@article{8a38d239e27848a6bb6f83f823afa19a,
title = "A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination",
abstract = "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 C{\^o}te d{\textquoteright}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.",
keywords = "Badnavirus, Caulimoviridae, DsDNA plant virus, Emerging diseases",
author = "Roberto Ramos-Sobrinho and Nomatter Chingandu and Gutierrez, {Osman A.} and Marelli, {Jean Philippe} and Brown, {Judith K.}",
note = "Funding Information: Funding: R.R.-S., N.C., and J.K.B. acknowledge the United States Department of Agriculture–Agricultural Research Service (USDA-ARS) for supporting this research through a Non-Assistance Cooperative Agreement numbers 6038-21000-023-13-S and 58-6038-6-008, and MARS Inc. for providing support through the USDA-ARS-MARS Trust Agreement number 6038-21000-023-12-T. Funding Information: R.R.-S., N.C., and J.K.B. acknowledge the United States Department of Agriculture-Agricultural Research Service (USDA-ARS) for supporting this research through a Non-Assistance Cooperative Agreement numbers 6038-21000-023-13-S and 58-6038-6-008, and MARS Inc. for providing support through the USDA-ARS-MARS Trust Agreement number 6038-21000-023-12-T. The authors wish to thank Lucien Diby (ICRAF) and George Ameyaw (CRIG Museum) for their support collecting cacao samples. Publisher Copyright: {\textcopyright} 2020 by the authors.",
year = "2020",
month = apr,
doi = "10.3390/v12040443",
language = "English (US)",
volume = "12",
journal = "Viruses",
issn = "1999-4915",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "4",
}