Abstract: Theobroma cacao is one of the most economically important tropical trees, being the source of
chocolate. As part of an ongoing study to understand the diversity of the badnavirus complex,
responsible for the cacao swollen shoot virus disease in West Africa, evidence was found recently of
virus-like sequences in asymptomatic cacao plants. The present study exploited the wealth of genomic
resources in this crop, and combined bioinformatic, molecular, and genetic approaches to report for
the first time the presence of integrated badnaviral sequences in most of the cacao genetic groups.
These sequences, which we propose to name eTcBV for endogenous T. cacao bacilliform virus, varied
in type with each predominating in a specific genetic group. A diagnostic multiplex PCR method was
developed to identify the homozygous or hemizygous condition of one specific insert, which was
inherited as a single Mendelian trait. These data suggest that these integration events occurred before
or during the species diversification in Central and South America, and prior to its cultivation in other
regions. Such evidence of integrated sequences is relevant to the management of cacao quarantine
facilities and may also aid novel methods to reduce the impact of such viruses in this crop.