Genome variability, species diversity, phylogenetic relationships, origin, and geographical distribution of badnaviruses involved in the cacao swollen shoot disease: the case of West Africa

Information on the various badnaviruses causing cacao swollen shoot disease (CSSD) or cacao swollen shoot virus disease (CSSVD) in West Africa is scattered. Several strains of the Cacao swollen shoot virus (CSSV) were assumed to cause CSSD; however, several recent studies have led to the discovery that CSSD is actually caused by many species of badnaviruses collectively called CSSD badnaviruses. This review seeks to present an update on the various CSSD-badnaviruses causing CSSD in the West African subcontinent, their geographical distribution, genome variability, species diversity, phylogenetic relationships, and possible origin. A comprehensive search of the scientific literature in relation to terms such as CSSV, CSSD, and CSSD-badnaviruses in Togo, Nigeria, Sierra Leone, Ghana, and Côte d’Ivoire was conducted. A total of seven cacao-infecting badnavirus species accepted by the International Committee on Taxonomy of Viruses (ICTV) were identified in this study to be the cause of CSSD in these countries. These are Cacao swollen shoot Ghana N virus (CSSGNV), Cacao swollen shoot CD virus (CSSCDV), Cacao swollen shoot Ghana Q virus (CSSGQV), Cacao swollen shoot CE virus (CSSCEV, also known as Cacao red vein virus, CRRV), Cacao swollen shoot Ghana M virus (CSSGMV; also known as Cacao red vein banding virus, CRVBV), Cacao swollen shoot Togo A virus (CSSTAV), and Cacao swollen shoot Togo B virus (CSSTBV; previously known as CSSV). All seven ICTV recognized CSSD badnaviruses were detected in the various cacao growing regions of Ghana and were also present in different combinations in other West African countries. Several genetic differences (arrangement of open reading frames (ORFs), genome size, and nucleotide sequences) were observed among the CSSD badnaviruses. Such studies are needed to help in the development of cacao germplasm which is resistant or shows some level of tolerance to CSSD badnaviruses.