Nucleotide sequence and genomic organization of cacao swollen shoot virus

Cacao swollen shoot virus is classified as a badnavirus based on its nonenveloped, bacilliform particle morphology and double-stranded DNA genome. A complete copy of the genome was cloned into a plasmid vector and the sequence was determined from 75 overlapping subclones covering both strands. The genome contains 7161 base pairs and possesses an intergenic region and five putative open reading frames (ORF) capable of coding for proteins > 10 kDa. All of the ORFs are present on the plus-strand. ORF 1 (17 kDa) and ORF 2 (14 kDa) encode proteins of unknown function. The large ORF 3 (211 kDa) encodes a polyprotein that can be divided into three regions. Based on distant homologies with viral movement proteins, region 1 may encode a protein involved in cell-to-cell spread, while region 2 encodes the viral capsid protein. Region 3 contains consensus sequences for viral aspartyl proteinase, reverse transcriptase, and ribonuclease H characteristic of pararetroviruses. The last two ORFs (13 and 14 kDa) overlap ORF 3 and are not present in the other badnaviruses described.