Skip to main content

Advertisement

SpringerLink
Log in

Molecular characterization and detection of a novel vitivirus infecting blackberry

  • Brief Report
  • Published:
Archives of Virology Aims and scope Submit manuscript

Abstract

Blackberries exhibiting yellow vein disease symptoms were found to be infected by a new virus, a putative member of the genus Vitivirus. Recombination assessment of several vitiviruses revealed multiple events involving the newly identified virus isolate. Occurrence in areas of high disease pressure was investigated and the population structure was studied using the movement and coat protein genes; both under purifying selection. This information was exploited in the development of a detection protocol for routine screening and Rubus certification programs around the globe.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

References

  1. Clark JR (2005) Changing times for eastern United States blackberries. Horttechnology 15:491–494

    Google Scholar 

  2. Strik BC, Clark JR, Finn CE, Bañados MP (2007) Worldwide blackberry production. Horttechnology 17:205–213

    Google Scholar 

  3. Martin RR, MacFarlane S, Sabanadzovic S et al (2013) Viruses and virus diseases of Rubus. Plant Dis 97:168–182

    Article  PubMed  Google Scholar 

  4. Jones AT, McGavin WJ, Gepp V et al (2006) Purification and properties of blackberry chlorotic ringspot, a new virus species in subgroup 1 of the genus Ilarvirus found naturally infecting blackberry in the UK. Ann Appl Biol 149:125–135

    Article  CAS  Google Scholar 

  5. Susaimuthu J, Tzanetakis IE, Gergerich RC, Martin RR (2008) A member of a new genus in the Potyviridae infects Rubus. Virus Res 131:145–151. https://doi.org/10.1016/j.virusres.2007.09.001

    Article  PubMed  CAS  Google Scholar 

  6. Hassan M, Di Bello PL, Keller KE et al (2017) A new, widespread emaravirus discovered in blackberry. Virus Res 235:1–5. https://doi.org/10.1016/j.virusres.2017.04.006

    Article  PubMed  CAS  Google Scholar 

  7. Thekke-Veetil T, Sabanadzovic S, Keller KE et al (2012) Genome organization and sequence diversity of a novel blackberry Ampelovirus. In: Proceedings of the 22nd international conference on virus and other transmissible diseases of fruit crops, Rome, Italy, pp 3–8

  8. Rush MC, Gooding GV, Ellis DE (1968) Wild Rubus spp as natural hosts of Tobacco ringspot virus. Phytopathology 58:1065

    Google Scholar 

  9. Sabanadzovic S, Abou Ghanem-Sabanadzovic N (2009) Identification and molecular characterization of a marafivirus in Rubus spp. Arch Virol 154:1729–1735. https://doi.org/10.1007/s00705-009-0510-x

    Article  PubMed  CAS  Google Scholar 

  10. Abou Ghanem-Sabanadzovic N, Tzanetakis IE, Sabanadzovic S (2013) Rubus canadensis virus 1, a novel betaflexivirus identified in blackberry. Arch Virol 158:445–449. https://doi.org/10.1007/s00705-012-1484-7

    Article  PubMed  CAS  Google Scholar 

  11. Sabanadzovic S, Abou Ghanem-Sabanadzovic N, Tzanetakis IE (2011) Blackberry virus E: an unusual flexivirus. Arch Virol 156:1665–1669. https://doi.org/10.1007/s00705-011-1015-y

    Article  PubMed  CAS  Google Scholar 

  12. Khadgi A (2015) Blackberry Virosome: a micro and macro approach. University of Arkansas

  13. Tzanetakis IE, Martin RR (2008) A new method for extraction of double-stranded RNA from plants. J Virol Methods 149:167–170. https://doi.org/10.1016/j.jviromet.2008.01.014

    Article  PubMed  CAS  Google Scholar 

  14. Ho T, Tzanetakis IE (2014) Developing a virus detection and discovery pipeline using next generation sequencing. Virology 471:54–60

    Article  PubMed  CAS  Google Scholar 

  15. Hall T (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98

    CAS  Google Scholar 

  16. Wheeler DL, Church DM, Federhen S et al (2003) Database resources of the National Center for Biotechnology. Nucleic Acids Res 31:28–33

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  17. Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874. https://doi.org/10.1093/molbev/msw054

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  18. Martin DP, Murrell B, Golden M et al (2015) RDP4: detection and analysis of recombination patterns in virus genomes. Virus Evol 1:1–5

    Article  Google Scholar 

  19. Korber B (2001) HIV signature sequences and similarities. In: Rodrigo GA, Learn GH (eds) Computational and evolutionary analysis of HIV molecular sequences. Kluwer Academic Publishers, Dordrecht, The Netherlands, pp 55–72

    Google Scholar 

  20. Adams M, Kreuze J (2016) Revision of family Betaflexiviridae, order Tymovirales. ICTV online. http://www.ictvonline.org/. Accessed 9 July 2018

  21. Minafra A, Saldarelli P, Grieco F, Martelli GP (1994) Nucleotide sequence of the 3′ terminal region of the RNA of two filamentous grapevine viruses. Arch Virol 137:249–261

    Article  PubMed  CAS  Google Scholar 

  22. Minafra A, Saldarelli P, Martelli GP (1997) Grapevine virus A: nucleotide sequence, genome organization, and relationship in the Trichovirus genus. Arch Virol 142:417–423

    Article  PubMed  CAS  Google Scholar 

  23. Galiakparov N, Tanne E, Sela I, Gafny R (2003) Functional analysis of the grapevine virus A genome. Virology 306:42–50

    Article  PubMed  CAS  Google Scholar 

  24. Haviv S, Moskovitz Y, Mawassi M (2012) The ORF3-encoded proteins of vitiviruses GVA and GVB induce tubule-like and punctate structures during virus infection and localize to the plasmodesmata. Virus Res 163:291–301. https://doi.org/10.1016/j.virusres.2011.10.015

    Article  PubMed  CAS  Google Scholar 

  25. Al Rwahnih M, Sudarshana MR, Uyemoto JK, Rowhani A (2012) Complete genome sequence of a novel vitivirus isolated from grapevine. J Virol 86:9545. https://doi.org/10.1128/JVI.01444-12

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  26. Nakaune R, Toda S, Mochizuki M, Nakano M (2008) Identification and characterization of a new vitivirus from grapevine. Arch Virol 153:1827–1832

    Article  PubMed  CAS  Google Scholar 

  27. Tzanetakis IE, Postman JD, Martin RR (2007) Identification, detection and transmission of a new vitivirus from Mentha. Arch Virol 152:2027–2033. https://doi.org/10.1007/s00705-007-1030-1

    Article  PubMed  CAS  Google Scholar 

  28. Dolja VV, Boyko VP, Agranovsky AA, Koonin EV (1991) Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. Virology 184:79–86

    Article  PubMed  CAS  Google Scholar 

  29. Chiba M, Reed JC, Prokhnevsky AI et al (2006) Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. Virology 346:7–14. https://doi.org/10.1016/j.virol.2005.09.068

    Article  PubMed  CAS  Google Scholar 

  30. Zhou ZS, Dell’Orco M, Saldarelli P et al (2006) Identification of an RNA-silencing suppressor in the genome of Grapevine virus A. J Gen Virol 87:2387–2395

    Article  PubMed  CAS  Google Scholar 

  31. Shi B-J, Habili N, Gafny R, Symons RH (2004) Extensive variation of sequence within isolates of Grapevine virus B+. Virus Genes 29:279–285. https://doi.org/10.1023/B:VIRU.0000036388.41242.c1

    Article  PubMed  CAS  Google Scholar 

  32. Mekuria TA, Gutha LR, Martin RR, Naidu RA (2009) Genome diversity and intra- and interspecies recombination events in Grapevine fanleaf virus. Phytopathology 99:1394–1402. https://doi.org/10.1094/PHYTO-99-12-1394

    Article  PubMed  CAS  Google Scholar 

  33. Marais A, Faure C, Mustafayev E, Candresse T (2015) Characterization of new isolates of Apricot vein clearing-associated virus and of a new prunus-infecting virus: evidence for recombination as a driving force in betaflexiviridae evolution. PLoS One 10:e0129469

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  34. Alabi OJ, Al Rwahnih M, Mekuria TA, Naidu RA (2014) Genetic diversity of grapevine virus A in Washington and California vineyards. Phytopathology 104:548–560. https://doi.org/10.1094/PHYTO-06-13-0179-R

    Article  PubMed  CAS  Google Scholar 

  35. Coetzee B, Maree HJ, Stephan D et al (2010) The first complete nucleotide sequence of a grapevine virus E variant. Arch Virol 155:1357–1360. https://doi.org/10.1007/s00705-010-0685-1

    Article  PubMed  CAS  Google Scholar 

  36. Candresse T, Theil S, Faure C, Marais A (2017) Determination of the complete genomic sequence of grapevine virus H, a novel vitivirus infecting grapevine. Arch Virol. https://doi.org/10.1007/s00705-017-3587-7

    Article  PubMed Central  PubMed  Google Scholar 

  37. Jo Y, Song M-K, Choi H et al (2017) Genome sequence of grapevine virus K, a novel vitivirus infecting grapevine. Genome Announc. https://doi.org/10.1128/genomeA.00994-17

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

The work presented here was funded by the USDA National Institute of Food and Agriculture-Specialty Crops Research Initiative (2009-51181-06022), USDA-NCPN (14-8130-0420-CA) and Hatch project 1002361.

Author information

Authors and Affiliations

  1. Division of Agriculture, Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA

    Mohamed Hassan, Muhammad S. Shahid & Ioannis E. Tzanetakis

  2. Agricultural Botany Department, Faculty of Agriculture, Fayoum University, El Faiyûm, Egypt

    Mohamed Hassan

  3. Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, 123, Al-Khod, Oman

    Muhammad S. Shahid

Authors
  1. Mohamed Hassan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Muhammad S. Shahid
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ioannis E. Tzanetakis
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ioannis E. Tzanetakis.

Ethics declarations

Conflicts of interest

The authors declare no conflicts of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Additional information

Handling Editor: Sead Sabanadzovic.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 573 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hassan, M., Shahid, M.S. & Tzanetakis, I.E. Molecular characterization and detection of a novel vitivirus infecting blackberry. Arch Virol 163, 2889–2893 (2018). https://doi.org/10.1007/s00705-018-3931-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00705-018-3931-6

Search

Navigation