Inconsistent PCR detection of Cacao swollen shoot virus (CSSV) is linked to the occurrence of different variants across the cocoa regions of Ghana

•The detection efficiency of ten (10) of the most utilized and novel CSSV primers were evaluated on isolates of the virus across Ghana through PCR assays.•Results from the PCR assays showed a highly variable and poor efficiency of the primers on the 189 samples of CSSV isolates evaluated.•Primer detection efficiency ranged from 4 % to 23 % with the four best performing primers being P4 (23%) > CSSD1 (21 %) > CSSD2 and BADNA (19 %).•The generally poor and inconsistent efficiency of the primers are discussed in the context of the genetic variability and also the occurrence of new variants of the virus in Ghana. Reliable diagnostic tools capable of detecting latent and asymptomatic infections are critically important to support the management of the cocoa swollen shoot virus disease (CSSVD) and also to complement research activities on screening for resistant cocoa varieties. Development of efficient polymerase chain reaction (PCR) assays sensitive for detection of CSSV infections has thus been a major research focus over the years. Advances in the full genome sequence information have resulted in the design of several Cacao swollen shoot virus (CSSV)-specific and degenerate primers. The objective of the present study was to further assess the detection efficiency of ten (10) of the most utilized and novel CSSV primers on isolates of the virus across Ghana. Results from the PCR assays showed a highly variable and poor efficiency of the primers on the 189 samples of CSSV isolates evaluated. The overall detection potential of the primers ranged from 4 % to 23 % with the four best performing primers in terms of PCR positivity being P4 (23 %), CSSD1 (21 %), JOEL (21 %) CSSD2 (19 %) and BADNA (19 %). The generally poor and inconsistent efficiency of the primers are discussed in the context of the genetic variability and also the occurrence of new variants of the virus in Ghana.