A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination

Authors: RAMOS-SOBRINHO, ROBERTO - University Of Arizona; CHINGANDU, NOMATTER - University Of Arizona; Gutierrez, Osman; MARELLI, JEAN-PHILIPPE - Mars, Inc; BROWN, JUDITH - University Of Arizona

Submitted to: Viruses
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/11/2020
Publication Date: 4/14/2020
Citation: Ramos-Sobrinho, R., Chingandu, N., Gutierrez, O.A., Marelli, J., Brown, J.K. 2020. A complex of badnavirus species infecting cacao reveals mixed infections, extensive genomic variability, and interspecific recombination. Viruses. 12, 443-461. https://doi.org/10.3390/v12040443.
DOI: https://doi.org/10.3390/v12040443

Interpretive Summary: Cacao swollen shoot virus disease (CSSD) has been affecting cacao production since the early 1930’s in West Africa. It produces the death of cacao trees within three years after initial infection. Currently, West Africa is responsible for 70% of the cacao production in the world and CSSD eradication programs have been conducted since the 1940s but have not been able to contain its spread. Since ~2000 intensified occurrence, severity, and dissemination of CSSD in cacao plantations has taken place in West Africa and this could be due to the occurrence of new viral strains. A genetic characterization of the complex badnavirus species associated-viruses causing CSSD in West Africa has not been completed. Researchers at the University of Arizona collaborated with USDA-ARS scientists to characterize genomic variability and genetic diversity of the badnavirus infecting cacao in Cote d’Ivoire and Ghana and causing CSSD in cacao producing countries in West Africa. Genome sequencing and phylogenetic analysis results indicated the existence of thirty new genomes that included previously described species such as Cacao swollen shoot virus (CSSV), Cacao swollen shoot CD virus (CSSCDV), and Cacao red vein virus (CRVV). Phylogenetic results also indicated recombination among badnavirus genomes as well as provided evidence of viral subpopulations geographically structured among Cacao red vein banding virus (CRVBV) isolates. These findings will help with development of new molecular diagnostic tools to identify all CSSD causing strains in West African countries and help to reduce the spread of CSSD.

Technical Abstract: The lychee erinose mite, Aceria litchii (Keifer) (Acari: Eriophyidae), is an important pest of lychee (Litchi chinensis Sonn., Sapindaceae). Its recent interception in Lee County, Florida resulted in a quarantine whereby no lychee material, including fruit, can be transferred outside the county. Therefore, there is an urgent need for post-harvest treatments that can disinfest the fruit from the pest. Results of this study indicate that postharvest dips in paraffinic oil solutions, 3-5%, for 60 seconds can achieve complete disinfestation of lychee fruit from A. litchii motile stages as well as other arthropods. In both ‘Mauritius’ and ‘Brewster’ cultivars the treatments had a beneficial effect on fruit quality for the first four days after treatment. Post-harvest dips in paraffinic oil showed quarantine control of A. litchii without reduction in fruit quality. Hence, this treatment might allow growers in Lee County to transport lychee fruit outside the quarantine zone.