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Topic 6: Sharing of experiences on detection, identification and monitoring of organisms, components and products of synthetic biology

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Welcome message - synbio forum - topic 6 [#9603]
Dear Participants,

We are approaching the end of this interesting forum, and we are now opening discussions for topic 6. You may have noticed that all other forum’ topics are related to the terms of reference of the synthetic biology AHTEG, and topic 6 is an exception. However, Paragraph 17 (f) of decision 14/19 request the Executive Secretary to convene discussions for sharing experiences on the detection, identification and monitoring of organisms, component and products of synthetic biology.

Based on this, participants are encouraged to share information related to experiences with the detection, identification and monitoring of organisms, components and products of synthetic biology.

Participants are kindly requested to be as specific as possible, and to provide examples of methodologies and strategies related to this forum's topic. The development, adaptation or use of existing tools for this purpose are key issues to be discussed. It would be important to share how these procedures are being performed or planned to be implemented.

Some guiding questions could be:

• Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?

• Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?

• Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?

When posting this information, participants are requested to provide their source of information, indicating if it is coming from a publication, their own work, or other type of source.

I finally take the opportunity to kindly suggest that you reply to this message when making interventions. This will facilitate the subsequent work on summarizing the information and writing the report. Please also refer to the # of a particular post if you are responding to it

Kind regards

Maria de Lourdes Torres
posted on 2019-03-18 01:03 UTC by Mr Austein McLoughlin, Secretariat of the Convention on Biological Diversity
RE: Welcome message - synbio forum - topic 6 [#9604]
Dear Colleagues,

Regarding the questions posed by the moderator related to detection, identification and monitoring of organisms, components and products of synthetic biology, I have the following comments:

1. Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
In the large majority of the cases the methods used for detecting, identifying and monitoring organisms of synthetic biology will be those used for LMOs, e.g. different types of PCR, hybridisation of nucleic acids, detection of proteins, sequencing, etc. There are some cases when there will be challenges (see the answer below).

2. Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?
There are two special cases when technical challenges might arise:

A. Organisms whose nucleic acids contain non-natural nucleotides and/or proteins contain non-natural amino acids.
In principle such amino acids and nucleotides can be detected, e.g. through different chromatographic techniques, mass-spectrometry, etc. If they are present in very small amounts though they can be below the detection limits. In principle methods for detection and identification of specific DNA/RNA sequences, e.g. PCR, hybridisation, sequencing, can be modified to accommodate the presence of non-natural nucleotides, if their positions are known. If the positions are not know there will be a much bigger challenge. One can imagine that some form of high-throughput sequencing technique will be used, but the process can be technically and financially demanding. Detection of non-natural amino acid residues probably will rely on mass-spectrometry and/or antibodies specifically detecting such residues.

B. Organisms whose genome has been edited.
Genome editing (which I do not consider synthetic biology as such) can introduce very small changes, even single nucleotide substitutions. The real challenge here is not only their detection but also distinguishing how such changes were introduced (natural mutations, chemical mutagenesis, classical genetic engineering, some genome editing technique). If the nature of the change is known in advance methods used at present will be applicable. If it is not known it will be much more difficult to detect the difference and probably high quality genome sequencing will be required, although it may not be sufficient. Deciding what is the origin of the change (assuming that we are manage to detect it) will rely heavily on contextual information, and the result is likely to be statistical, that is that different options will be given different probabilities and the results will reliable to different extend.

3. Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?
In principle the current techniques will be able distinguish in many cases between products of synthetic biology and their naturally occurring or chemically synthesized counterparts. Such distinction is likely to rely on the presence and absence of minor contaminants and/or modifications. One can expect that due to different chemistry of synthesis isotope composition (carbon, nitrogen) will show subtle differences between natural products and those produced through chemical synthesis. Whether such isotope differences will exist between the products of the natural producer (plant, animal, microorganism) and synthetic biology organism will depend on the specific set up.

Best Regards,
Nikolay
posted on 2019-03-18 07:35 UTC by Mr. Nikolay Tzvetkov, Bulgaria
RE: Welcome message - synbio forum - topic 6 [#9607]
Dear Colleagues,

Thank you Maria de Lourdes Torres For moderating this important topic. Although it might not be included in the terms of reference of the synthetic biology AHTEG, detection and identification of synbio product is a fundamental issue that precedes risk assessment, monitoring and labelling.

Re. Question 1) To date, LMOs/GMOs have been largely detected and identified by unique DNA sequences contained in their transgenes or neighboring sequences through PCR amplification. These sequences were also used to develop LMO/GMO unique identifiers. In the EU, for example, other methods are not considered under labelling and traceability law and guidelines.  Therefore, it is important to stress analytical methods available for the detection of DNA sequences and other molecules to the analytical methods used in routine analysis and which have been harmonized and validated. This is especially important if there is a need to implement other analytical methods than PCR amplification because they need to follow a list of minimum required criteria (the EU has guidelines for that) in order to be able to be implemented in a systematic way.

Re. Question 2) I agree with Nikolay on the two technical challenges. I would also agree that at some point, LMOs/GMOs can be detected by current analytical methods but they would face challenges for their identification, meaning, defining LMO/GMO unique identifiers. I tend to disagree however that we need to identify what techniques have been used. This has never been implemented or seems to be relevant under the Protocol. We need to generate LMOs/GMOs unique identifiers, and this is also necessary for liability purposes.

Re. Question 3) Because gene-editing organisms might contain DNA changes that are similar or somewhat identical (at least using current analytical methods) to those found in nature (e.g. a single point mutation in maize that already occurs in landrace or wild varieties) the DNA modification might not be suitable for identification purposes and the generation of a unique identifier. In such cases, I suggest other parts of the genome to be used. A multi-target approach would include the identification of DNA changes in other genomic sites than the intended one (i.e. off-target sites). Gene-editing modification cannot yet be confined to a target site and off-target modification is a reality in the large majority of experimental setups. Recently, CRISPR nickases have also shown off-target activity in two recent papers in Science (http://science.sciencemag.org/content/early/2019/02/27/science.aav9973; http://science.sciencemag.org/content/early/2019/02/27/science.aaw7166). Statistical considerations, as well as heterogeneous samples might require new guidance. My suggestion is that the Network of Laboratories work together with the EU ENGL network, as done in the past, to develop on the issue.

Best regards,
Sarah
posted on 2019-03-18 14:14 UTC by Ms. Sarah Agapito-Tenfen, Brazil
RE: Welcome message - synbio forum - topic 6 [#9618]
Dear Forum Participants,

I am aware that in these past weeks we have been asking for your contributions on different topics related to SynBio, and your support has been amazing.

I would like to thank Nikolay (#9604) and Sarah (#9607) for their contributions under the topic “Sharing of experiences on detection, identification and monitoring of organisms, components and products of synthetic biology” and would like to encourage other participants to share information related to this topic, that could contribute to the work of the AHTEG in the coming months.

Kind Regards,

Maria
posted on 2019-03-21 02:39 UTC by Ms. Maria de Lourdes Torres, Universidad San Francisco de Quito
RE: Welcome message - synbio forum - topic 6 [#9620]
Dear participants,

Thanks again for the moderator and for the opportunity to comment on this new topics:

• Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?

The most living organisms already developed or currently under research and development through techniques of synthetic biology, including organisms containing engineered gene drives, fell under the definition of LMOs as per the Cartagena Protocol and in this case the methods for detection, identification and quantification will be the methods used for LMOs. The PCR is the method used in the routine analysis in the official laboratories in Brazil and new protocols are constantly developed and validated according to the strategy for LMO monitoring and inspections.


Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?

Any analytical tool for detection and monitoring needs to be adapted or developed according to the scientific advances. That is not the case only for synthetic biology but it´s the case for genetic engineer since the beginning and that’s why nowadays its possible to use a broad range of analytical tools to obtain results in a short time, reliable and in a cost effective way. It is also important to highlight the importance of mechanisms already established, such as methods database, standard validation procedures, interlaboratorial programs, certified material etc that supports the development of new methods and information sharing.   


Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?

I agree with the #9604 that in principle the current techniques will be able distinguish between the products. But although for a scientific point of view could be interesting to distinguish the difference, if the risk assessment concludes that there are no risks for biodiversity of a certain product produced by synthetic biology, natural production or chemical synthesis I do not see the necessity of distinguish between them.

Best regards,
Luciana - Ministry of Agriculture
posted on 2019-03-21 13:54 UTC by Ms. Luciana Ambrozevicius, Brazil
RE: Welcome message - synbio forum - topic 6 [#9626]
Hi this is certainly not a profound comment, but when detecting entities or events which do not involve DNA, then older techniques based on antibodies eg western blotting or ELISA can still be very relevant and even preferred .  A recent example would be sensitive detection of a transgene expressed from an RNA virus infecting plants, see page 4
https://www.regulations.gov/document?D=EPA-HQ-OPP-2018-0040-0007
see Citrus_GM_viruses_CBD.pdf for more context if required.

Even the detection of RNA viruses can in some instances be better achieved than using antibodies  rather than cDNA approaches.

So while I agree with Nikolay [#9604] point 2a, I suspect that the role of antibodies will continue to extend beyond “Detection of non-natural amino acid residues probably will rely on mass-spectrometry and/or antibodies specifically detecting such residues.”

Thanks

Guy
posted on 2019-03-21 20:31 UTC by Dr. Guy Reeves, Max-Planck-Institut für Evolutionsbiologie
RE: Welcome message - synbio forum - topic 6 [#9630]
Dear Maria, dear all,


Here my answers to the guiding questions posed by our chair,
In general, they are in line with responses #9604, #9607, #9620, #9626.

• Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?

There are a number of methods to detect LMOs. Since all organisms so far fall under the LMO definition, methods for detecting, identifying and monitoring of LMOs are also applicable for organisms obtained by synthetic biology. These methods are mainly based on PCR-based methods to detect detecting specific and unique sequences in the genome. These unique sequences can result from insertion(s), deletions(s) or changes in the genome of the organism. Alternatively, tools are developed to detect expression (or lack of expression) of the specific trait by phenotypic analysis, as indicated by (#9626). Also for components and products of synthetic biology the currently used methods for detection of LMO products are applicable. The method to be used will depend on the nature of the product and, if applicable, will be stipulated by the respective product regulation.
The underlying question is why organisms, components and products of synthetic biology should be monitored, detected and identified. I would suppose this necessity is based on a specific risk posed by the specific organism, component or product. This specific risk could determine which organisms, components and products should be monitored and the most suitable method to be used.

• Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?

The novelty that some organisms, components and products of synthetic biology might present is in itself no reason to develop additional detection, identification and monitoring tools. Only in case this novelty is likely to result in adverse effects on the three objectives of the Protocol, the development of additional tools could be required. On the other hand, as also stated by (#9620), analytic tools for detection and monitoring need to be updated according to scientific advances for any organism, components or product, not only for those derived from synthetic biology.

• Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?

Given the fact that so far there are no differences between products of synthetic biology and their naturally occurring or chemically synthesized counterparts, the current analytical techniques can still be used for synbio products. In cases where there are no differences, or minor differences that would not result in a change in the nature of the product, there is also no need to use analytical techniques for distinction. In case distinction is warranted due to an (additional) risk of the synbio product, analytical methods could be used or developed that focus on these unique and specific differences. As indicated by #9604, the method to used will depend on what one wants to detect.

Kind regards,
Boet
posted on 2019-03-22 08:52 UTC by Ms. Boet Glandorf, Netherlands
RE: Welcome message - synbio forum - topic 6 [#9634]
Dear Maria, Dear All,

I would like to add some thoughts to this interesting discussion.

It is not obvious to me that the necessity to monitor, detect and identify an organism, component or product of synthetic biology should be triggered by a specific related risk as stated in [#9630]. I agree that the major concern when considering biodiversity are potential risks threatening the same. However, my understanding is that the necessity to develop detection methods also depends on the legislation in place, and market demands. I believe that it is commonly agreed that synbio organisms fall under the definition of LMOs. Now, applicants have to propose a detection method for any GMO that is applied for placing on the market in the European Union. Not only for this reason the development of detection methods for any organism, component or product falling under the definition of LMOs seems mandatory. It also allows labelling, and thus consumers to choose between GM and organically or traditionally produced food (which I consider a market demand).

Further, I agree with the expectation expressed in [#9604] that subtle differences might be expected between natural products and those produced through chemical synthesis. I would like to extend this to gene edited organisms. In case of GE, I would expect to find traces or patterns resulting from the specific GE approach applied, which could be the basis for screening and monitoring of such organisms.

I would like to point out that I am not convinced that organisms resulting from synbio are potentially similar to naturally occurring ones as proposed in [#9630]. In this context, I should probably add that I agree with [#9604], and that I similarly consider organisms resulting from GE not as products of synthetic biology. Therefore, I see the discussion on the detection of GE organisms and synbio organisms as two different topics.

Consequently, referring to the question whether products of synthetic biology could be distinguished from naturally occurring or chemically synthesized counterparts I expect organisms resulting from synbio approaches to be sufficiently different to distinguish them. Surely, distinguishability is a major issue when considering the origin of changes to the genome that would typically be introduced by applying GE techniques.

Which possibilities for detection are in place? In any case, one prerequisite for detection is prior knowledge on the alteration. Given this information, for most of the LMOs under question the currently available methods (basically PCR-based methods) are suitable.

What has to be developed? A major challenge remains when it comes to organisms and products where the changes are unknown, for instance because the organisms/products are neither authorized nor under an authorization request. It remains to be seen whether there are features that could be used to trace them in the sense of a monitoring system. In all other cases, the detection method will be event-specific, which means that the change has to be known (which, per definition, here is not the case). Research is needed to see the possibilities and limitations of laboratory methods, e.g. to check whether screening strategies are feasible. Currently, in many cases there is not enough experimental information to conclude on the technical possibilities.
For the time being, organisms, components or products of synthetic biology (and also gene editing) that are not authorized (e.g. in the European Union or other countries worldwide) but somewhere else could be collected in specific and ideally international databases. These could be maintained by regulatory authorities and might also include prior information on the changes to the genome, regardless of the specific technique used to create an organism falling under the definition of LMOs. Another possibility could be to collect information on the development and marketing of synbio products, which is ideally also done on an international basis. Currently, to my knowledge such attempts are only pursued in project-related endeavors.

Thank you and best regards!

Alexandra Ribarits – Austrian Agency for Health and Food Safety
posted on 2019-03-22 15:59 UTC by Ms. Alexandra Ribarits, Austrian Agency for Health and Food Safety
RE: Welcome message - synbio forum - topic 6 [#9636]
Dear Moderators and Forum,

My name is Jim Thomas with the ETC Group - an international  civil society organization that tracks emerging technologies, human rights and biodiversity. Thank you for the opportunity to comment on this extremely important topic of  detection, identification and monitoring of components, organisms and products of Synthetic Biology .  While ETC Group do not have on-staff technical expertise for lab detection methods we have been engaged in a number of  discussions with analytical laboratories, testing experts as  well as companies, standard-setting bodies and trade associations who are grappling in real time with the challenge of identifying organisms and products of synthetic biology as they enter the market place. My comments below are based on some of what we have learned in those discussions.

In particular we would point out that there is developing a considerable expertise on this topic  from those responsible for stewarding organic and non-GMO supply chains and we would encourage the CBD to reach out to these stakeholders in its furtehr work meeting the charge under decision 17f of decision 14/9.  The Non-GMO Project for example is a US-based organization that administers a popular technical standard which requires companies to explicitly exclude ingredients such as flavours, fragrances and sweeteners derived from biosynthetic organisms and also excludes the products of gene-edited organisms . That verification standard is applied to over fifty thousand commercial products  across North America and so the Non-GMO Project, like organic standards bodies, is developing significant expertise in identification and monitoring of organisms and components of synthetic biology including gene-edited ingredients. Natural products companies (who have a legal duty to their customers to live up to their self-description as ‘natural’ as well as organic food and product companies and supplement companies (with a legal duty to affirm the identity of their ingredients) also have a strong interest in ensuring they have strong systems for detection, identification and monitoring. It would be be useful for the CBD to draw on the expertise of these industries as well as the laboratories that work with them, in answering the charge of this question. This also I think speaks to the question raised by some of 'why' it is neccesary to have detection, identification and monitoring - important economic sectors who are involved in stewarding and sustainable use of biodiversity require these tools.

In response to the Guiding Questions:

A full answer to this question requires teasing out the different tools relevant to  a) detection and  identification as opposed to b) monitoring and teh relationship between those activities. Also the answer varies whether one is addressing the products of biosynthetic production organisms  (e.g. Syn Bio vanillin produced in a vat) , of living organisms released into open use (e.g. gene-edited organisms crops, insects or livestock) or the use of synthetic biology components (e.g. engineered siRNA in  an on-field system such as RNA sprays or transient expression approaches). To answer this question I am using the broad ‘operational definition of Synthetic biology that has been agreed by the parties as a useful starting point for these conversations. I am focusing on organsism and products but want to acknowledge tehre is outstanding questions about monitoring for syntehtci Biology components used in both commercial and open-air settings.

As already identified by others, many of the same tools available for detecting ‘first generation’ transgenic LMO’s are also  applicable to ‘next generation’ or ‘synthetic biology’ derived organisms including gene-edited organisms. These methods include  basic observation of the characteristics of the new GMO (e.g. how a herbicide-tolerant GMO reacts to a herbicide or if a yeast produces a novel molecule such as vanillin) as well as amplification of genetic targets and whole genome sequencing.  Most use techniques such as PCR (polymerase chain reaction) or NASBA (nucleic acid sequence based amplification). Methods range from qualitative (identifying if a GM trait is present) to quantitative (measuring how much GM material is present).

A recent and useful review of this topic by Dr Yves Bertheau explores whether these same approaches can continue to apply to the detection and identification of gene-edited organisms and derived products and the author concludes that indeed they can. Dr Bertheau is  director of research at the French National Institute for Agricultural Research (INRA) and former co-chair of a European working group on identification of unknown GMO’s.

see :  Bertheau, Yves. (2019). New Breeding Techniques: Detection and identification of the techniques and derived products. In: Melton L et al (eds.) (2019). Encyclopedia of Food Chemistry. Reference Module in Food Science. Elsevier. 320-336. 10.1016/B978-0-08-100596-5.21834-9. https://www.sciencedirect.com/science/article/pii/B9780081005965218349?via%3Dihub

It should be pointed out that in discussions about identification of new, especially gene-edited, genetic techniques there is occasionally a misleading political claim made that gene edited alterations cannot be detected since there are not necessarily the same identifying general marks , ‘scars’ and elements that GMO detection laboratories routinely use to scan for GMO - e.g. use of acommon  promoters such as the Cauliflower mosaic virus. Detection of first generation GMO’s has  often involved a simple  matrix approach that scans for all of these common elements in the genome  as a way of showing that genetic engineering has occurred. Proponents of deregulating the techniques may wish to claim that since such existing matrices may not pick up gene-edited changes then the genetic alterations are not detectable and so not regulate-able. This is primarily a politcial claim that relies on a lack of imagination.

In fact it is our understanding from others that with study it may be seen thattools such as CRISPR, ZFN and TALENS may indeed leave their own scars and signatures such as chromosomal rearrangements , certain patterns of indels etc that show that genetic engineering has been at work.  Dr Bertheau’s review for example points out that the sequence of the RNA that guides the CRISPR site-directed nuclease complex to the site within the host genome to be modified (the guide RNA) possesses a specific invariant sequence component, technically known as the PAM – the protospacer adjacent motif. The guide RNA, including the PAM, constitutes a recognition sequence that is unique to the given CRISPR system being used. A detection test can therefore  be applied that looks for the recognition sequence of a given CRISPR complex at the site of alteration of the genome. Apparently the genomic signatures of other gene-editing tools can in theory be similarly identified. (e.g. for  ZFN and TALEN gene-editing tool),

Such novel signatures aside, what is much clearer is that if a detection lab is seeking to identify a particular engineered organism  and has information about the genetic alteration that they are looking for then all the normal genomic identification tools can be applied to look for that alteration - including PCR based methods, next generation sequencing etc  That is, provided the  developer of the syn bio or gene-edited organism makes available sufficient identification information on the sequence of its creation then detection and identification  should be straightforward. Dr John Fagan, chief scientist at the Health Research Institute Labs , and the pioneer of commercial GMO Food testing in the 1990’s has commented  about Syn-bio and gene-edited organisms:

"Descriptions can be formulated that make it sound like the new GMOs are special, different, and difficult or impossible to test for. In practice they are not more difficult to test for than the old fashioned GMOs. Enough information will be available in the patents and applications for approvals so that with just a little bit of molecular biological detective work, tests can be designed. And because these are commercial products, as soon as they enter the market, it will be possible, in one way or another, to obtain a sample that can be used to verify the tests designed. This is exactly how labs have been developing GMO tests since 1996. Whether you call it genetic engineering or gene editing, the fact remains that these methods change the DNA sequence. The changed sequences are discoverable. And with that, a test can be developed.”

The key requirement is not new testing methods per se, but political will by authorities to require developers of synthetic biology organisms to make available samples and ideally also  validated protocols for detection and identification of their genetic inventions before anything moves onto the market or out into the environment.

A useful overview of methods to detect and  identify both engineered organisms is to be found in this 2017 report of the Network of European GMO Laboratories "Detection, Interpretation and Reporting on the presence of authorised and unauthorised genetically modified materials"
http://gmo-crl.jrc.ec.europa.eu/ENGL/docs/WG-DIR-Final-Report.pdf  This JRC report proposes a different approach to GMO testing that moves away from the general ‘matrix’ model to what it calls a knowledge-driven  approach. Key to this is being able to use informatics tools to assemble a range of information and knowledge of what may be ‘out there’  and then applying this knowledge with bioinformatics tools to  sequenced genomes to pick up indications that a genetic engineering process may have taken place.  Interestingly this approach mirrors a project funded by US intelligence research agency IARPA called FELIX (Finding  Engineering Linked Indicators). FELIX aims to use machine learning, bioinformatics data mining and other tools and technologies to create a platform able to detect signatures that a biological system has been engineered. IARPA’s call for proposals describes

"The FELIX program aims to develop a suite of tools for the agnostic detection of engineered biological organisms, ranging from viruses, bacteria, insects, animals and plants that are either purposefully or accidentally developed and/or released with the potential to cause harm. Ideally, the tools will expand the quality and amount of information available to distinguish engineered organisms from natural organisms, i.e., natural variation from intentional engineering. These may include technologies such as novel methods and high throughput techniques in genomics, systems biology, bioinformatics and evolutionary biology. The tools should be able to improve the confidence in determining whether a system has been engineered. Examples include identifying signatures that were previously not accessible, using data from multiple interrogation points, increasing sensitivity, improving the quality of the data, and leveraging technologies that can increase throughput and reduce the complexity of sample analysis” - see https://www.iarpa.gov/index.php?option=com_content&view=article&id=999&Itemid=397    Companies now working on the IARPA FELIX project include defence contractor Raytheon and Syn Bio firm Mission Bio - see https://www.raytheon.com/news/feature/rise-double-felix

Parties to the CBD may be concerned that so far as the technology of general detection and identification of organisms of synthetic biology is now under development, it will be in the hands of the US Intelligence establishment and private defense contractors. Parties may feel that the  United Nations shoudl consider action to bring those same detection technologies into open, shared and non-proprietary use.

What the approach advocated by JRC and also IARPA’s FELIX  indicates is that successful detection and identification of engineered organisms using novel techniques is likely to rely heavily on the third element - namely monitoring - particularly maintaining as comprehensive as possible a knowledge base about likely engineered organisms, traits and applications from which a screening approach can be developed. Again this fits with work that the CBD may consider as being exactly under its purview (including the Biosafety Clearing House and embryonic discussions about horizon scanning mechanisms)

ETC has a small bit of experience in this with the development of the GMO 2.0 ingredients database (http://database.synbiowatch.org) that was already reported to the last Online Forum process. Through patent searches, web searches, citation and journal searches and news-monitoring ETC Group was able to compile a database of over 350 instances where biosynthetic organisms were being developed or used to produce novel flavours, fragrances, sweeteners and other ingredients. We have been told by natural product industry players that they routinely use this database as part of their own monitoring and screening systems to identify ‘at risk’ ingredients. It is only a partial resource however at present there exists no other public authoritative database for monitoring of this sector. ETC would be happy to work with intergovernmental bodies to share the underlying data in an open source monitoring project.

The 3rd guiding question asked "Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?” We are told by analytical laboratories and experts in natural product chemistry that , as with detection of engineered organisms, detection of products of synthetic biology (e.g. biosynthetic versions of vanillin, resveratrol, stevia compounds or other single molecules or compounds for commercial use) should be  straightforward to identify using analytical chemistry techniques so long as reference samples exist and again so long as the developers of synthetic biology are required (e.g. by  law or contract) to provide information about their products before putting them onto the market, including ideally sharing validated testing protocols to help differentiate their product from natural or non-syn bio version. This is again a matter for political will by regulators not a technical barrier at the  laboratory bench.

The natural and botanical products industry has developed considerable expertise at identifying synthetic versions of natural products used to spike or counterfeit natural ingredients and woudl have much expertise to bring to this question of detectiona dn identification. Tehre are detectable differences between different vanillins for example and also, as mentioned by Nikolai, tehr eis the option to look for teh contaminants arising from the genetic engineering and  fermentation process.  I would particularly draw the attention to the Botanical Adulterants programme of  the American Botanical Council which provides standard monograms on laboratory procedures for identification of synthetic versions of natural products- see http://cms.herbalgram.org/BAP/index.html?ts=1553198694&signature=ea21c6212624aefd9336c15e0505960d


In the absence of validated tests, the current standard within the ‘non-GMO’, Organic and natural sector to identify and exclude the presence of biosynthetic ingredients is the use of monitoring activities in combination with identity preservation and traceability systems. For example its my understanding that the Non-GMO Project referred to above maintains  full time staff capacity to monitor the presence of biosynthetic, Syn Bio and gene-edited ingredients that may be on or close to market, provides companies who apply its standard with a regularly updated ‘at risk’ list and then requires firms to obtain legal affidavits if they use ingredients flagged under the 'at risk' list (e.g. if they use Vanilla flavour or stevia sweeteners). Assuring traceability of a natural product from seed to stomach is something that non-GMO producers have practiced for almost 20 years now and it give co-benefits of better transparency through the supply chain and teh ability to identify adverse efefcts and put in place recalls. However it is unfortunate that the costs of preserving the identity of natural ingredients  have to be borne by those who choose to exclude engineered ingredients  - not by the biotechnology companies who by not labelling their ingredients are muddying teh supply chains for everyone else. In ETC Group’s view the cost of developing tests, making sure they are publicly available and supporting monitoring databases should be borne by the industry that wishes to introduce these novel organisms and their products into the marketplace.

In her response to this topic Ms Luciana Ambrozevicius of Brazil asserted that " if the risk assessment concludes that there are no risks for biodiversity of a certain product produced by synthetic biology, natural production or chemical synthesis I do not see the necessity of distinguish between them. “. I am a bit confused by this viewpoint especially since as i see it  the risk assessment does not allow for the right question to be asked to address all 3 aims of teh CBD. The three aims of the CBD include safeguarding  ‘sustainable use’ of biodiversity - for example the sustainable growing and harvesting of natural products. In Brazil for example this might include Babassu nut cultivation for sustainable lauric oils. If a biosynthetic lauric oil is developed (e.g. from synthetic biology algae in a fermentation vat) that negatively impacts sustainable use of Babassu by undercutting that market this may be considered against the aims of the convention and it would be important to be able to identify that oil and allow measures to be taken against it (either.legally or in the marketplace). There is in fact such a biosynthetic oil (sold by Corbion - formerly Solazyme/Terravia) and it is approved for use in Brazil (in Lux  soaps) but to my understanding this new oil never underwent a risk assessment that asked about the impact on sustainable use of Babassu. The third aim of the convention deals also with biopiracy (the equitable sharing of benefits arising from utilization of genetic resources) Here again if a biosynthesized version of a natural product will undercut the value of the natural product and is based upon an engineered organism that contains sequences taken from a natural source then any fair ABS arrangement would need to identify the extent and value of the use of the biopirated version of the natural compound. Detection, identification and monitoring will be key to that.

Finally I would just like to notice that the charge under decision 17f of decision 14/9 was not to teh online forum but to convene stakeholders including the Network of laboratories for teh detection of LMO's and otehr analytical labs. We very much hope these further stakeholders are brought into the conversation and useful guidance to the parties is prepared..

Many thanks

Jim Thomas
Co_Executive Director ,  ETC Group (Canada)
(edited on 2019-03-22 17:29 UTC by Jim Thomas)
posted on 2019-03-22 17:18 UTC by Mr. Jim Thomas, ETC Group
RE: Welcome message - synbio forum - topic 6 [#9643]
Dear Collegues,

First off all I would like to thank Maria guide us through the several questions of this online forum.

I would like to start my intervention with a seemingly simple but nevertheless crucial thought: Detection is only possible, if we know, what we are looking for:

Detection of LMO/GMO is currently based on analysis of changes in the DNA sequence. E.g. in the EU, screening for GMO is based on PCR technologies that cover a range of events. This approach is intended to be robust, cheap and fast. However conceptually it requires a certain amount of a priori knowledge to be able to detect GMO. The example of unauthorised transgenic petunias which have supposedly been on the EU market for more than a decade or the import of unauthorized transgenic rice have shown that the detection system can only work for what is known. Transgenes that either lack any of the standard elements or are incorporated into organisms, which are not tested, cannot be detected by the current system in place. Therefore, we will need to discuss on an information platform to ensure that the knowledge on the released events is available. The BCH is the obvious context to develop such an international registry.

Secondly, I would like to share some thought on cases where genome editing has been applied, but no transgenic sequences remain in the final LMO. As with transgenic LMO, the detection of such LMO remains challenging, because no standard element remains in the LMO. A specific challenge was identified in the detection limit of methods that discriminate single nucleotide variants (SNV) and in the collection of evidence that this SNV is the result of genome editing. The second challenge can be solved by investigating the peripheral sequences in known events.
A recent publication (DOI: 10.1038/s41598-019-38701-9) for example reports the transfer of a method developed for the identification of rare cancer mutations to sequences originating from transgenic plants: “Simple, multiplexed, PCR-based barcoding of DNA for Sensitive mutation detection using Sequencing (SiMSen-Seq). This method lowers detection limits by mitigating errors in PCR and by sequencing.
As Sarah suggested (#9607) a combination of techniques such as simsen-seq with third generation sequencing (long reads) could identify the characteristic sequence diversity in the periphery of the target change (in the case of SDN-1) and to unequivocally assign a sequence to a LMO and determine its quantity in a given sample.

With kind regards
Margret
posted on 2019-03-23 09:10 UTC by Dr. Margret Engelhard, Germany
RE: Welcome message - synbio forum - topic 6 [#9646]
Dear Maria
With regards to the posed questions I have the following comments:
1. Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
The methods used for detecting, identifying and monitoring organisms of synthetic biology are essentially the same methods used for LMOs and include analytical methods for
- detecting unique DNA sequences (resulting from insertion(s), deletions(s) or changes in the genome of the organism) contained in their transgenes or neighboring sequences (e.g. PCR amplification, sequencing...)
- detecting expression (or lack of expression) of the specific trait by phenotypic analysis (e.g. detecting transgenic protein using ELISA…)

2. Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?
The currently available methods are mostly event specific. Thus, they are suitable for the identification of all genetically modified organisms if you have a prior knowledge/expectation on the alteration. This also applies for organisms subject to gene editing where tools such as CRISPR, ZFN and TALENS leave their own scar/marks such as chromosomal rearrangements and these patterns can be identified.
The challenge is when the alterations are unknown. Some form of high-throughput detection technique need to be used. This process involves a multi-target approach and can be technically and financially very demanding . I believe a specific software linked to databases to assist such screening process could be very useful.

3. Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?
In principle the current techniques are able distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts. Such distinction is likely to rely on the presence and absence of minor contaminants and/or modifications.
The process will depend on what one wants to detect (the alteration and its expression) and in this regards it is important to highlight the Cartagena Protocol’s definition of the terms products thereof ” processed materials that are of living modified organism origin, containing detectable novel combinations of replicable genetic material obtained through the use of modern biotechnology. “
Best regards,
posted on 2019-03-23 11:15 UTC by Mr. Ossama Abdelkawy, Syrian Arab Republic
RE: Welcome message - synbio forum - topic 6 [#9647]
Dear Colleagues :  I have read with interest responses to topics 5 and 6 and agree with most of the scientific responses so I wont respond in detail to them .
In relation to Topic 5: I agree that synbio organisms should be classed as LMOs. However synbio and associated techniques can/could be used to produce novel viruses, viroids, prions, free DNA, RNA, novel proteins etc. which are not generally classified as organisms since they are not cellular or free living. However these products could “migrate” into non-transformed cells and produce cells with different phenotypes or inheritance characteristics.
In relation to Topic 6.
1. Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
I agree that the methods used for detecting, identifying and monitoring organisms of synthetic biology are essentially the same methods used for other LMOs. Each new LMO will be required to have a unique identifier which is accepted by testing authorities. In the case of the EU this is established by the developer and accepted by the JCR together with the European Network of GM Laboratories (ENGL). If no unique identifier can be developed or accepted then the LMO cannot be commercialised. It is important that these identifiers are used internationally as standards to avoid confusion or mis-diagnosis.
2. Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?
The complexity of some future synbio organisms containing a range of new and/or previously registered genetic events and modifications may complicate diagnostics and make identification and differentiation more difficult.  Particularly this will be the case where movement will involve mixtures of products with a range of genetic composition. This problem already arises when trying to distinguish stacks from single events in bulk commodities, particularly of F2 generation products where segregation has occurred. 
3. Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?
Generally I agree that current techniques can be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts, if required. I refer to my comment 1 above that many authorities will require unique identifiers for LMOs and also for their products if they contain transgenic DNA.
However some GM/LMO products cannot currently be identified from “natural” products ( e.g. refined oils and sugars) and this will also be the case for some synbio products. In some countries products of GM microrganisms or products produced using processes which involve GMMs and do not contain trans DNA, do not need to be labelled and thus no identifers are developed. Some countries use this rule also for GM plant products where DNA is absent or denatured (e.g fibres, oils, refined products). Thus we already have a situation where some LMO products are not characterised and I anticipate that similar Synbio products will be treated in the same way.   

The main issue will be where unapproved or unregistered LMOs and products enter into supply chains. I am not a molecular biologist but I am aware that there are a range of techniques which can be used and many have been mentioned by other responders to these Topics. I think the magnitude of changes envisaged in Synbio organisms, as compared to other genetic techniques, will generally mean that they are detectable. However identification of products will be more problematic especially for processed products, where proteins and/or DNA are denatured or removed.
Best wishes
Jeremy Sweet ( JTEC, Cambridge, UK)
posted on 2019-03-23 12:36 UTC by Mr. Jeremy Sweet, JT Environmrntal Consultants Ltd
RE: Welcome message - synbio forum - topic 6 [#9651]
Dear Colleagues,

Thank you Moderator for the opportunity to share on this topic.

Q1: Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?

The current tools that are available to the detection, identification and monitoring of LMOs both DNA-based techniques (e.g. quantitative real-time PCR) and protein-based techniques (e.g. ELISA and Western blot) could also be used for organisms developed through synthetic biology. It’s more precise if the developers will provide the methodologies or reference materials for detection.

Q2: Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?

There are challenges of detection regarding some organisms develop through synthetic biology that might be small sequence change of DNA or no novel protein expression. 

Q3: Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?

As indicated by participants, the current analytical techniques can be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts. It depends on the kind of the products that will be detected. 

Best regards,

Chalinee
posted on 2019-03-23 19:34 UTC by Ms. Chalinee Kongsawat, Thailand
RE: Welcome message - synbio forum - topic 6 [#9652]
My thoughts on identification methods and respond to questions 1-3 are in the same line as in posts [# 9604] and [# 9607]. Many LMOs obtained by synthetic biology methods can currently be identified using methods of molecular biology, physical and biochemical methods. Also, of course, it is not necessary to discount methods based on protein [#9626] which are also important for large scale monitoring and could be helpful for monitoring of unauthorized or accidental releases (although in our country this methods are also not included in the list of state standards by which we can detect LMOs).
Some LMOs that will dramatically differ from the parent organism (e.g. synthesize new substances non speсific for species / genus, or differ phenotypically from species or genus, retaining some of the traits) can be quite easily detected by biochemical methods, mass spectrometry methods, or simply by phenotype.
Screening schemes for permitted and unauthorized LMOs, such as those developed by JRC and ENGL, could undoubtedly be useful for identifying. But here, unfortunately, there will be two issues on how to adapt such techniques to an ever-expanding series of events, including those not authorized in a particular country. How to include in these schemes methods based not only on PCR.
Finally the cost of such analyzes could be a big obstacle for a number of countries. The subsequent development of screening schemes as dialogue between both LMO detection laboratories and laboratories that are currently engaged in a wider range of tests using other methods than PCR e.g. hygiene laboratories, pharmacology laboratories, etc. in this area seems to me very important. Consideration of creation of a database of such screening methodologies on BCH seems also important.

Best wishes,
Galina
(edited on 2019-03-23 21:40 UTC by Galina Mozgova)
posted on 2019-03-23 21:36 UTC by Dr. Galina Mozgova, Belarus
RE: Welcome message - synbio forum - topic 6 [#9653]
Thank you Maria for your assistance to us all to make the forum a success.

Dear colleagues

There have been many excellent contributions to this thread but I think it is worth emphasising Margaret’s [#9643] point that: "Detection is only possible, if we know, what we are looking for”. (See also e.g. [#9646] by Ossama and [#9634] by Alexandra.)

This is perhaps the most important reason for the Protocol and the CBD, because it codifies the international consensus that each and every country has the legitimate right to know and, regardless of contrary decisions made by others, these rights must be respected.

On a more technical basis, Margaret’s point can be illustrated by two scenarios. First, that a modification is made that our current techniques cannot definitively statistically distinguish from background variation. To some this means that the product itself is of no concern because it is indistinguishable from natural, but I would disagree. There are many relevant changes at this level that are important but not revealed until we see the phenotype. At that point, there may have been already too many releases to contain harm.

Second, and we already well know this issue with current LM crops, our detection methods may not be sensitive enough to detect relevant levels when admixed with non-LMOs.

This was already said much better by others. What I want to emphasise is that the existence of techniques that can be used for identification, particularly techniques with sensitivities that do not effectively scale like those that target nucleic acid sequences, do not by their existence alone provide a basis for reassurance that detection is possible on a practical level.

Therefore, it is important for the AHTEG to consider the limits of detection of techniques, not just a list of techniques.

Detection limits may be pertinent to the RA of synthetic biology products if they cannot be detected at levels that would permit monitoring to be an effective risk mitigation strategy or would compromise a country’s right to prior informed consent.

In contrast to Luciana’s view [#9620] that indistinguishability of things determined to have no risks for biodiversity may be interesting but possibly not necessary, we have Alexandra’s view [#9634] that there is more to the Protocol (and CBD) than just this. And I agree. The Protocol also recognises risks to human health and socioeconomic implications. In addition to Alexandra’s examples I add that two “identical” traits made by different means will have different intellectual property rights instruments covering them in some countries, leading to potentially very different socioeconomic benefits to some, harm to others.

With best regards to everyone
Jack
posted on 2019-03-23 21:40 UTC by Mr. Jack Heinemann, University of Canterbury
RE: Welcome message - synbio forum - topic 6 [#9660]
Dear Colleagues,
I also find very important Margaret's [# 9643] point that: "Detection is only possible, if we know what we are looking for." At the same time, I would like to add one more point to the first well noted consideration – we need to account what is the purpose of our search. There could be different scenarios, e.g.
1. Scenario 1. We are accredited laboratory of the particular country and looking for lines approved in this particular country in grain, food, feed products (lines have been approved in the country, passed risk assessment and listed as lines that need to be detected). Currently, approved lines are detected by using validated methods (qualitative, quantitative) of the “gold standard” RT-PCR. An accredited LMO detection laboratory use for these purposes only validated methods, for which repeatability, reproducibility, LOD, etc. are shown. Firstly laboratory use screening, e.g. screen CaMV 35S, FMV 35S, NOS, SSuAra, E9, nptII; some lines are added to the screening scheme, since they cannot be detected by using the above mentioned promoters and terminators. This is followed by methods for identifying each line of an authorized LMO that is “suspected” due to the identified elements. There are also screening methodologies for unresolved lines by screening cp4Epsps, pat, bar, cry3A etc., which allow to suspect lines that have not been approved, and schemes for such screening. But here, as always, there is uncertainty - other LMOs appear that cannot be identified with the help of the promoters, terminators, target genes mentioned above. This suggests that constant horizontal screening of new developments need to be done, also in this context application of unique identifiers for all new LMOs is very important (Sarah [# 9607]). For me equally important is the database of validated methods. Such databases exist and available in JRC and other organizations. But once again, I think it is very important also to have one on the BCH, including validated methods developed by different organizations.
2. Scenario 2. An unintended or deliberate release of an unapproved or unauthorized LMO in the country has occurred. It is necessary to monitor, for example, landings. We can use the PCR method, but in the large-scale analysis it can be very expensive and, in this situation usually we need to act fast. For preliminary rapid screening in the fields (or in other situations including accidents with involvement of organisms different from plants), faster could be methods based on proteins. If we have this method and the method is validated, why not use it. And then confirm the PCR in the laboratory. It is clear of course that method based on protein has its detection limit and will not be used anywhere to detect the GM component for processed products.
3. The company manufactures the product in contained systems, for example, it is the production of substances in bioreactors by using LMOs. Here, all the more, a method must be developed and validated from the very beginning for screening in case of emergency situations. For this particular scenario we don`t need use all screening methodology, but use only one reliable method. Detection method may be the “gold standard”PCR in one case, and in the other, the other methods maybe will be more reliable for some synbio organisms.
In any case, any method must show its accuracy, reliability, levels of detection, etc. I support the reasoning of Jack [#9653], but with a small consideration. Discussion of method`s LOD is very important, but it seems to me that this should be done by the forum of LMO detection laboratories, not by this AHTEG. At the same time, in any case, these two forums need to be contacted in order for the laboratories to have as much information as possible about those LMOs that cannot be identified by PCR.

One more consideration. Why it is necessary to develop a method, even if a risk assessment has passed in a particular country and this particular LMO has been approved for the market and it has been stated in this country that LMO does not bear any risks. What is approved in one market may not be an authorized event in another market. The list of allowed lines in a particular country or community is different. There may be a number of reasons for that. For example, the answer to one of them is given by the risk assessment procedure itself. Risk assessment takes into account many things, e.g. not only changes in the parent organism, but also protection goals. For example in one country there are no centers of biodiversity, wild relatives, in the other they are. And the risk assessment in the first country showed that there is no any risk in it. The risk assessment in the second country when new line has come to the market determined that the release can damage its biodiversity. That is why identification methods should be developed not only for those LMOs that a priori can obviously have some negative effect, but also for LMOs whose effects may not be entirely obvious.

Best wishes,
Galina
posted on 2019-03-24 11:16 UTC by Dr. Galina Mozgova, Belarus
RE: Welcome message - synbio forum - topic 6 [#9657]
Dear forum participants,

I will address this topic in regard to organisms, specifically crops. As I (and others) have commented previously in this discussion, the Global Industry Coalition does not believe that crops developed with the use of genome editing belong in discussions on synthetic biology, and where they are LMOs, they are in the scope of the Cartagena Protocol. But, given that genome editing continues to feature I will add the developer perspective in regard to detection.

The requirement to detect and uniquely identify an organism developed using biotechnological tools is connected to its regulatory status – where the organism is regulated as an LMO/GMO, developers may be required to develop methods that enable the organism to be detected in trade once it is commercialized, e.g. in bulk shipments of grain. As already mentioned, these are validated PCR-based methods. They must also conform with certain performance criteria as set out in the Codex guideline CAC/GL 74-2010, and be practically feasible for use with bulk commodities. Such methods and links to Certified Reference Material providers are routinely posted in the database: http://www.detection-methods.com.

Where organisms are not within the scope of LMO/GMO regulation, there should not be a requirement for a specific detection method to uniquely identify them.

Where an organism developed with the use of certain genome editing approaches is regulated as an LMO/GMO, the ability to develop sufficiently sensitive detection methods depends on the type of edit. Where the edit involves the incorporation of a DNA sequence of sufficient size for the design of PCR primers (e.g. a gene cassette), PCR-based detection methods can be developed – this is same approach used for the development of detection methods for currently commercialized LM crops.

This is less straightforward where applications of genome editing in plants have comparable outcomes to conventional breeding approaches. While it may be technically feasible to detect DNA sequence changes, as pointed out by others (e.g. #9604) it is expected to be difficult to distinguish how a specific change arose during the breeding process – as a result of the use of a genome editing tool, conventional mutagenesis, or spontaneous mutations – because their outcomes are similar. The plasticity of plant genomes is well-documented in the scientific literature, with point mutations, insertions, and rearrangements commonplace (e.g. Arber 2010; Custers et al 2019; Schnell et al 2015; Weber et al 2012). Therefore, detection methods for such organisms are expected to have several limitations: difficulties with meeting established performance criteria, false positives, and impracticality for use with bulk shipments. Also, a DNA sequence change is unlikely to uniquely identify a specific technology, product, or developer.

References cited:

Arber W (2010) Genetic Engineering Compared to Natural Genetic Variations, New Biotechnology 27: 517-521. 

CAC/GL 74-2010 Guidelines on performance criteria and validation of methods for detection, identification and quantification of specific DNA sequences and specific proteins in foods. Available at: http://www.fao.org/fileadmin/user_upload/gmfp/resources/CXG_074e.pdf.

Custers R, Casacuberta JM, Eriksson D, Sági L, Schiemann J (2019) Genetic alterations that do or do not occur naturally; consequences for genome edited organisms in the context of regulatory oversight, Frontiers in Bioengineering and Biotechnology 6: 213. doi:10.3389/fbioe.2018.00213.

Schnell J, M Steele, J Bean, M Neuspiel, C Girard, N Dormann, C Pearson, A Savoie, L Bourbonnière, P Macdonald (2015) A comparative analysis of insertional effects in genetically engineered plants:  consideration for pre-market assessments, Transgenic Research 24: 1-17.

Weber N, C Halpin, LC Hannah, JM Jez, J Kough, W Parrott (2012) Crop genome plasticity and its relevance to food and feed safety of genetically engineered breeding stacks, Plant Physiology 160: 1842-1853.
posted on 2019-03-24 00:56 UTC by Ms. Felicity Keiper, BASF
RE: Welcome message - synbio forum - topic 6 [#9661]
Dear All, thanks to the moderators and contributors for this very constructive discussion.

I would like to reiterate previous comments (e.g. #9643, 9634, 9636) that emphasise that existing techniques and approaches allow for the detection of synbio organisms and product, particularly those developed using genome editing techniques.

I would also like to re-emphasise the point that in order to be able to do that, as Margret pointed out, we need to know what we are looking for, which relies on developers providing the necessary information including details of changes (on-target, off-target), testing protocols, samples. Such provisions are crucial for upholding obligations of free, prior informed consent for communities, particularly indigenous people and local communities, and nations. 

As highlighted in a recent policy and practice article compiled by members of regulatory, industry and academic institutions:

"It has been argued that the detectability of genome edited products is technically harder compared to GMOs, and that therefore there is no point in having them regulated. In terms of policymaking, this argument is moot. Products are regulated because sectors of society want them to be regulated. If there are technical tools to detect the product the better, but if not, regulation can also be based on a system of sworn statements, traceability, etc.

For most products of genome editing, there is a clear signature in the DNA, for instance the exact stretch of nucleotides erased. If that signature is revealed by the developer, the same PCR technology used for detecting GMOs can be applied to the detection and monitoring of genome-edited products in most cases." https://www.frontiersin.org/articles/10.3389/fbioe.2018.00079/full

Many thanks to all.
(edited on 2019-03-24 15:07 UTC by Eva Sirinathsinghji)
posted on 2019-03-24 15:01 UTC by Dr. Eva Sirinathsinghji, Third World Network
RE: Welcome message - synbio forum - topic 6 [#9664]
I would like to support in part the comments provided by Jim Thomas (#9636) in relation to tracking products of synthetic biology. While I was working at the Woodrow Wilson Center we developed what we believe was the first database of synthetic biology products (http://www.synbioproject.org/cpi/) and nanotechnology products (http://www.nanotechproject.org/cpi/). These database are no longer maintained.

The database Jim Thomas has developed, along with a new version of the Wilson Center database being developed by the Environmental Law Institute (https://www.futurebioengineeredproducts.org/) with support from the U.S. Department of Agriculture, fills a much needed void.  As Jim Thomas, and other have mentioned, these databases are only as good as the information available; which is usually provided by the manufactures, patent searches or through advertisements of products. Speaking from experience, we frequently had companies demanding to be removed, or added, to the database depending on the public perception of their products at the time; and rarely based on evidence that the products in question were all of a sudden "absent of", or "developed with", synthetic biology. 

Through my experiences of developing consumer products inventories for both synthetic biology and nanotechnology, and the criticisms against those databases, important issues will need to be addressed if these types of databases were to be used by the CBD including but not limited to:

1. Who should be in charge of maintaining these types of databases in order for them to be trusted?
2. Where is the funding coming from to maintain these types of databases?
3. How to develop a system of inclusion and to verify claims of a product being the result of synthetic biology?

Kindest regards,

Todd Kuiken
(edited on 2019-03-24 17:50 UTC by Todd Kuiken)
posted on 2019-03-24 17:45 UTC by Mr. Todd Kuiken, North Carolina State University
RE: Welcome message - synbio forum - topic 6 [#9668]
Dear colleagues

Thank you Maria for your moderation of this topic. As you note, this topic might not be included in the terms of reference of the synthetic biology AHTEG but it is an important subject. Detection and identification of a LMO/GMO/synthetic biology organism is fundamental to our ability to implement our domestic legislative framework.  We have restricted our comments to organisms.

Our comments are as follows:

1. Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?

As noted in posts #9604, #9607, and #9620, the current internationally validated tools for detecting LMOs (which includes organisms developed using synthetic biology as defined in decision XIII/27) consist of PCR-based methods to detect specific sequences in LMOs. We consider that the current tools used for LMOs will continue to be relevant for synthetic biology organisms and in the future (and validated as needed), also as noted in comments posted in #9604, #9607 and #9620. 

2. Does the novelty that some organisms, components and products of synthetic biology might present, require the development of additional detection, identification and monitoring tools, other than those that already exist?

We strongly agree with the response in #9620 regarding this question. Additionally, we note that there are technologies, some of which have been mentioned in comments in earlier topics in this online forum, as well as those that have been mentioned under this topic (#9604, #9607) as possibly requiring the development of additional detection, identification, and monitoring tools.

Most organisms that might fall in this category remain as laboratory experiments / demonstrations, rather than any organism that is used commercially, unlike LMOs with validated detection methods. Notably, the first organisms with non-natural amino acids were first created well before the term ‘synthetic biology’ ever came into use (Mehl et al, 2003. J Am Chem Soc 125: 935-939). However, even organisms such as these could presumably be detected using established PCR-based technologies. This is because such organisms require the use of ‘bespoke’ transfer RNA molecules, the genes for which could presumably be detected using PCR-based techniques. Such detectability would be achievable regardless of how low the levels of the non-natural amino acid in the organism might be.

It is by no means clear that gene-edited organisms are synthetic biology organisms, and even if they were considered to be so, there is the potential that at least some gene-edited organisms might be created using technology that does not meet the definition of “modern biotechnology” in Article 3 of the Cartagena Protocol, and thus would not require detection methods to be developed. We do not view this statement as being a potential cause for concern. Rather, we note that the overwhelming majority of crop species that are safely consumed around the world every day were bred and modified in ways that are not covered under the Protocol’s definition of “modern biotechnology”.

In summary, it is our view that, in much the same way that the risk assessment of LMOs must be done on a case-by-case basis, taking the characteristics of the LMO into account, the methods for detection, identification and monitoring of synthetic biology organisms must also be carried out on a case-by-case basis, considering the characteristics of such organisms carefully with regard to existing detection methods before embarking on the development of any new method.

3. Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?

Please refer back to our statement above regarding the products of synthetic biology.

With regards,
Mariska
posted on 2019-03-24 20:54 UTC by Ms. Mariska Wouters, New Zealand
RE: Welcome message - synbio forum - topic 6 [#9671]
Dear Forum Participants,

Thank you very much for all your contributions during this week under Topic 6:  "Sharing of experiences on detection, identification and monitoring of organisms, components and products of synthetic biology".

Best Regards,

Maria
posted on 2019-03-24 22:21 UTC by Ms. Maria de Lourdes Torres, Universidad San Francisco de Quito
RE: Welcome message - synbio forum - topic 6 [#9674]
Dear forum participants,

Thank you for your interventions. This topic is now closed for comments.

Secretariat
posted on 2019-03-25 01:00 UTC by Mr Austein McLoughlin, Secretariat of the Convention on Biological Diversity