Involves the activities of two units, namely the DISEASE MANAGEMENT unit and the PEST MANAGEMENT​​ unit. The Institute strongly supports an integrated program to control pests (IPM) on tropical and subtropical crops. The emphasis is on biological control and a reduction in the use of toxic pesticides, to promote a more sustainable, envi​ronment friendly approach of pest management. Another important aspect of this division is the management the Citrus post-entry quarantine (PEQ) process using shoot tip grafting (STG) for elimination of quarantine diseases. Plant Quarantine is the effort to prevent entry, establishment and spread of a foreign pest in the country through legal restriction of plant and plant products.​​​

  1. ​Diagnostic test for potato spindle tuber viroid (pdf) ​​

  2. Othe​r diagnostic services for identification of virusses, viroids as well as fungal pathogens​ (pdf)



The Disease Management divi​sion offers diagnostic and research services on primarily fungal and viral diseases with main focus on partnerships with the macadamia, avocado, citrus, mango, litchi and banana industries but also offers support to smaller industries on demand.


  • ​Diagnostic Services (pdf)

Isolation from plant samples, growing media, soil and water 

Morphological identification 

​​Molecular identification (PCR and sequencing)

  • ​Current Research Focus

Diseases affecting macadamia: Phomopsis Husk rot, Dry Flower disease, Blossom blight, Phytophthora root rot and stem canker.

Glasshouse trials on efficiency of fungicides and biological control products

Contact: Maritha Schoeman, Email: Maritha@arc.agric.za, Tel: (0)13 753 7115

Husk rot on 'Nelmak'.

 Husk rot on 'Beaumont'.​​
Phytophthora root rot.jpg
Phytophthora root rot.
Blossom blight​.
Dry flower disease.



  • Post Entry Quarantine of Citrus

The Disease Management Unit at the Agricultural Research Council's Tropical and Subtropical Crops, Nelspruit campus (ARC-TSC) is a role player in the mandate of the Citrus Improvement Scheme (CIS) to ensure the supply of pathogen free propagation material to the South African citrus industry. The Post Entry Quarantine (PEQ) function, assigned by the Department of Agriculture, Forestry and Fisheries (DAFF) to ARC-TSC, is critical to ensure no introduction of foreign pathogens via imported budwood. Budwood imports are subjected to shoot tip grafting (STG), to eradicate graft transmissible pathogens, i.e viruses, viroids and bacteria. Once STG is complete the material is indexed on biological indicators and molecular tests to detect various pathogens, including quarantine pathogens. Seed imports are subjected to grow out tests and subsequent molecular detection for pathogens listed on the quarantine pathogen list, including Citrus leaf blotch virus (CLBV). The role of the ARC-TSC lab in the PEQ of citrus is therefore critical and the importance to comply with PEQ standards and depend on the timely execution of STG procedures and subsequent indexing.

Contact: Dr Elize Jooste, Email: JoosteE@arc.agric.za, Tel: (0)13 753 7128 or Zama Theledi, Email: Zama@arc.agric.za, Tel: (0)13 753 7124​

  • Diagnostic Services

    • ​​Avocado sunbloch viroid (ASBVd)

Sensitivity of ASBVd detection is reliant on two critical aspects, firstly the yield efficacy of the RNA extraction and secondly the sensitivity of the RT-PCR assay. In both aspects, the ARC ASBVd detection pro​tocol was developed to maximize​ detection based on optimal yield and sensitivity. This means that for samples with low viroid titre, the ARC-TSC method would have the highest probability of extracting and detecting ASBVd. The RT-qPCR was optimized using a template with known concentration to determine the efficiency and sensitivity of the assay.  With a seven point 10× dilution standard curve we showed an amplification efficiency of 1.03 with a linearity correlation coefficient (R2) of 0.999, this is proof for optimal detection. 

More information can be found on the ASBVd info sheet and the Sample submission form should accompany all samples.

Contact: Dr Elize Jooste, JoosteE@arc.agric.za, 013 753 7128


Typical avocado sunblotch viroid symptoms on fruit​.

    • ​Other virus and viroid-related diagnostics

The plant virology unit offers general viral diagnosis which can be customized to individual needs. Various molecular tests are available which targets viral families and can be used to detect viruses from different crops. Common crops screened for viruses in the unit include granadilla, macadamia and citrus, however, general viral diagnostics are not limited to these crops and a best-fit diagnostics can be found for specific/individual needs.

Contact: Dr Ronel Roberts, Email: ViljoenR@arc.agric.za,  Tel: (0)13 753 7027

  • Current Research Focus

The unit, in collaboration with South African Macadamia (SAMAC), is currently researching the effects of a newly discovered Orthotospovirus on the yield of macadamia nuts. This novel virus was identified within the unit by high-throughput sequencing technologies and was shown to be wide-spread in Macadamia orchards, being detected in Mpumalanga, Limpopo and Kwazulu Natal. The virus causes characteristic ringspot symptoms on infected macadamia leaves from various cultivars and the presence of the virus can be confirmed by diagnostics developed within the lab.

A loop-mediated isothermal (LAMP) assay was developed by the unit for the detection of the causal agent of citrus Huanglongbing and Citrus Greening disease i.e. 'Candidatus Liberibacter asiaticus' (Las) and 'Ca. L. africanus' (Laf). The project was conducted in collaboration with Citrus research International (CRI). This tests aims to serve as a rapid in-field diagnostic to pre-screen citrus samples for the presence of HLB, which is currently not detected in South Africa. This disease has the potential of devastating the industry as it has done elsewhere in the world, and therefore it is vital that a first incursion of Las be detected as fast as possible to limit the spread of this fastidious bacterium. 

Contact: Dr Ronel Roberts, Email: ViljoenR@arc.agric.za. Tel: (0)13 753 7027​

Ringspot symptoms associated with the novel
Orthotospovirus identified from macadamia.

The unit is also involved in research on avocado sunblotch viroid (ASBVd) for South African avocado industry (funding through SAAGA). In this project, different aspects are investigated to understand field spread of ASBVd better and to determine the best management strategies for the viroid.

Contact: Dr Elize Jooste, Email: JoosteE@arc.agric.za, Tel: (0)13 753 7128

Plant infected with BBTV​.

​​Banana bunchy top disease is a major threat to banana cultivation in the South Coast region of KwaZulu-Natal. The virus associated with the disease, banana bunchy top virus (BBTV), was detected there in 2015 on a commercial farm in the region and since then has spread to the rural communities in the surrounding 30 – 40 km radius. Management strategies, the control of the aphid vector and removal of infected plants, are implemented on commercial farms but​​ in the rural communities continuous spread of the virus is recorded. The ARC collaborates with DALRRD and DARD to assist with management strategies in the region.​

​The banana aphid vector, Pentalonia nigronervosa, that transmit banana bunchy top (BBTV).