Pathogen testing is essential for ensuring clean, disease-free cannabis crops. But with so many potential threats, which pathogens should growers prioritize? Here’s the most critical seed-borne pathogens, their risks, and why targeted testing matters.

Numerous pathogens can be transmitted via cannabis seed, including viruses, viroids, fungal pathogens, oomycetes, and bacteria. Knowing which pathogens to test for, and why, is essential for ensuring a successful crop while avoiding unnecessary costs on tests for pathogens that are not seed-borne or unlikely to cause significant damage.

So, which pathogens could be harbored in cannabis seed?

Seed-borne Viroids in Cannabis

Among the most insidious seed-borne pathogens are viroids. The symptoms of viroid infections often begin subtly, initially mimicking abiotic stress, making early detection difficult. As a result, infections are frequently identified only after significant spread has occurred.

Among these, Hop Latent Viroid (HLVd) currently poses the greatest threat to cannabis cultivation. Like all viroids, HLVd is a tiny molecular parasite that spreads mechanically, through water runoff, and likely via insect vectors(1,2,3). Infected plants exhibit stunted growth, poor root development, decreased biomass, and severely reduced cannabinoid content. While research on HLVd seed transmission is still emerging, multiple studies(4,5) have reported transmission rates ranging from 50% to 90%.

Cannabis flower from infected plants also accumulates a substantial viroid load, suggesting seed surface contamination by HLVd may also be an important source of infection spread. Studies conducted at TUMI Genomics further support these findings, showing that seed-to-seedling transmission ranges from 20% to 50% when originating from a HLVd positive mother plant, depending on factors such as strain, infection level of the mother plant, and seed age.

Additionally, TUMI Genomics has observed HLVd seed transmission from infected males - but at a much lower rate (~5%). However, rates of HLVd infection in seedlings due to positive male plants has been shown to be as high as 80% by others(5).

hop latent viroid seed transmission through cannabis and hemp seeds

HLVd is widespread in both indoor and outdoor cannabis cultivation, with research showing that over 50% of symptomatic plants test positive for the viroid(1,2,6). TUMI Genomics studies further indicate that around 75% of cultivation facilities around the world have either an active or past HLVd infection, highlighting its prevalence across the industry. Given seed transmission of HLVd is highly efficient, it is extremely likely that a given seed batch could contain seeds from infected plants. The ease with which HLVd spreads and the significant impact it has on plant health and yields makes testing seed batches for this pathogen critical to ensuring a successful, disease-free crop.

Seed-borne Viruses in Cannabis

Beyond viroids like Hop Latent Viroid (HLVd), viral pathogens can be a significant concern, especially for outdoor cannabis growers. Among them, Beet Curly Top Virus (BCTV) is one of the most prevalent and damaging. BCTV causes severe upward leaf curling, leaf yellowing and growth defects. The virus is transmitted by the beet leafhopper (Circulifer tenellus), an insect endemic to the western United States and several other states. During times of high leafhopper prevalence, the percentage of BCTV infected plants can approach 90% in symptomatic plants(7).

While multiple sources suggest that BCTV is not seed-borne, no comprehensive study has been conducted to confirm or refute this mode of transmission in cannabis. However, research on petunias demonstrated BCTV seed transmission rates between 38% and 78%(8), suggesting that seed transmission remains a possibility.

Listed below are several other viral pathogens that infect cannabis and have evidence for seed transmission:

Tobacco streak virus (TSV): This virus was found to infect cannabis in studies conducted in both Colorado and New York(9,10) and has shown seed transmission rates between ~7% to 48% in other crops(11).
Alfalfa mosaic virus (AMV): AMV has been identified in cannabis(12) and shows a seed-borne transmission rates up to 90% in other types of plants(13).

Other viruses that do not currently pose an immediate threat to outdoor cannabis cultivation due to seed-borne transmission include:

Lettuce chlorosis virus (LCV): Not seed-borne, and no published reports of incidence in the United States(14).
Cannabis cryptic virus (CanCV): Asymptomatic, with no confirmed impact on plant health(15).
Tobacco mosaic virus (TMV): No reported natural infections in cannabis, and forced laboratory inoculation studies show no induced symptoms(16).
Citrus yellow vein-associated virus (CYVaV): Reported to infect cannabis is several studies(10,17), but no evidence of seed transmission(18).

Testing for BCTV in cannabis seeds followed by TSV and AMV are important steps to ensure a healthy crop. However, LCV, CanCV, TMV and CYVaV are unlikely to cause major economic issues due to seed-borne transmission and are therefore not priorities for screening prior to planting.

Seed-borne Fungal Pathogens in Cannabis

Seed-borne fungal pathogens pose a significant risk to cannabis growers, as they can be present both internally and externally on seeds. Internally infected seeds may carry fungal pathogens that cause disease from within, while externally contaminated seeds can transfer pathogens to seedlings during germination. Once infected plants exist in a field, fungal pathogens can spread quickly through water-run off, insects and sporulation in the air, making these pathogens a major risk to entire crops. Additionally, many fungal pathogens produce mycotoxins or cause dangerous infections in immunocompromised individuals which can be harmful to human health(19). Because of this, ensuring high-quality, disease-free cannabis and hemp seed is not only essential for a successful harvest but also for consumer safety.

Critical Seed-borne Fungal Pathogens

The following fungal pathogens can infect the interior of seeds, leading to damping off, root rot, wilting, and rapid plant death in seedlings(20). These pathogens may also persist on the seed coat, increasing the risk of disease transmission(21-27).

Fusarium spp.
Rhizoctonia solani
Sclerotinia sclerotiorum
Alternaria spp.
Stemphylium vesicarium
Rhizopus Spp

Seeds infected with these pathogens often exhibit low germination rates and may introduce persistent fungal contaminants into the growing environment. Spores from many of these fungi can survive in soil for years, making it critical to prevent their introduction through rigorous seed screening.

Externally Contaminated Seeds & Secondary Transmission

Other fungal pathogens, while less likely to be present internally, can contaminate the exterior of seeds and transfer to seedlings during germination. A recent study on hemp seed found that up to 75% of seeds were surface contaminated with fungal pathogens(23), including:

Penicillium spp.
Cladosporium spp.
Pythium spp.
Chaetomium spp.
Aspergillus spp.

These fungi can proliferate in seedlings and soil, increasing the risk of crop loss and long-term contamination. Seed sterilization prior to planting is critical to prevent fungal outbreaks and ensure healthy germination.

Seed-Borne Bacterial Pathogens in Cannabis

Bacterial diseases in cannabis are less common than fungal or viral pathogens but can still cause significant crop damage. While many bacterial diseases have been reported in outdoor cannabis and hemp, their prevalence is not well understood. Among bacterial pathogens, seed-borne bacteria transmitted by beet leafhoppers are a significant concern due to the widespread presence of these insects in the western United States. These pathogens include both phytoplasmas and Spiroplasma citri.

Spiroplasma citri appears to be significantly less common than phytoplasma pathogens. Recent studies indicate that while phytoplasmas are detected in approximately 21% of symptomatic cannabis plants, Spiroplasma citri is identified in only about 3% of cases(28,29). However, if beet leafhoppers are highly prevalent in the region where the seed was sourced, the risk of Spiroplasma citri infection should still be considered.

Phytoplasmas are cell wall-lacking bacteria that inhabit the plant phloem and are primarily transmitted by insect vectors such as the beet leafhopper. However, they can also be spread through vegetative propagation and seed(30). Phytoplasma infections can cause stunting, small and malformed leaves and highly branched stems (aka “witches broom”). Multiple phytoplasma species that have been identified in cannabis/hemp (28,31,32) including:

Candidatus Phytoplasma asteris
Candidatus Phytoplasma trifolii

While phytoplasmas can be transmitted via seed, infected mother plants often produce low-quality, malformed, or reduced seed yields, making it less likely infected mothers will contribute to seed lots. However, increased risk of seed transmission can arise when seeds are sourced from outdoor-grown plants in regions where the primary vector of phytoplasmas, beet leafhoppers, is endemic namely; Arizona, California, Colorado, Idaho, Oregon, Utah and Washington. If sourcing seed from outdoor cultivators in these areas, phytoplasma screening of seed lots is advisable.

The Bottom Line

Screening for seed-borne pathogens is critical to safeguarding crops. The most prevalent and damaging seed-borne pathogens in cannabis include:

Hop Latent Viroid (HLVd)
Beet Curly Top Virus (BCTV)
Alfalfa Mosaic Virus (AMV)
Tobacco Streak Virus (TSV)
Fusarium spp.
Rhizoctonia solani
Sclerotinia sclerotiorum
Alternaria spp.
Stemphylium vesicarium
Candidatus Phytoplasma asteris
Candidatus Phytoplasma trifolii

For cultivators facing budget constraints, prioritizing pathogen screening is essential to maximizing crop protection with limited resources. Among the seed-borne pathogens listed, HLVd, BCTV, Fusarium, Alternaria, Rhizoctonia solani and Sclerotinia sclerotiorum pose the greatest threat, as they are common, have the potential to cause widespread infection quickly, and can lead to catastrophic crop loss.

HLVd silently spreads through propagation material, leading to stunted, low-yielding plants, while BCTV can quickly devastate entire fields through insect transmission during times when beet leafhoppers are common. Fusarium, Alternaria, Sclerotinia sclerotiorum, and Rhizoctonia solani are aggressive fungal pathogens causing poor germination, seedling collapse and plant death and can persist in soil for years, making them particularly difficult to eradicate once introduced.

Given the potential economic impact of these diseases, allocating resources to test for these high-risk pathogens is a strategic investment in the long-term success of a cultivation operation.

Stronger plants start with testing

TUMI Genomics offers testing for seeds, plant tissue, growing medium, and air and water systems. Some of the pathogens mentioned in this article can be tested upon request.

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References

About TUMI Genomics

TUMI Genomics is a biotechnology company specializing in advanced pathogen detection and genomic solutions. Their flagship product, the TUMIGlow on-site testing device, is designed to support agricultural industries with precise, efficient, and reliable testing technology.

Media Contact: Hailey Spencer, Marketing Director

hailey@tumigenomics.com

Sales Inquiries: Luke Horst, Sales Director

luke@tumigenomics.com

Protecting Your Crop: Which Pathogens to Test in Cannabis Seeds