Distribution and genetic diversity of Coguvirus eburi in South African citrus and the development of a real-time RT-PCR assay for citrus-infecting coguviruses.

Citrus virus A (CiVA), a novel negative-sense single-stranded RNA virus assigned to the species Coguvirus eburi in the genus Coguvirus , was detected in South Africa with the use of high-throughput sequencing (HTS) after its initial discovery in Italy. CiVA is closely related to citrus concave gum-associated virus (CCGaV), recently assigned to the species Citrus coguvirus. Disease association with CiVA is however incomplete. CiVA was detected in grapefruit ( Citrus paradisi Macf.), sweet orange ( C. sinensis (L.) Osb.) and clementine ( C. reticulata Blanco) in South Africa and a survey to determine the distribution, symptom association and genetic diversity was conducted in three provinces and seven citrus production regions. The virus was detected in 'Delta' Valencia trees in six citrus production regions and a fruit rind symptom was often observed on CiVA-positive trees. Additionally, grapefruit showing symptoms of citrus impietratura disease were positive for CiVA. This virus was primarily detected in older orchards that were established prior to the application of shoot tip grafting for virus elimination in the South African Citrus Improvement Scheme. The three viral encoded genes of CiVA isolates from each cultivar and region were sequenced to investigate sequence diversity. Genetic differences were detected between the 'Delta' Valencia, grapefruit and clementine samples, with greater sequence variation observed with the nucleocapsid protein (NP) compared to the RNA-dependent RNA polymerase (RdRp) and the movement protein (MP). A real-time detection assay, targeting the RdRp, was developed to simultaneously detect citrus infecting coguviruses, CiVA and CCGaV, using a dual priming reverse primer to improve PCR specificity.