Could Cannabis Labs Help With COVID-19 Testing Backlogs?
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On January 21 this year, the first genome sequence of the virus from Wuhan China that came to be known as SARS-CoV-2 and the causative agent of COVID-19 was preprinted in bioRxiV. Less than 24 hours later, a corrected and improved version was posted on the same site. There were some rumblings at the time of how severe this virus was going to be, of course, but this was somewhat unprecedented. Science is methodical – and slow. You don’t drop new results and then fix them the next day. That’s not how this works. This is when a lot of us in the scientific community who aren’t directly involved in epidemiology or viruses realized that something bad was coming.
The very next day the US Center for Biotechnology Information had translated, and retranslated, the genome sequences into protein information. Out of boredom, I took these sequences and assembled them into a single file in the correct format for proteomics software and put that file on news in Proteomics Research, a site I run largely for making mass spectrometry memes. The next day I was shocked by the number of views my site had received. That’s when I realized something very bad was coming.
That weekend I took those protein sequences and ran them through some mass spectrometry programs, including a new deep learning program, and came up with some theoretical methods for detecting the virus in patient samples. It was a fun exercise and we learned some new tools, and that’s what my friends and I do some weekends, but then we sat on it.
Come on, what are two mass spectrometrists going to contribute to some virus? This is just a crazy idea and, at best, we’ll look like we’re grabbing at headlines. There are genomics experts and epidemiologists and the Centre for Disease Control (CDC) and the World Health Organization, they’ll get this in hand. Why would we need to propose something different?
You know the story. The problems with the detection kits. The reagent shortages. I have a rule about any idea. I take that idea and I talk about it with smart people and I encourage them to shoot it down. I’m lucky enough to have friends much smarter than I am and many of my ideas stop there. This one didn’t because this crazy idea looked like it would be better than no ideas. Finally, over a month after we’d finished it, we dropped the preprint and I nervously waited for a response. It was cleared and rapidly posted and eight days later it was the most read thing I’ve written in a 15-year career of writing far too much.
'Crazy Idea Number 1' all the sudden didn’t seem so out of place with what was happening to the world around us. With traditional systems breaking down under the pressure of this unprecedented global pandemic, is it time to knock down the walls and think about science and diagnostics in a new way?
The goal of our little team is to build new instrument applications on the equipment that people already have. We work under the principle that any piece of analytical equipment, particularly mass spectrometers, can be refitted to do just about anything if you’re creative enough. Covid-19 is just a new challenge in the long line of those we’ve worked on. In this one, the stakes are just higher.
In our study we propose this idea: ‘Hey – if you don’t have access to a Covid-19 testing kit, but you have access to a mass spectrometer, you could use it and here is the method you’d need for these five different brands of instrument.’ And the paper ends with an invitation to contact us for help. And people did. A day hasn’t gone by that I haven’t been contacted by someone working on implementing these assays.
Crazy? Yes. Here is an unvalidated method created entirely by computer programs and things are so bad that people are forced to give it a try.
It gets crazier. The backlogs of testing are still horrendous. It doesn’t matter where you are today. Yes, there is reason for optimism from the new tests in the headlines and it’ll get better, but right now the lines are growing.
While sitting on a teleconference with some government scientists from a wide range of institutions, someone mentioned as a joke something like, ‘what about cannabis labs, they have many of the right instruments…’ And we laughed and then we stopped laughing. Cannabis compliance labs do have the right instruments.
We’ve tinkered in the cannabis industry for the last year or so. We designed, built, and validated a lab in Maryland in 2019 and our design was replicated for a lab that was just validated in California earlier this year. We learned a lot about the cannabis industry and the people in it, but the instrumentation was all the same. The same that we’d used in the past for systems as diverse as anthrax and cancer cells, and viruses.
The detection assays for SARS-CoV-2 are of two main types. By far, the most common, including those developed by the CDC use quantitative polymerase chain reaction (qPCR) instruments. Nearly all cannabis testing labs use that same hardware for testing for microbial pathogens. I’m estimating this number based on visiting a few dozen labs in North America, but I’d guess that 80 percent of cannabis labs in the US use the Medicinal Genomics qPCR assays. The hardware used for these assays are the exact same instruments used for the CDC assays. In fact, as I’m currently consulting on the construction of Coral Reef Labs in Jonestown, PA, we are finding it difficult to even obtain instruments. The manufacturers are having trouble keeping up with the demand from the Covid-19 assays.
The second type of assays are protein based. Antibodies are raised against SARS-CoV-2 proteins and these assays can be cheaper, faster, but far less sensitive. It takes a long time to generate antibodies, but these should be hitting the market soon. In the clinical labs nearly every year another antibody-based assay is replaced by the faster, more sensitive, and more reproducible assays performed by liquid chromatography–mass spectrometry (LCMS).
Every cannabis compliance lab in North America has LCMS. This is how potency is often determined and always how products are screened for pesticide contamination and growth regulators. Some labs even utilize LCMS for the determination of terpene levels. LCMS is great for all these things – and it’s also great for monitoring for viral peptides in human body fluids. Researchers at Duke have been developing virus assays on LCMS platforms for at least a decade and they’re not the only ones. SARS-CoV-2 isn’t special. Once you have the targets set up, you can detect the virus proteins or peptides, or the human proteins formed in response to the virus. Along with our preprint we provided resources for testing for SARS-CoV-2 infection using Waters, Agilent, Shimadzu, Agilent, and Thermo instruments.
We weren’t the first ones to come up with this idea. By March 27, Health Canada was already approaching cannabis testing labs to see if they could help with the testing backlog. We haven’t heard much more about it, but the problem in almost every diagnostic technology is the same: who is going to develop the assay and train technicians in how to perform it.
And here is the craziest idea yet: we will. We’re open to ideas. We’ll need help and labs that are interested or required to divert their resources from testing cannabis to screening patients for SARS-CoV-2 can reach out to us. We’ll do everything we can. We’re also feverishly writing grants to find funding to pull in more resources in case this gets worse and we have to divert resources from many labs to this endeavor.
Here is the summary: during the progression of Covid-19 I’ve stopped several times because I thought I was being crazy. I’m done questioning. If you are in an area where there isn’t enough testing, maybe it’s time to go to the cannabis labs. They’ve got the right equipment. They’ve got trained staff. Some areas may be closing these valuable labs. If you need help, reach out to us. We’ll do what we can. I hope we never need to go this far, and this idea is just a backup plan won’t ever be employed.
In this time of crisis, the established plans haven’t been doing enough. Maybe it’s time for the crazy ideas. And this is craziest idea I’ve got.
Benjamin Orsburn is the chief scientific officer at Proteomic and Genomic Sciences.