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Research Project: Genetic Improvement of Cacao Through Genomics-Assisted Breeding

Location: Subtropical Horticulture Research

Title: The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease

Author
item Chingandu, Nomatter - University Of Arizona
item Kouakou, Koffie - Centre National De Recherche Agronomique (NCAR)
item Aka, Romain - Centre National De Recherche Agronomique (NCAR)
item Ameyaw, George - Cocoa Research Institute Of Ghana
item Gutierrez, Osman
item Herrmann, H - University Of Arizona
item Brown, Judith - University Of Arizona

Submitted to: Virology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/11/2017
Publication Date: 10/19/2017
Citation: Chingandu, N., Kouakou, K., Aka, R., Ameyaw, G., Gutierrez, O.A., Brown, J.K. 2017. The proposed new species, cacao red vein virus, and three previously recognized badnavirus species are associated with cacao swollen shoot disease. Virology Journal. 14:199. doi:10.1186/s12985-017-0866-6.
DOI: https://doi.org/10.1186/s12985-017-0866-6

Interpretive Summary: Currently, West Africa is responsible for 70% of the cacao production in the world. Cacao swollen shoot virus is severely affecting the cacao production since it causes the death of the tree within three years of the initial infection. Recent virus epidemics have been characterized by an unusually rapid weakening and death of the infected trees. The inability of current available assays to detect the presence of the virus, suggests the presence of new viral strains. Therefore, new viral detection assays are urgently needed. The purpose of this study was to develop new molecular diagnostic tools that are capable of identifying all the swollen shoot virus shoot virus strains in Cote d’Ivoire and Ghana. Genome sequence analysis of viral sequences amplified from infected cacao leaf samples indicated the presence of four distinct viral species groups. Further phylogenetic analysis showed statistical support for up to three separate clades. These results suggest that the cacao swollen shoot virus may be complex of multiple species.

Technical Abstract: The production of cocoa in West Africa, which produces over 70% of the world’s supply, is threatened by Cacao swollen shoot virus (CSSV) (Caulimoviridae, Badnavirus) infection. Recent CSSV outbreaks in West Africa are characterized by atypical rapid tree decline symptoms together with shoot swelling and reduced pod set in cacao trees. Serological and molecular methods that previously detected CSSV have proven ineffective, suggesting the emergence of new or previously uncharacterized CSSV-like variants. The genome variability among extant CSSV isolates was investigated for symptomatic cacao samples from Cote d’Ivoire and Ghana using the Illumina HiSeq platform, with validation by Sanger DNA sequencing. Pairwise nucleotide analysis of the 14 full-length genomes determined herein, and of the taxonomically informative RT-RNase H coding region, overall distinguished four groups based on the 80% species demarcation. Phylogenetic analysis of the RT-RNase H region and full-length genome of 87 badnavirus sequences resolved a well-supported clade containing all 14 and seven GenBank CSSV sequences, indicating that the 14 genomes are related to CSSV. The CSSV subclade was further distinguished by having two clades containing isolates with different genome arrangements. Four full-length genome sequences of isolates from Cote d’Ivoire and Ghana contained four open reading frames (ORFs), and grouped together in a previously undescribed clade, separate from the clade harboring published CSSV isolates, having either five or six ORFs. All isolates, regardless of the genome arrangement, contained similar functional protein domains. The results suggest that CSSV is a complex of multiple species that can differ by ORF arrangement, and by having similar and unique conserved protein domain architecture.