According to a press release published earlier this month, the Bio-Rad iQ-Check Aspergilllus Real-Time PCR Detection Kit has received AOAC International approval. The test covers detection for four different Aspergillus species: A. flavus, A. fumigatus, A. niger, and A. terreus.
The detection kit covers those Aspergillus species for testing in cannabis flower and cannabis concentrates, produced with our without solvents. The PCR detection kit was validated through the AOAC Research Institute’s Performance Tested Method Program. They conducted a study that resulted in “no significant difference” between the PCR detection kit and the reference method.
The kit was evaluated on “robustness, product consistency, stability, inclusivity and exclusivity, and matrix studies,” the press release says. Bio-Rad also received approval and validation on the iQ-Check Free DNA Removal Solution, part of the workflow for testing cannabis flower.
The test kit uses gene amplification and real-time PCR detection. Following enrichment and DNA extraction, the test runs their PCR technology, then runs the CFX Manager IDE software to automatically generate and analyze results.
Bio’Rad has also recently received AOAC approval for other microbial testing methods in cannabis, including their iQ-Check Salmonella II, iQ-Check STEC VirX, and iQ-Check STEC SerO II PCR Detection Kits.
Cannabis laws are changing at a rapid pace across all 50 states and around the world. Currently, Cannabis is legal in 11 states for adults over the age of 21, and legal for medical use in 33 states.
Across the nation, many states have been struggling to enact a viable medical and potential adult use cannabis system since Initiative 59 and the “Legalization of Marijuana for Medical Treatment Initiative of 1998.”
Unfortunately, the program has been continuously impacted by the federal government’s presence, first with the passage of the Barr Amendment by Congress overturning the early legalization progress and continuing to delay the onset of the first medical sale at a dispensary until 2013. The federal government continues to exert influence and control over the program expansion including adding Congressional riders on every proposed update including the latest “Safe Cannabis Sales Act of 2019.”
In Washington DC for example, 18 organizations including the National Cannabis Industry Association (NCIA), the ACLU and Law Enforcement Action Partnership petitioned the US House and Senate Financial Services Subcommittees to remove the rider given that “[the] Current law has interfered with the District’s efforts to regulate marijuana, which has impacted public safety. Without the ability to regulate marijuana sales, the grey market for marijuana flourishes despite the need and want of the District leadership and residents alike to establish a regulatory model.”
States with limited availability of medical cannabis, possession laws or with the ability to legally gift up to one ounce and the constant pressure by the federal government, the grey market has expanded with public safety and the safety of these pop-up businesses put at risk. The current state health and safety laws require a seed-to-sale tracking system and testing at independent labs for all medical cannabis, however the grey market consumers are afforded no such protection. The District of Columbia is unique in the US cannabis landscape as it grapples with the local government trying to provide clarity, safety and equity to a medical and adult use community, but it is hampered by what it can and cannot control through federal influence.
As the United States continues to recover from the effects of the COVID-19 pandemic, control and use of tax revenue will move to center stage in all these communities and the cannabis tax revenue will return to focus.
Cannabis tax revenue has shown a massive disparity between projection and reality. In 2018, California projected upwards of one billion dollars in cannabis tax revenue, but in reality was only able to recover a third of that amount. California in response continues to increase the excise tax and even proposed changes to taxes dependent on the amount of THC, creating new pressure on producers, in-part pushing some back into the grey market.
During the pandemic, Colorado enacted emergency rules to extend cannabis sales online. Allowing customers to pay for cannabis via the web and then pick up their purchases at the store. In a testament to what is considered a “critical businesses” the cannabis industry is given opportunity to expand during the pandemic, but still hampered by severely limited access to standard e-commerce options as credit card merchants still remain concerned that cannabis sales are illegal under US federal law. Alaska, Massachusetts, Michigan, Illinois and Oregon also allowed online sales and curbside pick-up, but remain limited in sales as federal banking and access to credit is limited as the Secure and Fair Enforcement (SAFE) Banking Act remains in limbo.
Overarching technologies such as DNA tracking that provide a clear indicator that the cannabis is produced and tested from legal sources, can be proven safe and protects local legal businesses’ products against out of market cannabis would provide such clarity.
As the country moves forward from the COVID-19 health crisis, all legal and safe ways to rapidly restart the economy will be needed, the cannabis economy will be no exception. We should be looking to this emerging market right now to help safely drive revenue and taxes into our states.
In 1887, Julius Petri invented a couple of glass dishes, designed to grow bacteria in a reproducible, consistent environment. The Petri dish, as it came to be known, birthed the scientific practice of agar cultures, allowing scientists to study bacteria and viruses. The field of microbiology was able to flourish with this handy new tool. The Petri dish, along with advancements in our understanding of microbiology, later developed into the modern field of microbial testing, allowing scientists to understand and measure microbial colonies to detect harmful pathogens in our food and water, like E. coli and Salmonella, for example.
The global food supply chain moves much faster today than it did in the late 19th century. According to Milan Patel, CEO of PathogenDx, this calls for something a little quicker. “Traditional microbial testing is tedious and lengthy,” says Patel. “We need 21st century pathogen detection solutions.”
Milan Patel first joined the parent company of PathogenDx back in 2012, when they were more focused on clinical diagnostics. “The company was predominantly built on grant funding [a $12 million grant from the National Institute of Health] and focused on a niche market that was very specialized and small in terms of market size and opportunity,” says Patel. “I realized that the technology had a much greater opportunity in a larger market.”
He thought that other markets could benefit from that technology greatly, so the parent company licensed the technology and that is how PathogenDx was formed. Him and his team wanted to bring the product to market without having to obtain FDA regulatory approval, so they looked to the cannabis market. “What we realized was we were solving a ‘massive’ bottleneck issue where the microbial test was the ‘longest test’ out of all the tests required in that industry, taking 3-6 days,” says Patel. “We ultimately realized that this challenge was endemic in every market – food, agriculture, water, etc. – and that the world was using a 140-year-old solution in the form of petri dish testing for microbial organisms to address challenges of industries and markets demanding faster turnaround of results, better accuracy, and lower cost- and that is the technology PathogenDx has invented and developed.”
While originally a spinoff technology designed for clinical diagnostics, they deployed the technology in cannabis testing labs early on. The purpose was to simplify the process of testing in an easy approach, with an ultra-low cost and higher throughput. Their technology delivers microbial results in less than 6 hours compared to 24-36 hours for next best option.
Out of all the tests performed in a licensed cannabis testing laboratory, microbial tests are the longest, sometimes taking up to a few days. “Other tests in the laboratory can usually be done in 2-4 hours, so growers would never get their microbial testing results on time,” says Patel. “We developed this technology that gets results in 6 hours. The FDA has never seen something like this. It is a very disruptive technology.”
When it comes to microbial contamination, timing is everything. “By the time Petri dish results are in, the supply chain is already in motion and products are moving downstream to distributors and retailers,” Patel says. “With a 6-hour turnaround time, we can identify where exactly in the supply chain contaminant is occurring and spreading.”
The technology is easy to use for a lab technician, which allows for a standard process on one platform that is accurate, consistent and reproduceable. The technology can deliver results with essentially just 12 steps:
Take 1 gram of cannabis flower or non-flower sample. Or take environmental swab
Drop sample in solution. Swab should already be in solution
Transfer 1ml of solution into 1.5ml tube
Conduct two 3-minute centrifugation steps to separate leaf material, free-floating DNA and create a small pellet with live cells
Conduct cell lysis by adding digestion buffer to sample on heat blocks for 1 hour
Conduct Loci enhancement PCR of sample for 1 hour
Conduct Labelling PCR which essentially attaches a fluorescent tag on the analyte DNA for 1 hour
Pipette into the Multiplex microarray well where hybridization of sample to probes for 30 minutes
Conduct wash cycle for 15 minutes
Dry and image the slide in imager
The imager will create a TIFF file where software will analyze and deliver results and a report
Their DetectX product can test for a number of pathogens in parallel in the same sample at the same time down to 1 colony forming unit (CFU) per gram. For bacteria, the bacterial kit can detect E. coli, E. coli/Shigella spp., Salmonella enterica, Listeria and Staph aureus, Stec 1 and Stec 2 E.coli. For yeast and mold, the fungal kit can test for Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger and Aspergillus terreus.
Their QuantX is the world’s first and only multiplex quantification microarray product that can quantify the microbial contamination load for key organisms such as total aerobic bacteria, total yeast & mold, bile tolerant gram negative, total coliform and total Enterobacteriaceae over a dynamic range from 100 CFU/mL up to 1,000,000 CFU/mL.
Not all of the PathogenDx technology is designed for just microbial testing of cannabis or food products. Their EnviroX technology is designed to help growers, processors or producers across any industry identify areas of microbial contamination, being used as a tool for quality assurance and hazard analysis. They conducted industry-wide surveys of the pathogens that are creating problems for cultivators and came up with a list of more than 50 bacterial and fungal pathogens that the EnviroX assay can test for to help growers identify contamination hotspots in their facilities.
Using the EnviroX assay, growers can swab surfaces like vents, fans, racks, workbenches and other potential areas of contamination where plants come in contact. This helps growers identify potential areas of contamination and remediate those locations. Patel says the tool could help growers employ more efficient standard operating procedures with sanitation and sterilization, reducing the facility’s incidence of pathogens winding up on crops, as well as reduction in use of pesticides and fungicides on the product.
Deploying this technology in the cannabis industry allowed Milan Patel and the PathogenDx team to bring something new to the world of microbial testing. Their products are now in more than 90 laboratories throughout the country. The success of this technology provides another shining example of how the cannabis market produces innovative and disruptive ideas that have a major impact on the world, far beyond cannabis itself.
Microbial contamination on cannabis products represents one of the most significant threats to cannabis consumers, particularly immunocompromised patients who are at risk of developing harmful and potentially fatal infections.
As a result, regulatory bodies in the United States and Canada mandate testing cannabis products for certain microbes. The two most popular methods for microbial safety testing in the cannabis industry are culture-based testing and quantitative polymerase chain reaction (qPCR).
When considering patient safety, labs should choose a method that provides an accurate account of what is living on the sample and can specifically target the most harmful microbes, regardless of the matrix.
1. The Method’s Results Must Accurately Reflect the Microbial Population on the Sample
The main objective of any microbial safety test is to give the operator an indication of the microbial population present on the sample.
Culture-based methods measure contamination by observing how many organisms grow in a given medium. However, not all microbial organisms grow at the same rate. In some cases, certain organisms will out-compete others and as a result, the population in a post-culture environment is radically different than what was on the original sample.
One study analyzed fifteen medicinal cannabis samples using two commercially available culture-based methods. To enumerate and differentiate bacteria and fungi present before and after growth on culture-based media, all samples were further subjected to next-generation sequencing (NGS) and metagenomic analyses (MA). Figure 1 illustrates MA data collected directly from plant material before and after culture on 3M petrifilm and culture-based platforms.
The results demonstrate substantial shifts in bacterial and fungal growth after culturing on the 3M petrifilm and culture-based platforms. Thus, the final composition of microbes after culturing is markedly different from the starting sample. Most concerning is the frequent identification of bacterial species in systems designed for the exclusive quantification of yeast and mold, as quantified by elevated total aerobic count (TAC) Cq values after culture in the total yeast and mold (TYM) medium. The presence of bacterial colonies on TYM growth plates or cartridges may falsely increase the rejection rate of cannabis samples for fungal contamination. These observations call into question the specificity claims of these platforms.
The Live Dead Problem
One of the common objections to using qPCR for microbial safety testing is the fact that the method does not distinguish between live and dead DNA. PCR primers and probes will amplify any DNA in the sample that matches the target sequence, regardless of viability. Critics claim that this can lead to false positives because DNA from non-viable organisms can inflate results. This is often called the Live-Dead problem. However, scientists have developed multiple solutions to this problem. Most recently, Medicinal Genomics developed the Grim Reefer Free DNA Removal Kit, which eliminates free DNA contained in a sample by simply adding an enzyme and buffer and incubating for 10 minutes. The enzyme is instantaneously inactivated when lysis buffer is added, which prevents the Grim Reefer Enzyme from eliminating DNA when the viable cells are lysed (see Figure 2).
2. Method Must Be Able to Detect Specific Harmful Species
Conversely, qPCR assays, such as the PathoSEEK, are designed to target DNA sequences that are unique to pathogenic Aspergillus species, and they can be run using standard qPCR instruments such as the Agilent AriaMx. The primers are so specific that a single DNA base difference in the sequence can determine whether binding occurs. This specificity reduces the frequency of false positives in pathogen detection, a frequent problem with culture-based cannabis testing methods.
Additionally, Medicinal Genomics has developed a multiplex assay that can detect the four pathogenic species of Aspergillus (A. flavus, A. fumigatus, A. niger, and A. terreus) in a single reaction.
3. The Method Must Work on Multiple Matrices
Marijuana infused products (MIPs) are a very diverse class of matrices that behave very differently than cannabis flowers. Gummy bears, chocolates, oils and tinctures all present different challenges to culture-based techniques as the sugars and carbohydrates can radically alter the carbon sources available for growth. To assess the impact of MIPs on colony-forming units per gram of sample (CFU/g) enumeration, The Medicinal Genomics team spiked a known amount of live E. coli into three different environments: tryptic soy broth (TSB), hemp oil and hard candy. The team then homogenized the samples, pipetted amounts from each onto 3M™ Petrifilm E. coli / Coliform Count (EC) Plates, and incubated for 96 hours. The team also placed TSB without any E. coli onto a petrifilm to serve as a control. Figures 3 and 4 show the results in 24-hour intervals.
This implies the MIPs are interfering with the reporter assay on the films or that the MIPs are antiseptic in nature.
Many MIPs use citric acid as a flavoring ingredient which may interfere with 3M reporter chemistry. In contrast, the qPCR signal from the Agilent AriaMx was constant, implying there is microbial contamination present on the films, but the colony formation or reporting is inhibited.
This is not an issue with DNA-based methods, so long as the DNA extraction method has been validated on these matrices. For example, the SenSATIVAx DNA extraction method is efficient in different matrices, DNA was spiked into various MIPs as shown in Table 1, and at different numbers of DNA copies into chocolate (Table 2). The SenSATIVAx DNA extraction kit successfully captures the varying levels of DNA, and the PathoSEEK detection assay can successfully detect that range of DNA. Table 3 demonstrates that SenSATIVAx DNA extraction can successfully lyse the cells of the microbes that may be present on cannabis for a variety of organisms spiked onto cannabis flower samples.
For years we have heard about and sometimes experienced, white powdery mildew when growing cannabis. It is a problem we can see, and we have numerous ways to combat it. But now more and more states are introducing regulatory testing on our harvests and they are looking for harmful substances like Escherichia coli., Aspergillis Fumigatus, Aspergillis terreus, … just to name a few. Mycotoxins, mold and bacteria can render a harvest unusable and even unsellable- and you can’t see these problems with the naked eye. How much would it cost you to have to throw away an entire crop?
You bring in equipment to control the humidity. You treat the soil and create just the right amount of light to grow a superior product. You secure and protect the growing, harvesting, drying and production areas of your facility. You do everything you can to secure a superior yield… but do you?
Many of the organisms that can hurt our harvest are being multiplied, concentrated and introduced to the plants by the very equipment we use to control the growing environment. This happens inherently in HVAC equipment.
Your air conditioning equipment cools the air circulating around your harvest in a process that pulls moisture from the air and creates a perfect breeding ground in the wet cooling coil for growth of many of the organisms that can destroy your yield. As these organisms multiply and concentrate in the HVAC system, they then spew out into the very environment you are trying to protect at concentrated levels far greater than outside air. In effect, you are inoculating the very plants you need to keep safe from these toxins if you want to sell your product.
The cannabis industry is starting to take a page from the healthcare and food safety industries who have discovered the best way to mitigate these dangers is the installation of a proper UVC solution inside their air conditioning equipment.
Why? How does UVC help? What is UVC?
What is Ultraviolet?
Ultraviolet (UV) light is one form of electromagnetic energy produced naturally by the sun. UV is a spectrum of light just below the visible light and it is split into four distinct spectral areas – Vacuum UV or UVV (100 to 200 nm), UVC (200 to 280 nm), UVB (280 to 315 nm) and UVA (315 to 400 nm). UVA & UVB have been used in the industry to help promote growth of cannabis.
What is UVC (Ultraviolet C)?
The entire UV spectrum can kill or inactivate many microorganism species, preventing them from replicating. UVC energy at 253.7 nanometers provides the most germicidal effect. The application of UVC energy to inactivate microorganisms is also known as Germicidal Irradiation or UVGI.
UVC exposure inactivates microbial organisms such as mold, bacteria and viruses by altering the structure and the molecular bonds of their DNA (deoxyribonucleic acid). DNA is a “blue print” these organisms use to develop, function and reproduce. By destroying the organism’s ability to reproduce, it becomes harmless since it cannot colonize. After UVC exposure, the organism dies off leaving no offspring, and the population of the microorganism diminishes rapidly.
Ultraviolet germicidal lamps provide a much more powerful and concentrated effect of ultraviolet energy than can be found naturally. Germicidal UV provides a highly effective method of destroying microorganisms.
To better understand how Steril-Aire UVC works, it is important to understand the recommended design. Directed at a cooling coil and drain pan, UVC energy destroys surface biofilm, a gluey matrix of microorganisms that grows in the presence of moisture. Biofilm is prevalent in HVAC systems and leads to a host of indoor air quality (IAQ) and HVAC operational problems. UVC also destroys airborne viruses and bacteria that circulate through an HVAC system and feed out onto the crop. HVAC cooling coils are the largest reservoir and amplification device for microorganisms in any facility.
For the most effective microbial control, UV germicidal Emitters are installed on the supply side of the system, downstream from the cooling coil and above the drain pan. This location provides more effective biofilm and microbial control than in-duct UVC installations. By irradiating the contaminants at the source – the cooling coils and drain pans – UVC delivers simultaneous cleaning of surface microorganisms as well as destruction of airborne microorganisms and mycotoxins. Steril-Aire patented this installation configuration in 1998.
The recirculating air in HVAC systems create redundancy in exposing microorganisms and mycotoxins to UVC, ensuring multiple passes so the light energy is effective against large quantities of airborne mycotoxins and cleaning the air your plants live by.
Where are these mycotoxins coming from?
Aspergillus favors environments with ample oxygen and moisture. Most pre-harvest strategies to prevent these mycotoxins involve chemical treatment and are therefore not ideal for the cannabis industry.
Despite the lack of cannabis protocols and guidelines for reducing mycotoxin contamination, there are some basic practices that can be utilized from other agricultural groups that will help avoid the production of aflatoxins and ochratoxins.
When guidelines are applied correctly to the cannabis industry, the threat of aflatoxin and ochratoxin contamination can be significantly reduced. The place to start is a clean air environment.
Design to win
The design of indoor grow rooms for cannabis is critical to the control of airborne fungal spores and although most existing greenhouses allow for the ingress of fungal spores, experience has shown that they can be retrofitted with air filters, fans, and UVC systems to make them relatively free of these spores. Proper designs have shown clearly that:
Prevention via air and surface disinfection using germicidal UVC is much better than chemical spot treatment on the surface of plants
High levels of air changes per hour enhance UVC system performance in reducing airborne spores
Cooling coil inner surfaces are a hidden reservoir of spores, a fertile breeding ground and constitute an ecosystem for a wide variety of molds. Continuous UVC surface decontamination of all coils should be the first system to be installed in greenhouses to reduce mildew outbreaks.
UVC can virtually eliminate airborne contaminants
Steril-Aire was the first and is the market leader in using UVC light to eliminate mold and spores to ensure your product will not be ruined or test positive.
Mold and spores grow in your air handler and are present in air entering your HVAC system.
Steril-Aire UVC system installs quickly and easily in your existing system.
The Steril-Aire UVC system destroys up to 99.999% of mold/spores.
Plants are less likely to be affected by mold…with a low cost and no down time solution.
It’s time to protect your harvest before it gets sick. It’s time to be confident your yield will not test positive for the contaminants that will render it unusable. It’s time to win the testing battle. It’s time for a proper UVC solution to be incorporated throughout your facilities.
Genome sequencing has made remarkable strides since the initiation of “The Human Genome Project” in 1990. Still, there are many challenges that must be overcome before this methodology can reach its fullest potential and be useful in serving as a method of Cannabis sativa genetics verification and tracking throughout the cannabis supply chain. Several major milestones that must be realized include end-to-end haploid type (single, unpaired set of chromosomes instead of complete paired set or “diploid”), long read, resolved genome sequences at a reasonable cost within a reasonable timeframe and with confidence in accuracy (Mostovoy et al.). These genomes are typically generated as shorter reads that are then scaffolded (Fig 1.) or matched to reference genomes in order to build a longer continuous read. While shorter sequencing reads indeed lower the cost barrier for producing more genomic data, it has created another issue as a result of this short-read technology.
There are two main issues with the more affordable short read sequencing methodology, the first being that sequential variants are typically not detected, especially if they involve a ton of repeats/inverted repeats, due to the limitation of the current referenced Cannabis genomes and the mapping process of the short-read sequences. This is especially unfortunate because larger variants can have up to a 13% variance within a diploid multichromosomal genome, such as Cannabis sativa, and this variance is thought to largely contribute to disease in various species, or maybe terpene profile in Cannabis sativa. Not being able to detect these variances with more affordable sequencing methodologies is particularly problematic and reference genomes produced with short read sequences are typically highly fragmented. The second limitation is the inherent errors, gaps and other ambiguities associated with taking tons of short read sequences and combining them all, like a jigsaw puzzle, in order to draft the larger genomic picture. While there is software with algorithms to assist in deciphering raw sequences, there is still much more work to be done on this challenge, considering that cannabis genome sequencing is new genomics territory. Unfortunately, as researchers seek higher and higher levels of data quality, shortcomings of this type of sequencing technology begin to become apparent. This sort of sequencing methodology relies heavily on reference sequences. This isn’t much of an issue with microbial genomes, which tend to be rather short and typically have one chromosome, however, when seeking to analyze much longer genomes with multiple diploid chromosomes and tons of mono and dinucleotide repeats, problems arise (English et al.).
The other category of sequencing is long read sequencing. Long read sequencing is as it sounds, the deciphering of much longer DNA strands. Of course, the technology is limited by the quality of the DNA captured, therefore, special high molecular weight DNA extraction protocols must be deployed in order to obtain the proper DNA quality (Fig. 3). Once this initial limitation is overcome there is the stark cost of long read sequencing technology. PacBio without a doubt makes one of the highest quality long read sequence generating instruments that has ever graced the field of biotechnology, but due to the steep price tag of the machine, progress in this field has been stifled simply because it just isn’t affordable and the read depth for mammalian and plant genomes is currently almost completely prohibitive until read lengths double in length for this instrumentation. In order to produce what is considered to be a “validated genome” both short read and long read sequencing methodologies are combined. Long read sequencing data is used to produce the reference contigs because they are much easier to assemble, then short read sequencing is scaffolded against the reference contigs as a sort of “consensus validation” of the long read contigs.
Despite the shortcoming of utilizing short read sequencing technology for analysis of the cannabis genome, it is still useful especially when combined with other longer read sequencing technologies or optical mapping technologies. Kevin McKernan, chief scientific officer of Medicinal Genomics, has been working feverishly to bridge the information gap between the cannabis genome and other widely studied plant genomes. As a scientist that worked on the Human Genome Project in 2001, McKernan has a demonstrated history of brilliance in the field of genomics. This paved the way for him to coordinate the first crypto funded and blockchain notarized sequencing project (DASH DAO funded) (Fig. 2), which was completed in 60 days, and surprisingly showed that the cannabis genome is over 1 billion bases long which is 30% larger than any cannabis genome submitted prior to his work. By reaching the standard of 500kb N50 set forth by the Human Genome Project, Kevin McKernan was able to see new aspects of the cannabis genome that were not visible due to the fragmented genomic data previously generated. Information such as a possible linkage of THCA synthase and CBDA synthase genes is crucial when seeking to use the cannabis genome for verification and tracking purposes. This is because special linkages can be considered a type of “genetic marker” that may be used to differentiate cannabis cultivars and lineages. There are many types of genetic markers, including SNP (single nucleotide polymorphisms), VNTR (variable number tandem repeats) and even patterns of gene expression. Funding and recording of cannabis genomics must be further developed in order for potential markers to be identified and validated via larger scale genome-wide association studies.
These technologies, when combined, often reduce the number of scaffolds while increasing the percent of resolved genome by filling in gaps within the drafted genome. Nanopore sequencing is an especially interesting and innovative sequencing technology that is useful in many ways. One of the most powerful uses of this technology is its ability to upgrade the quality of draft and pushed genomes by resolving poorly organized genomes and genomic structure for a fraction of the time and cost of other long read sequencing platforms (Jian et al.), making it an excellent candidate for solving cost and time constraints. Nanopore’s portability and convenience makes it a real-time solution to solving genetics-based problems and questions. A notable use of this technology is recorded during an epidemiological outbreak in Africa, its proof of concept in pathogen detection in space, and its ability to detect base modifications during sequencing process. Even still there are more uses to this exciting technology and it has the potential to elevate cannabis genomics and the field of genomics entirely, while remaining portable and expeditious. A shortcoming of the Nanopore sequencing platform is its low sequencing coverage, which makes this platform inefficient for applications like haplotype phasing and single nucleotide variant detection due to the number of variants to be detected being smaller than the published variant-detection error rates of algorithms using MinION data. Single nucleotide variants can be considered to be genetic markers, especially markers for disease, so this is what inhibits Nanopore from resolving our cannabis genome sequencing problems, as of today.
There are genetic markers to discover, molecular biology protocols to optimize, and industry wide potential for exciting collaborationMany algorithmic problems seem to occur due to input data quality. Typical input data quality suffers as the reads get longer and the sequencing depth gets shorter, resulting in not enough data being generated by the sequencing to provide confidence in the genome assembly. To mitigate this, scientists may decide to fractionate a genome, sequence it, or they may clone a difficult to sequence region with highly repetitive regions in order to produce reads with greater depth and thus resolve the region. They can then perform single molecule sequencing to resolve genome structure then determine and confirm the place of the cloned region. Thus, it seems that the best solution to the limitation of algorithms is to be aware of sequencing platform limitations and compensate for these limitations by using more than one sequencing platform to obtain enough pertinent data to confidently produce authentic, “validated” genome assemblies (Huddleston et al.). With input data being critical in producing accurate sequencing data, standardization of DNA isolation protocols, extraction reagents and any enzymes utilized may be deemed necessary.
To conclude, the field of cannabis genomics is teeming with opportunities. There are genetic markers to discover, molecular biology protocols to optimize, and industry wide potential for exciting collaboration. More states will need to take into account the lack of federal government research grant availability and begin to think of creative ways to get cannabis science funds to continue the development of this industry. Specifically speaking, developing a feasible method for genetic tracking of cannabis plants will require improvements within the availability of sequencing technology, improvements in deploying the resources to these projects in order for them to be completed expeditiously, and standardization/validation of methods and SOPs used in order to increase confidence in the accuracy of the data generated.
A special thank you to all of my cannabis industry mentors that have molded and elevated my understanding of current needs and applied technologies within the cannabis industry, without you there would be no career within this industry for me. You are immensely appreciated.
Bickhart, D. M., Rosen, B. D., Koren, S., Sayre, B. L., Hastie, A. R., Chan, S., . . . Smith, T. P. (2017). Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics,49(4), 643-650. doi:10.1038/ng.3802
English, A. C., Salerno, W. J., Hampton, O. A., Gonzaga-Jauregui, C., Ambreth, S., Ritter, D. I., . . . Gibbs, R. A. (2015). Assessing structural variation in a personal genome—towards a human reference diploid genome. BMC Genomics,16(1). doi:10.1186/s12864-015-1479-3
Huddleston, J., Ranade, S., Malig, M., Antonacci, F., Chaisson, M., Hon, L., . . . Eichler, E. E. (2014). Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research,24(4), 688-696. doi:10.1101/gr.168450.113
Jain, M., Olsen, H. E., Paten, B., & Akeson, M. (2016). The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community. Genome Biology,17(1). doi:10.1186/s13059-016-1103-0
Mostovoy, Y., Levy-Sakin, M., Lam, J., Lam, E. T., Hastie, A. R., Marks, P., . . . Kwok, P. (2016). A hybrid approach for de novo human genome sequence assembly and phasing. Nature Methods,13(7), 587-590. doi:10.1038/nmeth.3865
Across the country, there is a patchwork of regulatory requirements that vary from state to state. Regulations focus on limiting microbial impurities (such as mold) present in cannabis in order for consumers to receive a safe product. When cultivators in Colorado and Nevada submit their cannabis product to laboratories for testing, they are striving to meet total yeast and mold count (TYMC) requirements.In a nascent industry, it is prudent for state regulators to reference specific testing methodologies so that an industry standard can be established.
TYMC refers to the number of colony forming units present per gram (CFU/g) of cannabis material tested. CFU is a method of quantifying and reporting the amount of live yeast or mold present in the cannabis material being tested. This number is determined by plating the sample, which involves spreading the sample evenly in a container like a petri dish, followed by an incubation period, which provides the ideal conditions for yeast and mold to grow and multiply. If the yeast and mold cells are efficiently distributed on a plate, it is assumed that each live cell will give rise to a single colony. Each colony produces a visible spot on the plate and this represents a single CFU. Counting the numbers of CFU gives an accurate estimate on the number of viable cells in the sample.
The plate count methodology for TYMC is standardized and widely accepted in a variety of industries including the food, cosmetic and pharmaceutical industries. The FDA has published guidelines that specify limits on total yeast and mold counts ranging from 10 to 100,000 CFU/g. In cannabis testing, a TYMC count of 10,000 is commonly used. TYMC is also approved by the AOAC for testing a variety of products, such as food and cosmetics, for yeast and mold. It is a fairly easy technique to perform requiring minimal training, and the overall cost tends to be relatively low. It can be utilized to differentiate between dead and live cells, since only viable living cells produce colonies.
There is a 24 to 48-hour incubation period associated with TYMC and this impedes speed of testing. Depending on the microbial levels in a sample, additional dilution of a cannabis sample being tested may be required in order to count the cells accurately. TYMC is not species-specific, allowing this method to cover a broad range of yeast and molds, including those that are not considered harmful. Studies conducted on cannabis products have identified several harmful species of yeast and mold, including Cryptococcus, Mucor, Aspergillus, Penicillium and Botrytis Cinerea. Non-pathogenic molds have also been shown to be a source of allergic hypersensitivity reactions.The ability of TYMC to detect only viable living cells from such a broad range of yeast and mold species may be considered an advantage in the newly emerging cannabis industry.
After California voted to legalize recreational marijuana, state regulatory agencies began exploring different cannabis testing methods to implement in order to ensure clean cannabis for the large influx of consumers.
Unlike Colorado, California is considering a different route and the recently released emergency regulations require testing for specific species of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus). While Aspergillus can also be cultured and plated, it is difficult to differentiate morphological characteristics of each species on a plate and the risk of misidentification is high. Therefore, positive identification would require the use of DNA-based methods such as polymerase chain reaction testing, also known as PCR. PCR is a molecular biology technique that can detect species-specific strains of mold that are considered harmful through the amplification and analysis of DNA sequences present in cannabis. The standard PCR testing method can be divided into four steps:
The double stranded DNA in the cannabis sample is denatured by heat. This refers to splitting the double strand into single strands.
Primers, which are short single-stranded DNA sequences, are added to align with the corresponding section of the DNA. These primers can be directly or indirectly labeled with fluorescence.
DNA polymerase is introduced to extend the sequence, which results in two copies of the original double stranded DNA. DNA polymerases are enzymes that create DNA molecules by assembling nucleotides, the building blocks of DNA.
Once the double stranded DNA is created, the intensity of the resulting fluorescence signal can uncover the presence of specific species of harmful Aspergillus mold, such as fumigatus.
These steps can be repeated several times to amplify a very small amount of DNA in a sample. The primers will only bind to the corresponding sequence of DNA that matches that primer and this allows PCR to be very specific.
PCR is a very sensitive and selective method with many applications. However, the instrumentation utilized can be very expensive, which would increase the overall cost of a compliance test. The high sensitivity of the method for the target DNA means that there are possibilities for a false positive. This has implications in the cannabis industry where samples that test positive for yeast and mold may need to go through a remediation process to kill the microbial impurities. These remediated samples may still fail a PCR-based microbial test due to the presence of the DNA. Another issue with the high selectivity of this method is that other species of potentially harmful yeast and mold would not even be detected. PCR is a technique that requires skill and training to perform and this, in turn, adds to the high overall cost of the test.
Both TYMC and PCR have associated advantages and disadvantages and it is important to take into account the cost, speed, selectivity, and sensitivity of each method. The differences between the two methodologies would lead to a large disparity in testing standards amongst labs in different states. In a nascent industry, it is prudent for state regulators to reference specific testing methodologies so that an industry standard can be established.
As both recreational and medical cannabis legalization continues to progress across the country, each state is tasked with developing regulatory requirements to ensure that customers and patients receive clean cannabis for consumption. This requires cannabis to undergo laboratory testing that analyzes the presence of microbial impurities including yeast and mold.
Some states, such as Colorado, Nevada, Maine, Illinois and Massachusetts use total yeast and mold count testing (TYMC) and set a maximum yeast and mold count threshold that cultivators must fall below. Other states, such as California, require the detection of species-specific strains of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus), which requires analyzing the DNA of a cannabis sample through polymerase chain reaction testing, also known as PCR.
Differences in state regulations can lead to different microbiological techniques implemented for testing.Before diving in further, it is important to understand the scientific approach. Laboratory testing requirements for cannabis can be separated into two categories: analytical chemistry methods and microbiological methods.
Analytical chemistry is the science of qualitatively and quantitatively determining the chemical components of a substance, and usually consists of some kind of separation followed by detection. Analytical methods are used to uncover the potency of cannabis, analyze the terpene profile and to detect the presence of pesticides, chemical residues, residuals solvents, heavy metals and mycotoxins. Analytical testing methods are performed first before proceeding to microbiological methods.
Microbiological methods dive deeper into cannabis at a cellular level to uncover microbial impurities such as yeast, mold and bacteria. The techniques utilized in microbiological methods are very different from traditional analytical chemistry methods in both the way they are performed and target of the analysis. Differences in state regulations can lead to different microbiological techniques implemented for testing. There are a variety of cell and molecular biology techniques that can be used for detecting microbial impurities, but most can be separated into two categories:
Methods to determine total microbial cell numbers, which typically utilizes cell culture, which involves growing cells in favorable conditions and plating, spreading the sample evenly in a container like a petri dish. The total yeast and mold count (TYMC) test follows this method.
Molecular methods intended to detect specific species of mold, such as harmful aspergillus mold strains, which typically involves testing for the presence of unique DNA sequences such as Polymerase Chain Reaction (PCR).
Among states that have legalized some form of cannabis use and put forth regulations, there appears to be a broad consensus that the laboratories should test for potency (cannabinoids concentration), pesticides (or chemical residues) and residual solvents at a minimum. On the other hand, microbial testing requirements, particularly for mold, appear to vary greatly from state to state. Oregon requires random testing for mold and mildew without any details on test type. In Colorado, Nevada, Maine, Illinois and Massachusetts, regulations explicitly state the use of TYMC for the detection of mold. In California, the recently released emergency regulations require testing for specific species of Aspergillus mold (A. fumigatus, A. flavus, A. niger and A. terreus), which are difficult to differentiate on a plate and would require a DNA-based approach. Since there are differences in costs associated and data produced by these methods, this issue will impact product costs for cultivators, which will affect cannabis prices for consumers.
Sunrise Genetics, Inc., the parent company for Hempgene and Marigene, announced last week they have successfully mapped the cannabis genome. The genome map was presented at the 26th Annual Plant and Animal Genome Conference in San Diego, CA during the panel “Cannabis Genomics: Advances and Applications.”
According to CJ Schwartz, chief executive officer of Sunrise Genetics, the full genome map will allow breeders to develop strains using DNA sequence information to complement phenotyping. “In this way a breeding program can be guided by the breeder versus blindly as it is for just pheno-hunting,” says Schwartz. “At the DNA level, we can identify what version of a set of genes a plant contains, and make predictions as to the phenotype, without ever growing the plant. As we make more and more gene markers, we have more genes to track, and breeding becomes more rapid, efficient and precise.” Schwartz says this is essential for breeding stable, repeatable plants. “A commercial strain will be grown in different environments, with solid genetics, the phenotype will mostly stay true, a term we call Genetic Penetrance.”
Determining a plant’s DNA can be extremely valuable and completing the map of the genome now makes this more precise. It can serve as a point of proof, according to Schwartz, providing evidence of lineage in a breeding project and confirming the uniqueness and identity of a strain. The genome map can also allow breeders to select specific genes to develop custom strains. And in addition to all that, it provides legal protection. “Knowing your plants DNA code is the first step to being able take action so no one else can protect it,” says Schwartz. “Well documented evidence in the development of a customized strains is essential to maintaining control of your plant and keeping those you distrust (big pharma) away, many of which have minimal interest in the whole plant anyhow.”
Schwartz says this project took them roughly 18 months to wrap up. “One of the biggest problems was just finding the right plants to grow,” says Schwartz. “In addition we used some emerging technologies and those had some challenges of their own.” According to Schwartz, a key aspect in all this was finding the right collaborators. They ended up working with CBDRx and the plant biology department at the University of Minnesota, where a DEA-licensed lab has been researching cannabis since 2002. “George Weiblen’s group at UM has been working on Cannabis for over a decade,” says Schwartz. “During that time they did repeated selfing to make highly inbred marijuana and hemp lines. The lines were instrumental in deterring the physical order of the genes.”
After finishing up some experiments, they expect to get the genome map published on public domain in less than a year, opening up their research to the general public and allowing breeders and growers to use their data. “This will be a very significant publication,” says Schwartz. “The genome assembly allows for the assimilation of all the currently incompatible Cannabis genome sequence datasets from academia and private companies,” says Schwartz. “Joining datasets from 1000s of strains, and from every continent, will generate an essential public resource for cannabis researchers and aficionados alike.” With a tool like this, we can discover the genes that help produce desirable traits. “This project is a major accomplishment for cannabis, bringing it on par with other important crops, providing a scientific tool to unravel the secrets of this incredibly versatile plant,” says Schwartz.
Sunrise Genetics is assisting cannabis businesses in evaluating strains and developing breeding programs, working with a number of customers currently to develop strains for many different specific traits. “We have the expertise to help select parental strains and guide the selection process at each generation using genotype and phenotype information,” says Schwartz. “Essentially we are bringing all the tools any modern plant breeder would use for improving strawberries to cannabis.”
Sunrise Genetics, Inc., the parent company of Marigene and Hempgene, announced their partnership with New Brunswick Research & Productivity Council (RPC) this week, according to a press release. The company has been working in the United States for a few years now doing genomic sequencing and genetic research with headquarters based in Fort Collins, CO. This new partnership, compliant with Health Canada sample submission requirements, allows Canadian growers to submit plants for DNA extraction and genomic sequencing.
Sunrise Genetics researches different cannabis cultivars in the areas of target improvement of desired traits, accelerated breeding and expanding the knowledge base of cannabis genetics. One area they have been working on is genetic plant identification, which uses the plant’s DNA and modern genomics to create authentic, reproducible, commercial-ready strains.
Matt Gibbs, president of Sunrise Genetics, says he is very excited to get working on cannabis DNA testing in Canada. “RPC has a long track record of leadership in analytical services, especially as it relates to DNA and forensic work, giving Canadian growers their first real option to submit their plant samples for DNA extraction through proper legal channels,” says Gibbs. “The option to pursue genomic research on cannabis is now at Canadian cultivator’s fingertips.”
Canada’s massive new cannabis industry, which now has legal recreational and medical use, sales and cultivation, previously has not had many options for genetic testing. Using their genetic testing capabilities, they hope this partnership will better help Canadian cultivators easily apply genomic testing for improved plant development. “I’m looking forward to working with more Canadian cultivators and breeders; the opportunity to apply genomics to plant improvement is a win-win for customers seeking transparency about their Cannabis product and producers seeking customer retention through ‘best-in-class’ cannabis and protectable plant varieties,” says Gibbs. The partnership also ensures samples will follow the required submission process for analytical testing, but adding the service option of genetic testing so growers can find out more about their plants beyond the regular gamut of tests.
RPC is a New Brunswick provincial research organization (PRO), a research and technology organization (RTO) that offers R&D testing and technical services. With 130 scientists, engineers and technologists, RPC offers a wide variety of testing services, including air quality, analytical chemistry of cannabis, material testing and a large variety of pilot facilities for manufacturing research and development.
They have over 100 accreditations and certifications including an ISO 17025 scope from the Standards Council of Canada (SCC) and is ISO 9001:2008 certified. This genetic testing service for cannabis plants is the latest development in their repertoire of services. “This service builds on RPC’s established genetic strengths and complements the services we are currently offering the cannabis industry,” says Eric Cook, chief executive officer of RPC.
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