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https://e-catalogs.taat-africa.org/gov/technologies/cassava-virus-indexing-molecular-diagnostics-for-cassava-seed-health-certification
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Cassava virus indexing: Molecular diagnostics for cassava seed health certification

Virus diagnostic tool for cassava seed health certification by seed producers and seed certifiers.

Cassava virus indexing is a technical process to detect and eliminate virus-infected cassava planting materials from the seed value chain, especially at the nucleus and early generation seed production stages. Virus indexing involves testing plants using sensitive diagnostic methods like Polymerase Chain Reaction (PCR) and isothermal amplification [e.g., Loop-mediated Isothermal Amplification (LAMP) ]to identify infected materials. Only virus-free plants are selected for early-generation seed production. This process safeguards seed quality, enhances crop resilience, and is essential for effective seed certification systems, supporting food security in cassava-growing regions. This technology is critical for nucleus and EGS cassava seed producers, as well as cassava seed regulatory (seed certifiers) for diagnostics-based certification of EGS fields (breeder and foundation seed).

This technology is pre-validated.

9•8

Scaling readiness: idea maturity 9/9; level of use 8/9

Adults 18 and over: No impact

Not applicable as technology is neutral to age and gender

The poor: Positive high

The technology helps prevent the introduction of invasive viruses and protect biodiversity and landraces.

Under 18: No impact

Not applicable as technology is neutral to age and gender; although not relevant to group under 18 years.

Women: No impact

Not applicable as technology is neutral to age and gender

Climate adaptability: Highly adaptable

As a laboratory tool, adoptable and usable under all conditions.

Farmer climate change readiness: Significant improvement

The technology reduces the risk of vector-borne viruses in the field, which are expected to increase under changing climate conditions.

Biodiversity: Positive impact on biodiversity

The technology helps prevention of introduction of invasive viruses and protect biodiversity and landraces

Problem

  • Undetected viral infections in planting materials: Many cassava plants used for seed production may carry viruses without showing clear symptoms, making infections difficult to detect visually.
  • High risk of virus transmission through vegetative propagation: Since cassava is propagated using stem cuttings rather than true seeds, viruses are easily passed from one generation to the next.
  • Widespread presence of destructive cassava viruses: Diseases like Cassava Mosaic Disease (CMD) and Cassava Brown Streak Disease (CBSD) are common in Africa and cause significant yield losses.
  • Lack of reliable diagnostic capacity: In many production areas, there are no tools or systems to accurately detect viruses before seeds are distributed to farmers.
  • Poor seed quality control: Without proper virus detection, infected seeds enter the value chain, compromising seed quality and threatening food security.
  • Reputation and economic losses for seed producers: Distributing virus-infected seeds can damage the trust and credibility of seed suppliers, leading to reduced market opportunities and financial losses.
  • Weak enforcement of seed certification standards: Regulatory bodies often struggle to verify seed health due to the absence of diagnostic-based certification systems.
  • Uncontrolled spread of viruses across farms and regions: The use of contaminated planting materials accelerates the regional spread of diseases, making control and recovery efforts more difficult and expensive.

Solution

  • Accurate virus detection: By using sensitive diagnostic methods like Polymerase Chain Reaction (PCR) and Loop-mediated Isothermal Amplification (LAMP), this technology can detect even low levels of viral infection in cassava plants.
  • Production of virus-free planting material: It ensures that only healthy, virus-free plants are selected for seed multiplication, improving the overall quality of cassava seed systems.
  • Improved seed certification processes: Virus indexing supports regulatory agencies in certifying cassava seed fields based on diagnostic evidence, leading to more reliable seed certification systems.
  • Stronger crop resilience and productivity: Using clean planting materials helps farmers grow healthier cassava crops, increasing yields and reducing losses caused by viral diseases.
  • Protection of seed producer reputation: Seed producers who adopt this technology can avoid distributing infected materials, maintaining trust and market credibility.
  • Slowed spread of cassava viruses: By removing infected plants early, the technology reduces the risk of virus transmission through vegetative planting material.
  • Support for food security: Healthier seed systems contribute to stable cassava production, which is crucial for food security in cassava-growing regions.
  • Scalable and replicable tools and protocols: The technology includes training, protocols, and lab setup guidance, making it possible to scale and replicate virus indexing across different regions and organizations.

Key points to design your project

Cassava Virus Indexing technology helps tackle major challenges in seed quality and virus spread in cassava production. By detecting and removing virus-infected planting materials early, it protects cassava yields, improves seed certification systems, and supports food security in cassava-growing regions—aligning with global sustainability and resilience goals.

To successfully integrate this technology into your national or regional projects, consider the following steps:

  • Assess needs and scale: Estimate the number of samples to be tested and determine equipment and consumables required (e.g., PCR machines, LAMP kits, nucleic acid extraction kits, primers, reagents).
  • Budget wisely: Include costs for lab setup (approx. USD 20,000), sample testing (starting at USD 3/sample), delivery, import duties, and maintenance.
  • Invest in capacity building: Develop a training program for lab technicians and field staff on sample collection, virus testing (PCR/LAMP), and result interpretation. Plan for ongoing technical support.
  • Develop outreach materials: Create simple communication tools (guides, posters, short videos) to promote awareness among seed producers and certifiers on the importance of virus indexing.
  • Engage key partners: Collaborate with research institutes, seed certification bodies, and cassava seed multipliers to embed virus indexing in seed production systems and policies.

20,000 USD

Initial setup cost for a diagnostic lab

3 USD

Cost per sample for testing

IP

No formal IP rights

Countries with a green colour
Tested & adopted
Countries with a bright green colour
Adopted
Countries with a yellow colour
Tested
Countries with a blue colour
Testing ongoing
Egypt Equatorial Guinea Ethiopia Algeria Angola Benin Botswana Burundi Burkina Faso Democratic Republic of the Congo Djibouti Côte d’Ivoire Eritrea Gabon Gambia Ghana Guinea Guinea-Bissau Cameroon Kenya Libya Liberia Madagascar Mali Malawi Morocco Mauritania Mozambique Namibia Niger Nigeria Republic of the Congo Rwanda Zambia Senegal Sierra Leone Zimbabwe Somalia South Sudan Sudan South Africa Eswatini Tanzania Togo Tunisia Chad Uganda Western Sahara Central African Republic Lesotho
Countries where the technology is being tested or has been tested and adopted
Country Testing ongoing Tested Adopted
Benin No ongoing testing Tested Not adopted
Burundi No ongoing testing Not tested Adopted
Côte d’Ivoire No ongoing testing Tested Not adopted
Democratic Republic of the Congo No ongoing testing Not tested Adopted
Ghana No ongoing testing Tested Not adopted
Kenya No ongoing testing Not tested Adopted
Malawi No ongoing testing Tested Not adopted
Nigeria No ongoing testing Not tested Adopted
Sierra Leone No ongoing testing Tested Not adopted
Tanzania No ongoing testing Not tested Adopted
Uganda No ongoing testing Not tested Adopted
Zambia No ongoing testing Tested Not adopted

This technology can be used in the colored agro-ecological zones. Any zones shown in white are not suitable for this technology.

Agro-ecological zones where this technology can be used
AEZ Subtropic - warm Subtropic - cool Tropic - warm Tropic - cool
Arid
Semiarid
Subhumid
Humid

Source: HarvestChoice/IFPRI 2009

The United Nations Sustainable Development Goals that are applicable to this technology.

Sustainable Development Goal 2: zero hunger
Goal 2: zero hunger

End hunger, achieve food security, and promote sustainable agriculture

Sustainable Development Goal 3: good health and well-being
Goal 3: good health and well-being

Ensure healthy lives through improved crop health

Sustainable Development Goal 12: responsible production and consumption
Goal 12: responsible production and consumption

Ensure sustainable consumption and production patterns

  • Set Up a Diagnostic Lab:

    • Equip the lab with necessary tools, including nucleic acid extraction kits, thermal cyclers, and reagents for PCR and LAMP tests.

  • Collect Plant Samples:

    • Sample cassava plants during early-generation seed production using a standardized protocol.

  • Virus Detection:

    • Use PCR or LAMP methods to test for viruses like CMD and CBSD in the plant tissue.

  • Select Virus-Free Plants:

    • Only select plants that test negative for viruses for early-generation seed production.

  • Train Personnel:

    • Train lab and field staff on virus testing, equipment use, and result interpretation.

  • Standardize Protocols:

    • Follow consistent protocols for sampling, testing, and interpreting results to ensure reliable outcomes.

  • Ensure Seed Integrity:

    • Regularly test seeds to maintain virus-free stock and update testing procedures as needed.

  • Integrate into Certification:

    • Use virus indexing results as part of the seed certification process for virus-free early-generation seeds.

Last updated on 2 May 2025