Immunocapture polymerase chain reaction for the detection and characterization of cacao swollen shoot virus 1 A isolates

Oligonucleotides derived from the flanking regions of the putative coat protein gene of the cacao swollen shoot badnavirus isolate 1 A (CSSV-1 A) were able to prime the synthesis of specific products directly from extracts from CSSV-1A-infected leaves by immunocapture polymerase chain reaction (IC-PCR), following trapping of virions with polyclonal antibodies to CSSV-1 A. CSSV isolates serologically distinct from CSSV-1 A were not detected by IC-PCR when the CSSV-1 A-derived primers were used following trapping with homologous antisera. IC-PCR was at least 100-fold more sensitive than double antibody sandwich (DAS)-ELISA in comparative tests on samples from greenhouse-grown cacao plants. The superior sensitivity of IC-PCR over DAS-ELISA was confirmed in attempts to detect and identify CSSV-1 A isolates in field samples and permitted detection of CSSV-1 A isolates even in symptomless leaves from plants showing stem swelling only. The IC-PCR products obtained from four randomly selected field samples were sequenced and shown to contain a region of the CSSV-1 A genome where ORF X overlaps ORF 3. Analysis of the partial amino acid sequences deduced from ORF 3 and ORF X of the four field isolates revealed a considerable variation in these CSSV-1 A gene products.