No established tests are in place

Here's an interesting and well researched article about GMO detection methods for gene-edited products. The article is from a surprising source: Labiotech.eu, which calls itself "the leading digital media covering the European Biotech industry".
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Detecting gene-edited food: The EU’s nightmare

By Jonathan Smith
Labiotech.eu, 3 Feb 2021
https://www.labiotech.eu/regulatory/gene-editing-food-europe/

The EU imposed stringent controls on the commercialization of gene-edited food back in 2018. Years later, regulators are still working in the dark, with no established tests in place.

The EU has some of the strictest food regulations in the world surrounding the cultivation and commercialization of genetically modified organisms (GMOs), which it defines as organisms whose “genetic material is modified artificially to give [them] a new property.” To get approval, GMO crops have to pass stringent assessments of their safety and environmental impact, and continue to be closely monitored after reaching the market.

To enforce GMO restrictions, EU member states first need a way to detect GMOs. So in 2002, the EU set up the European Network of GMO Laboratories (ENGL). This one of the main EU organizations developing methods for screening seeds, grains, food, and feed for signs of unauthorized bioengineering. One of the key weapons in its arsenal is polymerase chain reaction (PCR), where a telltale DNA sequence in a sample is captured and amplified in the lab.

In the early days, there were common genetic traces of bioengineering in multiple crop varieties. For example, many of the different foreign genes introduced in GMOs often shared specific DNA sequences, such as promoters and terminators (among others). This made these specific sequences a convenient smoking gun for PCR tests. But times have changed.

“In the last decade, many GMOs have been developed that don’t have any of those sequences,” said John Fagan, cofounder of the Health Research Institute in Iowa, US. “So for instance, right now, if you want to test for all varieties of genetically engineered maize that are on the market, you would have to run four or five separate PCR reactions. We’ll pick up maybe eight varieties, but then you come down to two varieties that don’t have any of those common elements.”

To develop tests for new GMOs, the ENGL has to get hold of samples of the GMOs and information about their specific genetic quirks. The onus falls on GMO developers applying for EU authorization to provide these reference samples and detection methods. But companies that are not bidding for the EU market have no incentive to share and may refuse. What happens if there are no samples and no information to help the ENGL?

“There easily could be unapproved GMOs on the market today in Europe … Old-fashioned recombinant DNA-generated GMOs,” said Fagan. “There could be one or more of those that are right out there in the marketplace, invisible to everybody.”

The GMO landscape has been shaken up by the advent of modern gene editing tools like CRISPR and TALENS. These tools are able to make tiny changes in the target DNA — down to a single nucleotide — that could conceivably arise naturally [GMW: There's no evidence that gene-edited organisms are the same as naturally bred organisms and every reason to think that they will be different, both at the genetic level and the composition level]. In contrast, older techniques to create GMOs generated much bigger modifications that can’t be found in nature.

In 2018, the EU Court of Justice decided that gene-edited organisms fall under GMO restrictions. The move was controversial and left the ENGL with the task of detecting unauthorized gene-edited organisms coming in from abroad. Examples include a Japanese gene-edited tomato, a soybean marketed in the US by the firm Calyxt, and a rapeseed plant sold in Canada by the US company Cibus.

More than two years after the EU’s decision to regulate gene-edited organisms as GMOs, there are zero approved gene-edited crops on the EU market. Moreover, the ENGL and the EU member states don’t appear to have PCR tests ready to detect unauthorized gene-edited organisms in food imports.

“To my knowledge, EU competent authorities aren’t testing for them,” said Franziska Achterberg, biodiversity campaigner at the Greens/European Free Alliance in the European Parliament. “There is some work ongoing in Germany, but overall, neither the EU nor EU governments are putting in the effort needed to resolve the challenges.”

Insufficient enforcement of the EU’s GMO regulations impacts everyone across the biotech industry regardless of their stance on gene editing. For example, an academic or a company following the strict guidelines required to develop a gene-edited crop could discover that a competitor’s gene-edited organisms entered the EU’s food chain without ever undergoing the costly approval process, giving them an unfair advantage.

In a 2019 report, the ENGL outlined some of the headaches it was facing. For example, edits of a single nucleotide are harder to pick up with PCR than the huge sequences traditionally inserted into GMOs. Additionally, the technique cannot distinguish gene-edited varieties from crops in which the same mutation arose naturally.

In September last year, Fagan’s research group published a PCR method aimed to detect Cibus’ gene-edited rapeseed plant, called SU Canola. The PCR test can distinguish between the DNA sequences of the SU Canola strain and those of other varieties that occur naturally.

“Nobody had actually gone into the lab and said ‘can we do it?’” said Fagan. “With our method, we were targeting the most difficult kind of gene editing, which is a single base pair change.”

“We were quite able, with just some standard tweaks that people do to optimize PCR, to make a technique that fully met the sensitivity requirements of the European regulatory bodies.”

However, the test only proves that a sample has the target DNA sequence, not whether it was a natural occurrence. This was a concern raised by Hendrik Emons, who leads the unit of Food and Feed Compliance at the European Commission’s Joint Research Centre, during a webinar discussing the PCR test in December.

“From a legal point of view, a regulatory point of view, you would not be able to clearly say that this single-nucleotide variant is a result of gene editing just with this detection method alone,” explained Emons.

Heike Moldenhauer, the EU policy advisor of the German Association for Food without Genetic Engineering (VLOG), countered that the PCR test doesn’t necessarily need to prove that gene editing has taken place, as long as it can pick up that particular strain of canola.

The discussion over the legal weight of this PCR test is just part of a much bigger debate: should gene-edited organisms be regulated as GMOs in the EU if the gene editing process can’t be detected? According to the Genetic Literacy Project and Euroseeds, a body representing seed producers, the answer is no.

“[The] lack of enforceability of the GMO regulation is recognized by a growing number of countries like the US, several South American countries, Australia, and Japan,” said Petra Jorasch, Euroseeds’ Manager of Plant Breeding Innovation Advocacy. That is one of the reasons these countries don’t include gene-edited organisms in their GMO controls.

However, Moldenhauer argued that it’s the EU’s responsibility to make it possible to enforce the control of gene-edited crops. The VLOG and other groups started the ball rolling by financing the development of Fagan’s PCR test.

“We stepped in as a consortium of non-GMO associations and non-governmental organizations because the responsible authorities failed to do their job,” Moldenhauer said in the webinar. “I think it’s not a model for the future.”

Practically speaking, if current tests can’t find traces of the gene editing process, then the ENGL relies even more on data and reference materials provided by the developers to identify each organism. But in the case of SU Canola, Cibus refused to provide the reference materials and data that the ENGL and other laboratories needed to validate a test.

“We are short of the tools to do our experimental work,” Emons said.

At the time of publication, Cibus wasn’t available to comment. The US biotech is not obligated to send testing materials to European regulators because it isn’t currently applying for EU authorization. This is a snag for regulators’ efforts to prevent the crop from illegally reaching European shores.

Fagan hinted that his team got hold of Cibus’ materials without asking the company directly. He added that the company’s opaque behavior is a common occurrence in the US agrobiotech industry, where regulation is less stringent than that of the EU. In contrast, the EU demands more transparency and consultation.

“This is something I always say to my friends in the industry: if you were just open and transparent about what you’re doing, consumers would begin to trust your products and accept them,” Fagan noted. “Instead of that, the strategy for so long has been just the opposite.”

While the EU is unprepared for detecting gene-edited organisms at the moment, there is still time to beef up its testing muscle. Gene-edited crops take years to reach the market, and those approved in the US, Canada, and Japan have a low chance of illegally entering the EU’s food chain for now. But, according to Moldenhauer, this is not an excuse for policymakers to lay idle.

“The member states refer to the European Commission, which refers to the member states. The result: nobody takes responsibility,” she said. “What is needed is a coordinating instance and that has to be the European Commission.”

A possible course of action would be for the European Commission to issue a call for research projects to improve testing methods for gene-edited organisms. In the case of the SU Canola, the Commission could also press Cibus and the Canadian authorities harder for the reference materials that the ENGL needs to do its job.

While there are currently no ways to fully confirm in the lab whether an organism has been gene-edited, Fagan believes this may not be the case forever. For example, genomic leftovers of the gene editing machinery could be sniffed out by sequencing the full genome and potentially with PCR further into the future.

“You do a full genome sequence, which costs less than €2,000 today,” said Fagan. “If there’s even a 25 base-pair fragment of the recombinant material left, you’re going to find it.”

Once more tests and funding become available to the EU’s GMO enforcers, opaque companies will be forced to tread more carefully. Furthermore, the availability of these tests could level the playing field for gene editing companies that wish to be transparent and follow the EU’s regulations.

“It’s time to grab the bull by the horns,” concluded Fagan. “It’s good for Europe to create that transparency.”

Note: There is some debate about whether Cibus’ SU Canola is truly gene-edited, since one recent Canadian regulatory document seems to contradict the idea. However, the European Food Safety Authority told me it will treat the crop as a GMO.