1887

Abstract

Hepaciviruses (HVs) have been detected in several domestic and wild animals and present high genetic diversity. The actual classification divides the genus into 14 species (), according to their phylogenetic relationships, including the bovine hepacivirus [ (HNV)]. In this study, we confirmed HNV circulation in Brazil and sequenced the whole genome of two strains. Based on the current classification of HCV, which is divided into genotypes and subtypes, we analysed all available bovine hepacivirus sequences in the GenBank database and proposed an HNV classification. All of the sequences were grouped into a single genotype, putatively named ‘genotype 1’. This genotype can be clearly divided into four subtypes: A and D containing sequences from Germany and Brazil, respectively, and B and C containing Ghanaian sequences. In addition, the NS3-coding region was used to estimate the time to the most recent common ancestor (TMRCA) of each subtype, using a Bayesian approach and a relaxed molecular clock model. The analyses indicated a common origin of the virus circulating in Germany and Brazil. Ghanaian sequences seemed to have an older TMRCA, indicating a long time of circulation of these viruses in the African continent.

Keyword(s): bayesian inferences , cattle , HCV , Hepacivirus and HNV
Loading

Article metrics loading...

/content/journal/jgv/10.1099/jgv.0.001082
2018-07-01
2024-03-28
Loading full text...

Full text loading...

/deliver/fulltext/jgv/99/7/890.html?itemId=/content/journal/jgv/10.1099/jgv.0.001082&mimeType=html&fmt=ahah

References

  1. Smith DB, Becher P, Bukh J, Gould EA, Meyers G et al. Proposed update to the taxonomy of the genera Hepacivirus and Pegivirus within the Flaviviridae family. J Gen Virol 2016; 97:2894–2907 [View Article][PubMed]
    [Google Scholar]
  2. Moradpour D, Penin F, Rice CM. Replication of hepatitis C virus. Nat Rev Microbiol 2007; 5:453–463 [View Article]
    [Google Scholar]
  3. Penin F, Dubuisson J, Rey FA, Moradpour D, Pawlotsky JM. Structural biology of hepatitis C virus. Hepatology 2004; 39:5–19 [View Article][PubMed]
    [Google Scholar]
  4. Corman VM, Grundhoff A, Baechlein C, Fischer N, Gmyl A et al. Highly divergent hepaciviruses from African cattle. J Virol 2015; 89:5876–5882 [View Article][PubMed]
    [Google Scholar]
  5. Baechlein C, Fischer N, Grundhoff A, Alawi M, Indenbirken D et al. Identification of a novel hepacivirus in domestic cattle from Germany. J Virol 2015; 89:7007–7015 [View Article][PubMed]
    [Google Scholar]
  6. Elia G, Lanave G, Lorusso E, Parisi A, Cavaliere N et al. Identification and genetic characterization of equine hepaciviruses in Italy. Vet Microbiol 2017; 207:239–247 [View Article][PubMed]
    [Google Scholar]
  7. Canal CW, Weber MN, Cibulski SP, Silva MS, Puhl DE et al. A novel genetic group of bovine Hepacivirus in archival serum samples from Brazilian cattle. Biomed Res Int 2017; 2017:1–4 [View Article][PubMed]
    [Google Scholar]
  8. Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P. Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 2005; 309:1577–1581 [View Article][PubMed]
    [Google Scholar]
  9. Thézé J, Lowes S, Parker J, Pybus OG. Evolutionary and phylogenetic analysis of the hepaciviruses and pegiviruses. Genome Biol Evol 2015; 7:2996–3008 [View Article][PubMed]
    [Google Scholar]
  10. Lyons S, Kapoor A, Sharp C, Schneider BS, Wolfe ND et al. Nonprimate hepaciviruses in domestic horses, United kingdom. Emerg Infect Dis 2012; 18:1976–1982 [View Article][PubMed]
    [Google Scholar]
  11. Kapoor A, Simmonds P, Gerold G, Qaisar N, Jain K et al. Characterization of a canine homolog of hepatitis C virus. Proc Natl Acad Sci USA 2011; 108:11608–11613 [View Article][PubMed]
    [Google Scholar]
  12. Drexler JF, Corman VM, Müller MA, Lukashev AN, Gmyl A et al. Evidence for novel hepaciviruses in rodents. PLoS Pathog 2013; 9:e1003438 [View Article][PubMed]
    [Google Scholar]
  13. Quan PL, Firth C, Conte JM, Williams SH, Zambrana-Torrelio CM et al. Bats are a major natural reservoir for hepaciviruses and pegiviruses. Proc Natl Acad Sci USA 2013; 110:8194–8199 [View Article][PubMed]
    [Google Scholar]
  14. Bukh J. Animal models for the study of hepatitis C virus infection and related liver disease. Gastroenterology 2012; 142:1279–1287 [View Article][PubMed]
    [Google Scholar]
  15. Voisset C, Dubuisson J. Functional hepatitis C virus envelope glycoproteins. Biol Cell 2004; 96:413 [View Article][PubMed]
    [Google Scholar]
  16. Chevaliez S, Pawlotsky S. HCV Genome and Life Cycle. Hepatitis C Viruses: Genomes and Molecular Biology Norfolk: Horizon Bioscience; 2006
    [Google Scholar]
  17. Earp FS, Bastian EF, Modenesi AM. Como vai o Brasil. A economia brasileira no terceiro milênio Modernização e produtividade da agropecuária no Brasil; 2018
    [Google Scholar]
  18. Linhares MYL. Pecuária, alimentos e sistemas agrários no Brasil (séculos XVII e XVIII)Arquivos do Centro Cultural Calouste Gulbenkian, Le Portugal et l’Europe Atlantique, le Brésil et l’Amérique Latine 1995 pp. 132–150
    [Google Scholar]
  19. Edgar RC, Drive RM, Valley M. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article]
    [Google Scholar]
  20. Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M et al. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 2012; 28:1647–1649 [View Article][PubMed]
    [Google Scholar]
  21. Uindon PG, Ranc J. New algorithms and methods to estimate maximum-likelihood phylogenies : assessing the performance of PhyML 3. 0; 2017; 59307–321
  22. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
    [Google Scholar]
  23. Muhire BM, Varsani A, Martin DP. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 2014; 9:e108277 [View Article][PubMed]
    [Google Scholar]
  24. Dereeper A, Guignon V, Blanc G, Audic S, Buffet S et al. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008; 36:W465–W469 [View Article][PubMed]
    [Google Scholar]
  25. Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 2010; 10:8 [View Article][PubMed]
    [Google Scholar]
  26. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 2007; 7:214–218 [View Article][PubMed]
    [Google Scholar]
  27. Pybus OG, Thézé J. Hepacivirus cross-species transmission and the origins of the hepatitis C virus. Curr Opin Virol 2016; 16:1–7 [View Article][PubMed]
    [Google Scholar]
  28. AJ RAD 2017; Tracer v1.4. http://beast.bio.ed.ac.uk/Tracer
http://instance.metastore.ingenta.com/content/journal/jgv/10.1099/jgv.0.001082
Loading
/content/journal/jgv/10.1099/jgv.0.001082
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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