European Journal of Plant Pathology

, Volume 155, Issue 4, pp 1373–1379 | Cite as

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

  • Glynnis CookEmail author
  • Wayne Kirkman
  • Rochelle Clase
  • Chanel Steyn
  • Elaine Basson
  • Paul H. Fourie
  • Sean D. Moore
  • Tim G. Grout
  • Elma Carstens
  • Vaughan Hattingh


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.


Citrus leprosis Dichorhavirus Orchid fleck virus Flat mite Brevipalpus californicus 



We wish to thank the Sundays River Citrus Company for rapid response to the outbreak and assistance in scouting and Dr. Edward Ueckermann for flat mite identification. We also acknowledge Dr. Elize Jooste of the Agricultural Research Council-Tropical and Subtropical Crops, for independent virus verification.

Funding information

This study was funded by Citrus Research International.

Compliance with ethical standards

The authors declare that this research did not involve testing of either human or animal subjects.

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  1. 1.Citrus Research InternationalNelspruitSouth Africa

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