Diagnosis of Cocoa Swollen Shoot Virus Disease by Polymerase Chain Reaction (PCR)

Abstract

Cocoa swollen shoot virus disease causes severe damage to cocoa farms leading to substantial losses in crop yield and therefore the country’s revenue from cocoa. This study set out to design new PCR primers for the detection of the virus that causes the disease. Thirty-six cocoa swollen shoot virus (CSSV) isolates, randomly selected from 5 main groups based on serological and biological properties from the CRIG museum at Tafo were used Viral DNA extracted and purified from the infected leaves were used for PCR using two sets of universal badna primers 2+T and 3+T. The multiple amplification bands produced were cut out, gel purified and hybridised against full length cloned PCR DNA of CSSV New Juaben probes to detect the amplification products of virus origin. These were then cloned, sequenced and new primers designed based on consensus sequences derived from the alignment of the CSSV sequences with sequences from other closely related badna viruses. The new pair of primers (badna primers 1+4) gave a single PCR amplification product of 600 base pairs. The thirty-six CSSV isolates from the CRIG museum were screened with the new primers to test the efficacy of these new primers. Out of the 36 isolates screened, 28 gave the expected amplification product and 8 did not give any amplification products. The new primers in comparison with the old primers can be said to be better at detecting CSSV.