C. M., Dyer K. D., Karpe K. A., Domachowske J. B., Rosenberg H. F. 2014; Eosinophils and respiratory virus infection: a dual-standard curve qRT-PCR-based method for determining virus recovery from mouse lung tissue. Methods Mol Biol 1178:257–266 [CrossRef]
     [Google Scholar]
  26. Renshaw R. W., Zylich N. C., Laverack M. A., Glaser A. L., Dubovi E. J. 2010; Pneumovirus in dogs with acute respiratory disease. Emerg Infect Dis 16:993–995 [View Article][PubMed]
     [Google Scholar]
  27. Renshaw R., Laverack M., Zylich N., Glaser A., Dubovi E. 2011; Genomic analysis of a pneumovirus isolated from dogs with acute respiratory disease. Vet Microbiol 150:88–95 [View Article][PubMed]
     [Google Scholar]
  28. Rodriguez L. L., Bunch T. A., Fraire M., Llewellyn Z. N. 2000; Re-emergence of vesicular stomatitis in the western United States is associated with distinct viral genetic lineages. Virology 271:171–181 [View Article][PubMed]
     [Google Scholar]
  29. Shan T., Li L., Simmonds P., Wang C., Moeser A., Delwart E. 2011; The fecal virome of pigs on a high-density farm. J Virol 85:11697–11708 [View Article][PubMed]
     [Google Scholar]
  30. Stephenson R. J., Trible B. R., Wang Y., Kerrigan M. A., Goldstein S. M., Rowland R. R. 2015; Multiplex serology for common viral infections in feral pigs (Sus scrofa) in Hawaii between 2007 and 2010. J Wildl Dis 51:239–243 [View Article][PubMed]
     [Google Scholar]
  31. Thorpe L. C., Easton A. J. 2005; Genome sequence of the non-pathogenic strain 15 of pneumonia virus of mice and comparison with the genome of the pathogenic strain J3666. J Gen Virol 86:159–169 [View Article][PubMed]
     [Google Scholar]
  32. Wang L.-F., Collins P. L., Fouchier R. A. M., Kurath G., Lamb R. A., Randall R. E., Rima B. K. 2011; The family Paramyxoviridae . In Virus Taxonomy – Ninth Report of the International Committee on Taxonomy of Viruses pp 672–685 Edited by King A. M. Q., Adams M. J., Carstens E. B., Lefkowitz E. J. London, UK: Elsevier/Academic Press;
     [Google Scholar]
  33. Zhang B., Tang C., Yue H., Ren Y., Song Z. 2014; Viral metagenomics analysis demonstrates the diversity of viral flora in piglet diarrhoeic faeces in China. J Gen Virol 95:1603–1611 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.000554
Loading
Feral swine virome is dominated by single-stranded DNA viruses and contains a novel Orthopneumovirus which circulates both in feral and domestic swine
J. Gen. Virol. 97, 2090 (2016); https://doi.org/10.1099/jgv.0.000554
/content/journal/jgv/10.1099/jgv.0.000554
/content/journal/jgv/10.1099/jgv.0.000554
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error