Cacao swollen shoot virus (CSSV) is the causal agent of the "Cocoa swollen shoot disease", one of the most devastating scourges of cacao (Theobroma cacao) that causes serious crop losses in many cacao growing areas of West Africa (Posnette 1947; Partiot et al. 1978). Mild and severe isolates have been found in CSSV-endemic regions (Castel et al. 1980; Dufour 1988) and to date six of them have been completely characterized and sequenced (Hagen et al. 1993; Muller and Sackey 2005). The most virulent isolate "CSSV-Agou1" from Togo (Hagen et al. 1993) is the reference sequence in our analyses. CSSV is a member of Caulimoviridae family, genus Badnavirus (International Committee on the Taxonomy of Viruses -ICTV- Fauquet et al. 2005), and according to Llorens et al. 2009 is located within Class 2 of the Caulimoviridae family.
CSSV is a small non-enveloped bacilliform virus which particles are approximately 28x112-130 nm (Brunt et al 1964) and contain a circular double-stranded DNA genome interrupted by site-specific discontinuities (Lot et al. 1991). DsDNA molecule, 7161 bp long, encodes for five open reading frames (ORFI, II, III, X, Y) located on the plus strand of the genome, some of which contain the highly conserved Badnavirus protein domains (Hagen et al. 1993; Muller and Sackey 2005). ORFI encodes a putative 16.8 kDa protein showing sequence similarity to the Caulimoviridae virion associated proteins (VAPs) encoded by the corresponding ORFs I. The ORFII product of 14.4 kDa has been demonstrated to possess a potentially nucleic acid-binding property (Jacquot et al. 1996). ORF III of about 211 kDa contains consensus sequences for a cell-to-cell movement protein (MOV), an RNA binding domain of the coat protein (COAT), an aspartyl proteinase (PR), a reverse transcriptase (RT) and a ribonuclease H (RH) (Hagen et al. 1993; Muller and Sackey 2005). In particular the COAT (gag)-like region includes the two cysteine-rich domains "C-X-C-X2-C-X4-H-X4-C" and "C-X2-C-X11-C-X2-C-X4-C-X2-C" only observed in Badna- and Tungroviruses and similar to those identified in the nucleocapsid domains of LTR retroelements (Hull 1996; Bouhida et al. 1993; Llorens et al. 2009). ORFs X and Y, corresponding to proteins of 13.2 and 14.2 kDa respectively, are located within ORF III (Hagen et al. 1993). ORF Y overlaps the end of ORF III as observed for Citrus yellow mosaic virus (CYMV)-ORF VI whose products show some sequence homologies (Huang and Hurtung 2001). No described protein similarities have been found to both ORF X and Y products (Hagen et al. 1993).
The typical "Cacao swollen shoot disease" symptomatology consists in shoot, stem and root swellings, leaf mosaic and chlorosis, red vein banding, defoliation and round pods, and die within three to four years following infection in susceptible cacao cultivars (Partiot et al. 1978; Castel et al. 1980). CSSV is naturally transmitted to cacao plants by several species of mealybug (Pseudococcidae), including Planococcus citri, in a semi-persistent manner (Dufour 1988), but it can also been transmitted by plant-agroinoculation (Jacquot et al. 1999) and seed-biolistic inoculation (particles bombardment, Hagen et al. 1994). Virus has been detected in both pollen and seed and considering that currently cocoa is propagated largely by seeds, exist considerable evidence that viruses have been introduced into many geographical regions by infected seeds and through increasing international germplasm exchanges (Quainoo et al. 2008).