Archives of Virology

, Volume 162, Issue 5, pp 1363–1371 | Cite as

Molecular characterization of previously elusive badnaviruses associated with symptomatic cacao in the New World

  • Nomatter Chingandu
  • Muhammad Zia-ur-rehman
  • Thyail N. Sreenivasan
  • Surendra Surujdeo-Maharaj
  • Pathmanathan Umaharan
  • Osman A. Gutierrez
  • Judith K. BrownEmail author
Brief Report


Suspected virus-like symptoms were observed in cacao plants in Trinidad during 1943, and the viruses associated with these symptoms were designated as strains A and B of cacao Trinidad virus (CTV). However, viral etiology has not been demonstrated for either phenotype. Total DNA was isolated from symptomatic cacao leaves exhibiting the CTV A and B phenotypes and subjected to Illumina HiSeq and Sanger DNA sequencing. Based on de novo assembly, two apparently full-length badnavirus genomes of 7,533 and 7,454 nucleotides (nt) were associated with CTV strain A and B, respectively. The Trinidad badnaviral genomes contained four open reading frames, three of which are characteristic of other known badnaviruses, and a fourth that is present in only some badnaviruses. Both badnaviral genomes harbored hallmark caulimovirus-like features, including a tRNAMet priming site, a TATA box, and a polyadenylation-like signal. Pairwise comparisons of the RT-RNase H region indicated that the Trinidad isolates share 57-71% nt sequence identity with other known badnaviruses. Based on the system for badnavirus species demarcation in which viruses with less than 80% nt sequence identity in the RT-RNase gene are considered members of separate species, these isolates represent two previously unidentified badnaviruses, herein named cacao mild mosaic virus and cacao yellow vein banding virus, making them the first cacao-infecting badnaviruses identified thus far in the Western Hemisphere.


Conserve Domain Database Cacao Tree Cacao Plant Polymerase Chain Reaction Premix Cacao Swell Shoot Virus 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Compliance with ethical standards


We gratefully acknowledge funding for this project from the USDA-ARS through the Specific Cooperative Agreement #6038-21000-023-07 titled: Development and Optimization of Molecular Diagnostics Method for Qualitative and Quantitative Detection of Cacao Swollen Shoot Virus with MARS Inc through Trust Agreement #58-6631-6-123, titled: Genetic Improvement of Theobroma cacao, and from the World Cocoa Foundation Borlaug Fellowship Program, USDA-Foreign Agricultural Services.

Conflict of interest

The authors declare that they have no potential conflict of interest.

This manuscript does not contain studies with human participants or animals.

Supplementary material

705_2017_3235_MOESM1_ESM.docx (49 kb)
Supplemental Table 1 Virus-specific primers are underlined, and expected amplicon sizes for cacao mild mosaic virus (CaMMV) and cacao vein-banding virus (CYVBV) are shown. The Not I restriction site added to facilitate cloning is shown in italics. Supplemental Table 2 Percentage pairwise nucleotide (nt) sequence identity for the RT-RNase H locus of cacao mild mosaic virus and cacao yellow vein-banding virus in relation to other badnavirus sequences using MUSCLE alignment implemented in SDTv1.2. The nt sequence identities are shown for GenBank sequences, and shading indicates >80% nt sequence identity, representing distinct species. Supplemental Table 3 Percentage pairwise nucleotide (nt) sequence identity for cacao mild mosaic virus and cacao yellow vein-banding virus complete genome sequences in relation to badnavirus sequences, using MUSCLE alignment, implemented in SDTv1.2. The nt sequence identities are shown for the sequences obtained from the GenBank database (DOCX 48 kb)


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Copyright information

© Springer-Verlag Wien 2017

Authors and Affiliations

  • Nomatter Chingandu
    • 1
  • Muhammad Zia-ur-rehman
    • 2
  • Thyail N. Sreenivasan
    • 3
  • Surendra Surujdeo-Maharaj
    • 3
  • Pathmanathan Umaharan
    • 3
  • Osman A. Gutierrez
    • 4
  • Judith K. Brown
    • 1
    Email author
  1. 1.School of Plant SciencesUniversity of ArizonaTucsonUSA
  2. 2.IAGSUniversity of PunjabLahorePakistan
  3. 3.Cocoa Research CentreThe University of the West IndiesSt. AugustineTrinidad and Tobago
  4. 4.USDA-ARS Subtropical Horticultural Research StationMiamiUSA

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