Cacao Swollen Shoot Virus: A Re-Emergent, Mealybug-Transmitted Virus Spreading in West Africa

Cacao swollen shoot virus (CSSV; genus, Badnavirus; family, Caulimoviridae) has re-emerged in cacao throughout West Africa, which supplies about 73% of the world’s cacao. This has made the development of molecular diagnostic tools essential to support programs aimed at developing virus resistant cacao germplasm for distribution to the cocoa farmers located in the pandemic zone.  The seven available CSSV genome sequences were aligned and used to design seven pairs of polymerase chain reaction (PCR) primers.  Primer detection for samples collected from cacao and wild hosts in Cote d’Ivoire ranged from 30-68%, indicating the genomic variation in extant isolates is greater than is represented in GenBank.  A number of isolates were highly similar to one group of reference sequences previously studied from Ghana.  None of the isolates shared high sequence identity with previously sequenced isolates from Cote d’Ivoire, suggesting broader sampling is needed, and/or that a shift in the predominant genomic variants has occurred.  Several other groups were represented for which no reference sequence was available, confirming the hypothesis that greater than genomic variability occurs in the CSSV complex in West Africa.  Deep sequencing of CSSV genomes for regionally representative samples and outside of and within the pandemic zone to fully appreciate the extent of variability and distribution of variants in West Africa.  This information will be valuable for informing the design of molecular diagnostic tools to assist breeding programs and to make epidemiologically informed management recommendations.