A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination

Roberto Ramos-Sobrinho, Nomatter Chingandu, Osman A. Gutierrez, Jean Philippe Marelli, Judith K. Brown

Research output: Contribution to journalArticle


The incidence of cacao swollen shoot disease (CSSD) in cacao (Theobroma cacao L.) has increased in West Africa since ~2000. To investigate the genomic and species diversity of the CSSD-badnaviruses infecting cacao in Côte d’Ivoire and Ghana, symptomatic leaves were subjected to high-throughput sequencing. Among the 30 newly determined genomes, three badnaviruses were identified, Cacao swollen shoot Togo B virus (CSSTBV), Cacao swollen shoot CD virus, and Cacao swollen shoot CE virus (CSSCEV). The phylogenetic trees reconstructed for the reverse transcriptase (RT) and ribonuclease H (RNase H) sequences were incongruent with the complete viral genomes, which had the most robust statistical support. Recombination seems to be involved in the CSSD-badnavirus diversification. The genomic diversity varied among different CSSD-badnaviruses, with CSSTBV showing the lowest nucleotide diversity (π = 0.06236), and CSSCEV exhibiting the greatest variability (π = 0.21911). Evidence of strong purifying selection was found in the coding regions of the CSSTBV isolates.

Original languageEnglish (US)
Article number443
Issue number4
StatePublished - Apr 2020



  • Badnavirus
  • Caulimoviridae
  • DsDNA plant virus
  • Emerging diseases

ASJC Scopus subject areas

  • Infectious Diseases
  • Virology

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