Orchid fleck virus associated with the first case of citrus leprosis-N in South Africa

Abstract

Citrus leprosis (CL) is prevalent in South and Central American countries and has not previously been reported on citrus outside the Americas. CL is caused by several RNA viruses which define the disease as either the cytoplasmic type (CL-C) or the nuclear type (CL-N). Symptoms typical for CL were observed on fruit, leaves and branches in Valencia and Navel orange orchards in the Eastern Cape province of South Africa. A CL-N associated virus belonging to the genus Dichorhavirus was detected in samples from 27 affected orchards on five farms by RT-PCR and amplicon sequencing. Full genome sequencing of the virus showed it to be a variant of orchid fleck virus (OFV) with closest sequence identity of 99% to an isolate described on orchids in the Cymbidium genus, but not to isolates previously reported on citrus. Infestations of Brevipalpus californicus flat mite, the natural vector of at least one of the CL-N associated viruses, were observed at find sites. Orchids were additionally sampled from nurseries in five provinces of South Africa and OFV was identified in samples from three provinces. The full-genome sequence determination of OFV from an infected Brassia sp. orchid showed 99% sequence identity to the genome of OFV found on citrus in South Africa. Phylogenetic analysis of the RNA-dependent RNA polymerase gene showed that OFV found in both citrus and orchids in South Africa cluster separately from OFV isolates from Mexico. CL-N in South Africa is likely to have originated from imported, infected orchids, based on the close sequence identity of OFV found on citrus and orchids.