Archives of Virology

, Volume 162, Issue 6, pp 1791–1794 | Cite as

New strains of chickpea chlorotic dwarf virus discovered on diseased papaya and tomato plants in Burkina Faso

  • Alassane Ouattara
  • Fidèle Tiendrébéogo
  • Pierre Lefeuvre
  • Murielle Hoareau
  • Sohini Claverie
  • Edgar Valentin Traoré
  • Nicolas Barro
  • Oumar Traoré
  • Arvind Varsani
  • Jean-Michel Lett
Annotated Sequence Record


This is the first description of full genome sequences of chickpea chlorotic dwarf virus (CpCDV; genus Mastrevirus; family Geminiviridae) identified in papaya and tomato plants sampled in Burkina Faso. The CpCDV full genome sequences from papaya and tomato share the highest pairwise sequence identity (84% and 93.5%) with Sudanese isolates of the CpCDV-K and CpCDV-M strains, respectively. Based on the strain demarcation threshold (>94% identity) for mastreviruses, we propose two new strains, CpCDV-Q and CpCDV-R, identified in papaya and tomato, respectively. Phylogenetic analysis confirmed that the sequences belong to a distinct clade of the highly diverse population of CpCDVs. Evidence of inter-strain recombination provided more support for the important role of recombination in CpCDV evolution. The discovery of CpCDV on papaya, a previously unsuspected host, raises many questions about the natural and potential host range of this dicot-infecting mastrevirus species that is reported to be emerging worldwide.


Faba Bean Dwarf Virus Full Genome Sequence Citrullus Lanatus Maximum Likelihood Phylogenetic Analysis 


Compliance with ethical standards


This study was funded by the European Union (FEDER), the Région Réunion and CIRAD (Action incitative renforcement des compétences des chercheurs du Sud). AO is a recipient of a PhD fellowship from CIRAD (2015-2017).

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

No studies involving human participants or animals performed by any of the authors are described in this article.

Supplementary material

705_2017_3262_MOESM1_ESM.docx (23 kb)
Supplementary Figure 1. Annotated genome sequences of CpCDV isolates from Burkina Faso. (DOCX 23 kb)
705_2017_3262_MOESM2_ESM.xls (41 kb)
Supplementary Table 1. Name, acronyms and GenBank/EMBL/DDBJ accession numbers of the mastreviruses used in this study. (XLS 41 kb)
705_2017_3262_MOESM3_ESM.xlsx (16 kb)
Supplementary Table 2. Matrix of pairwise nucleotide similarities inferred from alignments of complete genome sequences of two new strains of chickpea chlorotic dwarf virus from tomato and papaya from Burkina Faso (CpCDV-Q and CpCDV-R, respectively) and one or two isolates of each of the 16 strains of CpCDV (CpCDV-A to CpCDV-P), as well as the six other species of dicot-infecting mastreviruses. For mastrevirus acronyms, see Supplementary Table 1. (XLSX 15 kb)


  1. 1.
    Fahmy IF, Taha O, El-Ashry AN (2015) First genome analysis and molecular characterization of Chickpea chlorotic dwarf virus Egyptian isolate infecting squash. Virus Dis 26:33CrossRefGoogle Scholar
  2. 2.
    Hadfield J, Thomas JE, Schwinghamer MW, Kraberger S, Stainton D, Dayaram A, Parry JN, Pande D, Martin DP, Varsani A (2012) Molecular characterisation of dicot-infecting mastreviruses from Australia. Virus Res 166:13–22CrossRefPubMedGoogle Scholar
  3. 3.
    Kraberger S, Harkins GW, Kumari SG, Thomas JE, Schwinghamer MW, Sharman M, Collings DA, Briddon RW, Martin DP, Varsani A (2013) Evidence that dicot-infecting mastreviruses are particularly prone to inter-species recombination and have likely been circulating in Australia for longer than in Africa and the Middle East. Virology 444:282–291CrossRefPubMedGoogle Scholar
  4. 4.
    Kraberger S, Kumari SG, Hamed AA, Gronenborn B, Thomas JE, Sharman M, Harkins GW, Muhire BM, Martin DP, Varsani A (2015) Molecular diversity of Chickpea chlorotic dwarf virus in Sudan: High rates of intra-species recombination - a driving force in the emergence of new strains. Infect Genet Evolut 29:203–215CrossRefGoogle Scholar
  5. 5.
    Kraberger S, Mumtaz H, Claverie S, Martin DP, Briddon RW, Varsani A (2015) Identification of an Australian-like dicot-infecting mastrevirus in Pakistan. Arch Virol 160:825–830CrossRefPubMedGoogle Scholar
  6. 6.
    Manzoor MT, Ilyas M, Shafiq M, Haider MS, Shahid AA, Briddon RW (2014) A distinct strain of chickpea chlorotic dwarf virus (genus Mastrevirus, family Geminiviridae) identified in cotton plants affected by leaf curl disease. Arch Virol 159:1217–1221CrossRefPubMedGoogle Scholar
  7. 7.
    Martin DP, Murrell B, Golden M, Khoosal A, Muhire B (2015) RDP4: Detection and analysis of recombination patterns in virus genomes. Virus Evolut 1:vev003Google Scholar
  8. 8.
    Muhire B, Martin DP, Brown JK, Navas-Castillo J, Moriones E, Zerbini FM, Rivera-Bustamante R, Malathi VG, Briddon RW, Varsani A (2013) A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae). Arch Virol 158:1411–1424CrossRefPubMedGoogle Scholar
  9. 9.
    Muhire BM, Varsani A, Martin DP (2014) SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS One 9:e108277CrossRefPubMedPubMedCentralGoogle Scholar
  10. 10.
    Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0. Mol Biol Evolut 30:2725–2729CrossRefGoogle Scholar
  11. 11.
    Thomas JE, Parry JN, Schwinghamer MW, Dann EK (2010) Two novel mastreviruses from chickpea (Cicer arietinum) in Australia. Arch Virol 155:1777–1788CrossRefPubMedGoogle Scholar
  12. 12.
    Zaagueri T, Mnari-Hattab M, Zammouri S, Hajlaoui MR, Acotto GP, Vaira AM (2016) First Report of Chickpea chlorotic dwarf virus in watermelon (Citrullus lanatus) in Tunisia. Plant Dis 101:392CrossRefGoogle Scholar
  13. 13.
    Zia-Ur-Rehman M, Hameed U, Herrmann HW, Iqbal MJ, Haider MS, Brown JK (2015) First report of Chickpea chlorotic dwarf virus infecting tomato crops in Pakistan. Plant Dis 99:1287CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  1. 1.INERAOuagadougouBurkina Faso
  2. 2.CIRAD, UMR PVBMT, Pôle de Protection des PlantesSaint-PierreFrance
  3. 3.Université Ouaga I Professeur Joseph Ki-ZerboOuagadougouBurkina Faso
  4. 4.Laboratoire Mixte International Patho-BiosIRD-INERAOuagadougouBurkina Faso
  5. 5.The Biodesign Center for Fundamental and Applied Microbiomics, School of Life Sciences, Center for Evolution and MedicineArizona State UniversityTempeUSA

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