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Open AccessArticle

A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination

1
School of Plant Sciences, The University of Arizona, Tucson, AZ 85721, USA
2
USDA-ARS Subtropical Horticulture Research Station, Miami, FL 33158, USA
3
Mars Wrigley 434 G Street Suite 200, Davis, CA 95616, USA
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(4), 443; https://doi.org/10.3390/v12040443
Received: 25 March 2020 / Revised: 9 April 2020 / Accepted: 11 April 2020 / Published: 14 April 2020
(This article belongs to the Section Viruses of Plants, Fungi and Protozoa)
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. View Full-Text
Keywords: Badnavirus; Caulimoviridae; dsDNA plant virus; emerging diseases Badnavirus; Caulimoviridae; dsDNA plant virus; emerging diseases
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Ramos-Sobrinho, R.; Chingandu, N.; A. Gutierrez, O.; Marelli, J.-P.; K. Brown, J. A Complex of Badnavirus Species Infecting Cacao Reveals Mixed Infections, Extensive Genomic Variability, and Interspecific Recombination. Viruses 2020, 12, 443.

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