Virus Genes

, Volume 54, Issue 6, pp 768–778 | Cite as

Evaluation of the serum virome in calves persistently infected with Pestivirus A, presenting or not presenting mucosal disease

  • Matheus N. Weber
  • Samuel P. Cibulski
  • Simone Silveira
  • Franciele M. Siqueira
  • Ana Cristina S. Mósena
  • Mariana S. da Silva
  • Juliana C. Olegário
  • Ana Paula M. Varela
  • Thaís F. Teixeira
  • Matheus V. Bianchi
  • David Driemeier
  • Saulo P. Pavarini
  • Fabiana Q. Mayer
  • Paulo M. Roehe
  • Cláudio W. CanalEmail author


Bovine viral diarrhea virus 1, reclassified as Pestivirus A, causes an economically important cattle disease that is distributed worldwide. Pestivirus A may cause persistent infection in that calves excrete the virus throughout their lives, spreading the infection in the herd. Many persistently infected (PI) calves die in the first 2 years of life from mucosal disease (MD) or secondary infections, probably as a consequence of virus-induced immune depression. Here, high-throughput sequencing (HTS) was applied for evaluation of the total virome in sera of (i) PI calves displaying clinically apparent MD (n = 8); (ii) PI calves with no signs of MD (n = 8); and (iii) control, Pestivirus A-free calves (n = 8). All the groups were collected at the same time and from the same herd. Serum samples from calves in each of the groups were pooled, submitted to viral RNA/DNA enrichment, and sequenced by HTS. Viral genomes of Pestivirus A, Ungulate erythroparvovirus 1, bosavirus (BosV), and hypothetical circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses were identified. Specific real-time PCR assays were developed to determine the frequency of occurrence of such viruses in each of the groups. The absolute number of distinct viral genomes detected in both PI calf groups was higher than in the control group, as revealed by higher number of reads, contigs, and genomes, representing a wider range of taxons. Genomes representing members of the family Parvoviridae, such as U. erythroparvovirus 1 and BosV, were most frequently detected in all the three groups of calves. Only in MD-affected PI calves, we found two previously unreported Hypothetical single-stranded DNA genomes clustered along with CRESS-DNA viruses. These findings reveal that parvoviruses were the most frequently detected viral genomes in cattle serum; its frequency of detection bears no statistical correlation with the status of calves in relation to Pestivirus A infection, since clinically normal or MD-affected/non-affected PI calves were infected with similar U. erythroparvovirus 1 genome loads. Moreover, MD-affected PI calves were shown to support viremia of CRESS-DNA viral genomes; however, the meaning of such correlation remains to be established.


BVDV Persistent infection Mucosal disease Virome NGS 



Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul (FAPERGS), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES), and Propesq/UFRGS supported this study. Cláudio Wageck Canal and Paulo Michel Roehe are CNPq productivity research fellows. Matheus Nunes Weber was sponsored by a scholarship from CNPq (process 155366/2016-5) during this study. Funding was provided by Pró-Reitoria de Pesquisa, Universidade Federal do Rio Grande do Sul.

Author contributions

Conceptualization: MNW, SPC, FMS, SS, ACSM, MVB, DD and SPP. Data curation: MNW, SPC, SS, and JCO. Formal analysis: MNW, SPC, SS, FMS, MSS, and ACSM. Investigation: SS, MSS, ACSM, and MVB. Methodology: MNW, SPC, JCO, and FQM. Software: MNW, SPC, FQM, APMV, TFT, and PMR. Supervision: FQM, PMR, and CWC. Writing: MNW, FMS, FQM, PMR, and CWC.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.

Ethical approval

The project was registered with the Ethics Committee on the Use of Animals (CEUA) of Universidade Federal do Rio Grande do Sul under protocol number # 31976.

Supplementary material

11262_2018_1599_MOESM1_ESM.docx (15 kb)
Supplementary material 1 (DOCX 15 KB)


  1. 1.
    Yeşilbağ K, Alpay G, Becher P (2017) Variability and global distribution of subgenotypes of bovine viral diarrhea virus. Viruses 9:128. CrossRefPubMedCentralGoogle Scholar
  2. 2.
    Richter V, Lebl K, Baumgartner W et al (2017) A systematic worldwide review of the direct monetary losses in cattle due to bovine viral diarrhoea virus infection. Vet J 220:80–87. CrossRefPubMedGoogle Scholar
  3. 3.
    Smith DB, Meyers G, Bukh J et al (2017) Proposed revision to the taxonomy of the genus Pestivirus, family Flaviviridae. J Gen Virol 98:2106–2112. CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Simmonds P, Becher P, Bukh J et al (2017) ICTV virus taxonomy profile: Flaviviridae. J Gen Virol 98:2–3. CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Vilcek S, Paton DJ, Durkovic B et al (2001) Bovine viral diarrhoea virus genotype 1 can be separated into at least eleven genetic groups. Arch Virol 146:99–115CrossRefGoogle Scholar
  6. 6.
    Deng M, Ji S, Fei W et al (2015) Prevalence study and genetic typing of bovine viral diarrhea virus (BVDV) in four bovine species in China. PLoS ONE 10:e0134777. CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Baker JC (1995) The clinical manifestations of bovine viral diarrhea infection. Vet Clin North Am 11:425–445Google Scholar
  8. 8.
    MacLachlan NJ, Dubovi EJ (2011) Flaviviridae. In: MacLachlan NJ, Dubovi EJ (eds) Fenner’s veterinary virology, 4th edn. Academic Press, London, pp 467–481Google Scholar
  9. 9.
    Brock KV (2003) The persistence of bovine viral diarrhea virus. Biologicals 31:133–135. CrossRefPubMedGoogle Scholar
  10. 10.
    Bianchi MV, Konradt G, Souza SO et al (2016) Natural outbreak of BVDV-1d-induced mucosal disease lacking intestinal lesions. Vet Pathol 54:1–7. CrossRefGoogle Scholar
  11. 11.
    Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351. CrossRefPubMedGoogle Scholar
  12. 12.
    Kohl C, Nitsche A, Kurth A (2015) Metagenomics-driven virome: current procedures and new additions. Br J Virol 2:96–101. CrossRefGoogle Scholar
  13. 13.
    Virgin HW (2014) The virome in mammalian physiology and disease. Cell 157:142–150. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Moreno PS, Wagner J, Mansfield CS et al (2017) Characterisation of the canine faecal virome in healthy dogs and dogs with acute diarrhoea using shotgun metagenomics. PLoS ONE 12:e0178433. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Delwart EL (2007) Viral metagenomics. Rev Med Virol 17:115–131. CrossRefPubMedGoogle Scholar
  16. 16.
    Hoffmann B, Scheuch M, Hoper D et al (2012) Novel orthobunyavirus in cattle, Europe, 2011. Emerg Infect Dis 18:469–472. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Hause BM, Collin EA, Peddireddi L et al (2015) Discovery of a novel putative atypical porcine pestivirus in pigs in the USA. J Gen Virol 96:2994–2998. CrossRefPubMedGoogle Scholar
  18. 18.
    Ng TFF, Kondov NO, Deng X et al (2015) A metagenomics and case-control study to identify viruses associated with bovine respiratory disease. J Virol 89:5340–5349. CrossRefPubMedPubMedCentralGoogle Scholar
  19. 19.
    Sadeghi M, Kapusinszky B, Yugo DM et al (2017) Virome of US bovine calf serum. Biologicals 46:64–67. CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Toohey-Kurth K, Sibley SD, Goldberg TL (2016) Metagenomic assessment of adventitious viruses in commercial bovine sera. Biologicals 47:64–68. CrossRefGoogle Scholar
  21. 21.
    Wang H, Li S, Mahmood A et al (2018) Plasma virome of cattle from forest region revealed diverse small circular ssDNA viral genomes. Virol J 15:11. CrossRefPubMedPubMedCentralGoogle Scholar
  22. 22.
    Weber MN, Silveira S, Machado G et al (2014) High frequency of bovine viral diarrhea virus type 2 in Southern Brazil. Virus Res 191:117–124. CrossRefPubMedGoogle Scholar
  23. 23.
    Weber MN, Galuppo AG, Budaszewski RF et al (2013) Evaluation of prenucleic acid extraction for increasing sensitivity of detection of virus in bovine follicular fluid pools. Theriogenology 79:980–985. CrossRefPubMedGoogle Scholar
  24. 24.
    Thurber RV, Haynes M, Breitbart M et al (2009) Laboratory procedures to generate viral metagenomes. Nat Protoc 4:470–483. CrossRefPubMedGoogle Scholar
  25. 25.
    Sambrook J, Russel DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor, USAGoogle Scholar
  26. 26.
    Niel C, Diniz-Mendes L, Devalle S (2005) Rolling-circle amplification of Torque teno virus (TTV) complete genomes from human and swine sera and identification of a novel swine TTV genogroup. J Gen Virol 86:1343–1347. CrossRefPubMedGoogle Scholar
  27. 27.
    Bankevich A, Nurk S, Antipov D et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. CrossRefPubMedPubMedCentralGoogle Scholar
  28. 28.
    Gotz S, Garcia-Gomez JM, Terol J et al (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 36:3420–3435. CrossRefPubMedPubMedCentralGoogle Scholar
  29. 29.
    Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797CrossRefGoogle Scholar
  30. 30.
    Tamura K, Stecher G, Peterson D et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729. CrossRefPubMedPubMedCentralGoogle Scholar
  31. 31.
    Patience C, Wilkinson DA, Weiss RA (1997) Our retroviral heritage. Trends Genet 13:116–120. CrossRefPubMedGoogle Scholar
  32. 32.
    Katzourakis A, Gifford RJ (2010) Endogenous viral elements in animal genomes. PLoS Genet 6:e1001191. CrossRefPubMedPubMedCentralGoogle Scholar
  33. 33.
    Piccinini R, Luzzago C, Frigerio M et al (2006) Comparison of blood non-specific immune parameters in bovine virus diarrhoea virus (BVDV) persistently infected and in immune heifers. J Vet Med 53:62–67. CrossRefGoogle Scholar
  34. 34.
    Bolin SR, Ridpath JF (1989) Specificity of neutralizing and precipitating antibodies induced in healthy calves by monovalent modified-live bovine viral diarrhea virus vaccines. Am J Vet Res 50:817–821PubMedGoogle Scholar
  35. 35.
    Gånheim C, Hultén C, Carlsson U et al (2003) The acute phase response in calves experimentally infected with bovine viral diarrhoea virus and/or Mannheimia haemolytica. J Vet Med B 50:183–190CrossRefGoogle Scholar
  36. 36.
    Taxis TM, Bauermann FV, Ridpath JF, Casas E (2017) Circulating microRNAS in serum from cattle challenged with bovine viral diarrhea virus. Front Genet 8:91. CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Bohac JG, Yates WD (1980) Concurrent bovine virus diarrhea and bovine papular stomatitis infection in a calf. Can Vet J 21:310–313PubMedPubMedCentralGoogle Scholar
  38. 38.
    Ames TR (1986) The causative agent of BVD: its epidemiology and pathogenesis. Vet Med 81:846–869Google Scholar
  39. 39.
    Moustafa A, Xie C, Kirkness E et al (2017) The blood DNA virome in 8,000 humans. PLoS Pathog 13:e1006292CrossRefGoogle Scholar
  40. 40.
    Allander T, Emerson SU, Engle RE et al (2001) A virus discovery method incorporating DNase treatment and its application to the identification of two bovine parvovirus species. Proc Natl Acad Sci USA 98:11609–11614. CrossRefPubMedGoogle Scholar
  41. 41.
    Cotmore SF, Agbandje-Mckenna M, Chiorini JA et al (2014) The family Parvoviridae. Arch Virol 159:1239–1247. CrossRefPubMedGoogle Scholar
  42. 42.
    Xiao CT, Halbur PG, Opriessnig T (2013) Molecular evolutionary genetic analysis of emerging parvoviruses identified in pigs. Infect Genet Evol 16:369–376. CrossRefPubMedGoogle Scholar
  43. 43.
    Rosario K, Duffy S, Breitbart M (2012) A field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomics. Arch Virol 157:1851–1871. CrossRefPubMedGoogle Scholar
  44. 44.
    Rosario K, Duffy S, Breitbart M (2009) Diverse circovirus-like genome architectures revealed by environmental metagenomics. J Gen Virol 90:2418–2424. CrossRefPubMedGoogle Scholar
  45. 45.
    Castrignano SB, Nagasse-Sugahara TK, Kisielius JJ et al (2013) Two novel circo-like viruses detected in human feces: complete genome sequencing and electron microscopy analysis. Virus Res 178:364–373. CrossRefPubMedGoogle Scholar
  46. 46.
    Rosario K, Dayaram A, Marinov M et al (2012) Diverse circular ssDNA viruses discovered in dragonflies (Odonata: Epiprocta). J Gen Virol 93:2668–2681. CrossRefPubMedGoogle Scholar
  47. 47.
    Delwart E, Li L (2012) Rapidly expanding genetic diversity and host range of the Circoviridae viral family and other Rep encoding small circular ssDNA genomes. Virus Res 164:114–121. CrossRefPubMedGoogle Scholar
  48. 48.
    Steel O, Kraberger S, Sikorski A et al (2016) Circular replication-associated protein encoding DNA viruses identified in the faecal matter of various animals in New Zealand. Infect Genet Evol 43:151–164. CrossRefPubMedGoogle Scholar
  49. 49.
    Castrignano SB, Keico Nagasse-Sugahara T, Garrafa P et al (2017) Identification of circo-like virus-Brazil genomic sequences in raw sewage from the metropolitan area of São Paulo: evidence of circulation two and three years after the first detection. Mem Inst Oswaldo Cruz Rio Janeiro 112:175–181. CrossRefGoogle Scholar
  50. 50.
    Li L, Giannitti F, Low J et al (2015) Exploring the virome of diseased horses. J Gen Virol 96:2721–2733. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Matheus N. Weber
    • 1
  • Samuel P. Cibulski
    • 1
  • Simone Silveira
    • 1
  • Franciele M. Siqueira
    • 2
  • Ana Cristina S. Mósena
    • 1
  • Mariana S. da Silva
    • 1
  • Juliana C. Olegário
    • 1
  • Ana Paula M. Varela
    • 3
  • Thaís F. Teixeira
    • 3
  • Matheus V. Bianchi
    • 4
  • David Driemeier
    • 4
  • Saulo P. Pavarini
    • 4
  • Fabiana Q. Mayer
    • 5
  • Paulo M. Roehe
    • 3
  • Cláudio W. Canal
    • 1
    Email author
  1. 1.Laboratório de Virologia, Faculdade de VeterináriaUniversidade Federal do Rio Grande do Sul (UFRGS)Porto AlegreBrazil
  2. 2.Laboratório de Bacteriologia, Faculdade de VeterináriaUFRGSPorto AlegreBrazil
  3. 3.Laboratório de Virologia, Departamento de Microbiologia, Imunologia e ParasitologiaUFRGSPorto AlegreBrazil
  4. 4.Setor de Patologia Veterinária, Faculdade de VeterináriaUFRGSPorto AlegreBrazil
  5. 5.Laboratório de Biologia Molecular, Instituto de Pesquisas Veterinárias Desidério Finamor (IPVDF), Departamento de Diagnóstico e Pesquisa Agropecuária, Secretaria de Agricultura, Pecuária e IrrigaçãoEldorado do SulBrazil

Personalised recommendations