Tag Archives: diagnostic

Hop Latent Viroid (HLVd) & Pathogen Diagnostics: A Comprehensive Overview

By Tassa Saldi, Ph.D.
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Hop latent viroid (HLVd) has gained attention as the molecular cause of “dudding disease” and is causing significant economic losses in the cannabis industry.1,2 Estimates indicate that upwards of 4 billion dollars of market value are lost each year to this pathogen alone.3 The impact of HLVd on cannabis plants necessitates the development and implementation of effective pathogen diagnostics to mitigate its spread and minimize crop damage. With collaborative research efforts, we can gain valuable insights into the characteristics, spread, symptoms and preventive measures associated with HLVd in the cannabis industry.

Viroids: A Brief Overview

Figure 1: Virus vs Viroid

Viroids are unique infectious agents composed solely of genetic material, distinct from viruses. Unlike viruses, viroids lack a protective protein layer and solely rely on the host plant for replication and spread. Their stability and ability to persist in various environments make viroids a formidable threat to plant health.

Hop Latent Viroid: Origin and Global Spread

Hop latent viroid was initially identified in hop plants in 19884 and was found to be largely asymptomatic in this crop. Consequently, HLVd has spread worldwide, mostly unchecked by the hops industry. This pathogen has been identified on most continents and in some fields more than 90% of hops plants are infected.5 Hop latent viroid very likely jumped from hops into cannabis, due to similar genetics. The timing and mechanism of cross-species transmission to cannabis remains unknown, but the prevalence of HLVd suggests this viroid has been circulating within cannabis for an extended period. Data collected at TUMI Genomics indicates that HLVd is present in all states in the United States where cannabis is legal as well internationally including; Canada, the United Kingdom, France, the Netherlands, Thailand, Austria and Switzerland.

Symptoms and Impacts on Cannabis Plants 

Figure 2: HLVd Symptoms

HLVd exhibits a wide range of symptoms, which can vary from severe to subtle, affecting the growth, leaf development, flower quality and overall vitality of cannabis plants. Understanding these symptoms is crucial for timely diagnosis and appropriate disease management strategies.  However, HLVd can also present asymptomatically, especially in vegetative plants. The only way to determine if your plants are infected is by routine molecular testing.

Modes of Transmission

Mechanical Transmission: HLVd primarily spreads mechanically through contact with infected sap during activities like trimming and handling. Additionally, transmission through contaminated water and the potential role of insects, fungal pathogens and seeds in spreading HLVd have also been observed.

Seed Transmission: Although no published studies exist in cannabis describing the frequency of seed transmission, HLVd does transmit through seeds in hop plants at a rate of around 8%.7 Preliminary studies performed by TUMI Genomics in collaboration with EZ-genetics suggest cannabis seed transmission does occur at variable rates depending on strain and level of infection of the parent plants.

Water Transmission: It has also been observed that viroids are in high concentration in the roots8 and can move from the root into runoff water.9 Plants sharing a common water source with infected plants, such as recirculating water systems or flood and drain procedures, are at risk for transmission of the viroid.

Insect and Other Vector Transmission: The jury is still out as to whether or not insects can transmit HLVd. However, multiple viroids are transmitted via insects, so it is likely that HLVd insect transmission occurs. Recent studies also indicate that fungal pathogens, like Fusarium, can transmit viroid infections.6 While pathogenic fungus is a major concern for cannabis growers in its own right, limiting the prevalence and spread of fungal pathogens in your facility could help limit hop latent viroid transmission as well.

Therefore, implementing proper sanitation practices and limiting pest access can help minimize transmission risks.

Preventive Measures

Prevention plays a vital role in safeguarding cannabis crops against HLVd. The STOP program, developed by TUMI Genomics, offers a comprehensive approach that includes maintaining a Sterile environment, Testing mother plants regularly, Organizing the facility to minimize pathogen spread, and Protecting the facility’s borders from introduction of infected plant material, insects and contaminated water. More details on these preventative measures can be found here.

Pathogen Diagnostics

Protecting your plants from hop latent viroid requires accurate identification and removal of infected plants before the infection spreads to other plants. To accomplish this, several critical factors should be considered:

Type of test: HLVd and all viroids can only be detected by a molecular test (a test that detects the presence of DNA/RNA). Among common molecular tests, PCR is generally the most sensitive and accurate method. PCR can provide both a diagnosis and an approximate viroid level, allowing informed management decisions. Other types of molecular tests, such as LAMP and RPA, can formally be as sensitive as PCR, but the classic versions of these assays often suffer from false positive/negative results, reducing accuracy.

Figure 3: HLVd Levels and Distribution

Tissue type: An important consideration for HLVd detection is the plant tissue selected for testing, especially when identifying low-level or early infections when HLVd is not yet systemic. Studies completed by TUMI Genomics and others show root tissue contains the highest levels of HLVd and is the most reliable tissue for detection of viroid infection. While upper root tissue appears to contain the highest levels of viroid, roots from anywhere in the root ball are predictive of infection. Samples taken from the leaves/foliage tend to have lower levels of viroid and may produce false negative results.

Figure 4: Testing Schedule

Testing frequency: Routine pathogen testing is standard practice in general agriculture and is critical to maintain a healthy cannabis crop. Testing of mother plants every 4-6 weeks for economically critical pathogens (such as HLVd) will help ensure a successful run and a high-quality product.

Disinfection Methods

Studies have shown that viroids can remain infectious for longer than 24 hours on most common surfaces11 and 7 weeks in water.10 Making effective disinfection methods essential to limit the spread of HLVd. While common disinfectants like alcohol and hydrogen peroxide are ineffective against viroids, a 10% bleach solution has shown efficacy in destroying HLVd. Proper tool sterilization practices, such as soaking tools in bleach for 60 seconds, are crucial to prevent transmission during plant handling.

Figure 5: Bleach Dilution

Hop latent viroid poses a significant threat to the cannabis industry, leading to substantial economic losses. Timely and accurate pathogen diagnostics, along with stringent preventive measures, are essential for minimizing the impact of HLVd. Regular testing, proper disinfection protocols and adherence to pathogen prevention programs can help ensure the health and vitality of cannabis crops in the face of this global pandemic.


References

  1. Bektas, A., et al. “Occurrence of Hop Latent Viroid in Cannabis Sativa with Symptoms of Cannabis Stunting Disease in California.” APS Journals, 21 Aug. 2019, doi.org/10.1094/PDIS-03-19-0459-PDN.
  2. Warren, J.G., et al. “Occurrence of Hop Latent Viroid Causing Disease in Cannabis Sativa in California.” APS Journals, 21 Aug. 2019, doi.org/10.1094/PDIS-03-19-0530-PDN.
  3. Cooper, Benjie. “Hop Latent Viroid Causes $4 Billion Cannabis Industry Loss – Candid Chronicle.” Candid Chronicle – Truthful, Straightforward, Blunt Cannabis News, 16 Aug. 2021, candidchronicle.com/hop-latent-viroid-causes-4-billion-cannabis-industry-loss/.
  4. Puchta H, Ramm K, Sänger HL. The molecular structure of hop latent viroid (HLV), a new viroid occurring worldwide in hops. Nucleic Acids Res. 1988 May 25;16(10):4197-216. doi: 10.1093/nar/16.10.4197. PMID: 2454454; PMCID: PMC336624.
  5. Faggioli, Franceso, et al. “Geographical Distribution of Viroids in Europe.” Viroids and Satellites, 31 July 2017, www.sciencedirect.com/science/article/abs/pii/B9780128014981000449#bib47.
  6. Wei S, Bian R, Andika IB, Niu E, Liu Q, Kondo H, Yang L, Zhou H, Pang T, Lian Z, Liu X, Wu Y, Sun L. Symptomatic plant viroid infections in phytopathogenic fungi. Proc Natl Acad Sci U S A. 2019 Jun 25;116(26):13042-13050. doi: 10.1073/pnas.1900762116. Epub 2019 Jun 10. PMID: 31182602; PMCID: PMC6600922.
  7. Singh RP. The discovery and eradication of potato spindle tuber viroid in Canada. Virus disease. 2014 Dec;25(4):415-24. doi: 10.1007/s13337-014-0225-9. Epub 2014 Dec 2. PMID: 25674616; PMCID: PMC4262315.
  8. Jama, Aisha, et al. TUMI Genomics, Fort Collins, CO, 2022, Hop Latent Viroid Levels and Distribution in Cannabis Plant Tissue.
  9. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.
  10. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.
  11. Mackie AE, Coutts BA, Barbetti MJ, Rodoni BC, McKirdy SJ, Jones RAC. Potato spindle tuber viroid: Stability on Common Surfaces and Inactivation With Disinfectants. Plant Dis. 2015 Jun;99(6):770-775. doi: 10.1094/PDIS-09-14-0929-RE. Epub 2015 May 15. PMID: 30699527.

Smart Plants: A Q&A with Jonathan Vaught, CEO and Co-Founder of Front Range Biosciences

By Aaron Green
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Plant genetics are an important consideration for cultivators planning to grow cannabis crops. Genetics can affect how well a plant grows in a particular environment under various conditions and have a major impact on the production of cannabinoids, terpenes as well as other molecules and traits expressed by the plant.

Front Range Biosciences is a hemp and cannabis genetics platform company, leveraging proprietary next generation breeding and Clean Stock® tissue culture nursery technologies to develop new varieties for a broad range of product applications in the hemp and cannabis industries. FRB has global reach through facilities in Colorado, California and Wisconsin, and a partnership with the Center for Research in Agricultural Genomics in Barcelona, Spain. FRB is headquartered in Lafayette, Colorado.

We spoke with Jonathan Vaught, Ph.D., CEO and co-founder of Front Range Biosciences. Jonathan co-founded Front Range in 2015 after a successful career in the diagnostics and food testing industries.

Aaron Green: Jon, thank you for taking the time today. I saw in the news you recently sent tissue cultures to the International Space Station? I’d love to learn more about that!

Hemp tissue culture samples like these sat in an incubator aboard the ISS

Jonathan Vaught: This was a collaborative project between the BioServe group at the University of Colorado Boulder, which is a part of their aerospace engineering program. They do research on the International Space Station, and they have for quite some time. We partnered with them and another company, Space Technology Holdings, a group that’s working on applications of space travel and space research. We teamed up to send tissue culture samples to the space station and let them sit in zero gravity at the space station for about a month, and then go through the reentry process and come back to Earth. We brought them back in the lab to perform some genomic analyses and try to understand if there’s any underlying genetic changes in terms of the plants being in that environment. We wanted to know if there was anything interesting that we could learn by putting these plant stem cells and tissue cultures in an extreme environment to look for stress response, and some other possible changes that might occur to the plants by going through those conditions.

Aaron: That’s an interesting project! Are there any trends that you’re following in the industry?

Jon: We’re excited to see ongoing legalization efforts around the world. We’ve seen continued progress here in the United States. We still have a long way to go, but we’re excited to see the additional markets coming onboard and regulations moving in the right direction. Also, we’re excited to see some of the restorative justice programs that have come out.

Aaron: How did you get involved at Front Range Biosciences?

Jon: It really starts with my background and what I was doing before Front Range Biosciences. I’ve spent more than 15 years developing commercializing technologies in human diagnostics, food safety and now agriculture.

Jonathan Vaught, Ph.D., CEO and co-founder of Front Range Biosciences

I started my career during graduate school in biotech at the University of Colorado at Boulder, where I helped develop some of the core technology for a human diagnostic startup company called Somalogic here in Colorado. I went to work for them after finishing my dissertation work and spent about six years there helping them grow that company. We ended up building the world’s largest protein biomarker discovery platform primarily serving pharmaceutical companies, hospitals and doctors, with personalized medicine and lab tests for things like early detection of chronic illness, cancer, heart disease and inflammation.

I then went to another startup company called Beacon Biotech, that was interested in food safety. There I helped develop some similar technologies for detecting food-borne illness — things like salmonella, listeria and E. coli. That was my introduction to big food and big agriculture. From there, I went to help start another company called Velocity Science that was also in the human diagnostic space.

Along the way, I started a 501(c)3 nonprofit called Mountain Flower Goat Dairy, a dairy and educational non-profit that had a community milk-share, which included summer camps and workshops for people to learn about local and sustainable agriculture. I became more and more interested in agriculture and decided to take my career in that path and that’s really what set me up to start Front Range Biosciences.

Aaron: Do you have any co-founders?

Jon: I have two other co-founders. They both played various roles over the last four years. One was another scientist, Chris Zalewski, PhD. He currently works in the R&D department and helps oversee several different parts of the company including pathology and product development. My other co-founder, Nick Hofmeister served as chief strategic officer for the last few years, and has helped raise the majority of our funding. We’ve raised over $45 million dollars, and he played a big role in that.

Aaron: What makes you different from other cannabis seed companies?

John: We’ve built the first true cannabis genetics platform. What I mean by that is we built a platform that allows us to develop and produce new plant varieties that support both the hemp and the cannabis markets. To us, it’s all cannabis. Hemp and cannabis are scientifically the same plant. They just have different regulatory environments, different products and different markets, but we stay focused on the plant. Our platform is built on several different pillars. Genetics are one of the core pieces, and by genetics I mean, everything from molecular based breeding to marker assisted breeding to large germplasm collections. We collect different varieties of germplasm, or seed, from all over the world and use those to mix and match and breed for specific traits. We also have large nursery programs. Another one of our pillars of the platform includes greenhouse nursery production — everything from flowering cannabis plants to producing cannabis seeds to cloning and producing mother plants and rooted cuttings or clones.

Then tissue culture is another part of the platform, it’s basically the laboratory version of a greenhouse nursery. It’s housed in a sterile environment and allows us to produce plants that are clean and healthy. It’s a much more effective, modern way to manage the nursery. It’s part of our clean stock program, where we start clean, stay clean, and you can finish clean. It’s really built on all of those different pieces.

We also have capabilities in analytical chemistry and pathology, that allow us to better understand what drives performance and the plants, and both different regions as well as different cannabinoid products or terpene products. All of the science and capabilities of the platform are what allow us to create new varieties faster, better, stronger.

Aaron: It sounds like you’re vertically integrated on the front-end of cannabis cultivation.

Jon: Absolutely, that’s a great way to think about it.

The last piece I’d say is that we have areas of research and development that cover the full span of multiple product lines. We think about it from an ingredient perspective. Cannabinoids and terpenes are certainly what drive a large part of the cannabis market in terms of edibles, smokable flower, vapes and extracts and the different effects and flavors that you get. We also are looking at other ingredients, like plant-based protein and hemp as a viable protein source and the ability for hemp to produce valuable fiber for textiles, as well as industrial building materials and applications.

Lastly, there are additional small molecules that we’re working on as well from a food ingredients perspective. There are all kinds of interesting compounds. Everybody talks about the cannabinoids and terpenes, but there are also things like flavonoids, and some other very interesting chemistries that we’re working on as well.

Aaron: What geographies are you currently in?

Jon: Colorado and California primarily and we have a small R&D partnership in Barcelona.

Hemp clones and seeds is a big part of the Front Range Biosciences business

Aaron: Do you have plans for expansion beyond that?

Jon: Our current headquarters are out of Colorado, and most of our Colorado operations right now are all hemp. Our hemp business is national and international.

We work with a licensed cannabis nursery partner in California which is our primary focus for that market, but we will be expanding the cannabis genetics and nursery program into Colorado next year. From a regulated cannabis perspective, that’s the first move. Beyond that, we’re in conversations with some of the multi-state operators and cannabis brands that are emerging to talk about how to leverage our technology and our genetics platform across some of the other markets.

Aaron: How do you think about genetics in your products?

Jon: Genetics means a lot of things to different folks depending on your vantage point and where you sit in the supply chain. Our business model is based on selling plants and seeds. At the end of the day, we don’t develop oils, extracts and products specifically, but we develop the genetics behind those products.

For us, it’s not only about developing genetics that have the unique qualities or ingredients that a product company might want like CBD, or other minor cannabinoids like THCV for example, but also about making sure that those plants can be produced efficiently and effectively. The first step is to introduce the ingredient to the product. Then the second step is to make sure that growers can grow and produce the plant. That way they can stabilize their supply chain for their product line. Whether it’s for a smokable flower product, or a vape product, or an edible product, it’s really important to make sure that they can reproduce it. That’s really how we think about genetics.

Aaron: What is a smart plant? That’s something I saw on your website.

Jon: It’s really about plants that perform under specific growing regions, or growing conditions. For example, in hemp, it’s one thing to produce CBD or CBG. It’s another thing to be able to produce it efficiently in five different microclimates around the U.S. Growing hemp in Florida or Alabama down on the Gulf Coast versus growing on the Pacific Northwest coast of Washington, or Oregon are two very different growing conditions that require smart plants. Meaning they can grow and thrive in each of those conditions and still produce the intended product. Generally, the different regions don’t overlap. The genetics that you would grow in Pacific Northwest are not going to do as well as some better selected varieties for the South East.

It’s not only different outdoor growing regions, but it’s different production styles too. When you think about regulated cannabis the difference between outdoor and indoor greenhouse is mixed light production. Even with hydroponic type growing methods, there are lots of different ways to grow and produce this plant and it’s not a one size fits all. It’s really about plants that perform well, whether it’s different regions in the United States in outdoor production or different indoor greenhouses with mixed lights and production methods.

Aaron: You market CBG hemp as a product line. What made you start with CBG? Is that a pull from the market or something you guys see trending?

Jon: So I think it’s a little bit of both. We offer CBD dominant varieties and CBG dominant varieties of hemp. We also now have other cannabinoids in the pipeline that we’ll be putting out in different varieties next year. Things like CBC as well as varins, or propyl cannabinoids. Also things like CBDV, CBCV, or CBGV, which are the propylcannabinoid versions of the more familiar compounds.

Their nursery services include breeding, propagation and production of cannabis

There was a lot of market demand for CBG. It was a fairly easy cannabinoid to produce as a single dominant cannabinoid similar to CBD or THC. There’s a lot of up-and-coming demand for some of the other minor cannabinoids. Up until a few years ago, CBD was considered a minor cannabinoid. It wasn’t until Charlotte’s Web in the Sanjay Gupta story that it became a major cannabinoid. So I think we see some level of market pull across the category.

On the flip side of that, we have one of the world’s largest R&D teams and consolidated expertise in terms of cannabis. We see the potential for minor cannabinoids, and even terpenes and other compounds like flavonoids to have wide ranging implications in human health. Everything from wellness products, to active pharmaceutical ingredients, to recreational products. From our perspective, that’s the reason why we’re pushing these ingredients. We believe that there are a lot of good products that come out of this work and the genetics that produce these minor cannabinoids.

Aaron: Okay, great. And then last question, is there anything you’re interested in learning more about?

Jon: I think the most exciting thing for me, given my background in clinical diagnostics and human health, is to see more data around how all of these different compounds of the plant can support improved wellness, health and nutrition. I think we’ve only scratched the tip of the iceberg. This type of research and data collection takes years, even decades, especially to see outcomes over time of people using these products. I’m really excited to see more of that and also hopefully be able to make stronger conclusions about some of the benefits that can be had from this plant.

Aaron: That’s the end of the interview, thanks Jon!