Detection and Identification Online Discussions 2019

Dear Participants,

In decision 14/19 on synthetic biology, the Conference of Parties to the Convention on Biological Diversity requested the Executive Secretary to collaborate and convene discussions, including through the Network of Laboratories for the Detection and Identification of Living Modified Organisms, for sharing experiences on the detection, identification and monitoring of organisms, components and products of synthetic biology. Preliminary discussions were established from the discussions on Topic 6 of the Open-ended online forum on Synthetic Biology in March 2019. I invite you to review the previous discussions: https://bch.cbd.int/synbio/open-ended/discussion/?threadid=9603.

Under these discussions, I encourage you 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 the development, adaptation or use of existing or new tools for the detection, identification and monitoring of organisms, components and products of synthetic biology. 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; kindly provide the source, and indicate if it is coming from a publication, your own work, or any other source. In addition, if you would like to respond to another post, we request that you mention the # of the post you are responding to, for example: “in response to post # XXXX, …”. This will also facilitate the understanding of others. Please post your responses under this thread. We also advise you to review the general guidelines for the forum posted on the main webpage of the discussion.

Best regards,
Shakirat Ajenifujah-Solebo

- Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
Duplex, triplex, and pentaplex real-time PCR screening assays (Huber I, Block A, Sebah D et al, 2013), ELISA,

- 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?
Basic methods such as PCR and EISA can always be used. What may differ may be the reagents to be used for these techniques.

- Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?
I do not think these methods can distinguish between the natural and the synthetic/chemical counterparts.

Dear Stephen,

Thank you for  your post #9981 on the detection, identification and monitoring of organisms, components and products of synthetic biology.

Forum participants are invited to share more information on developments in the monitoring of organisms, components and products of synthetic biology. Are there specific references to some of these components and products? And what tools have been employed in their identification?

Thank you.

Shakirat

Dear all,
Thanks for the opportunity to  comment on this forum.
In respect to the following questions below;

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

The current techniques available for detecting and identifying LMOs can be applied to products of synthetic biology. These include the PCR based methods (Real time PCR, Nested PCR) and the Protein Based method of detection (ELISA). Also, Next Generation Sequencing (NGS) technique can be used. https://unctad.org/en/PublicationsLibrary/ditctedinf2019d12_en.pdf.

- 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 might present may not necessarily require any modification in the existing tools for identification.

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

Current analytical tools an be employed to distinguish between products of synthetic biology and their naturally occurring counterparts.

Hullo Participants,

We thank those who have responded to this Topic. In Uganda, we are still in the infancy stages of developing capacity for detection and identification of SB products.

As shared in Topic 1 and 3, we need collaborative and joint regional capacity building opportunities in African regions. During such interactions, we also need to harmonize our SOPs to adopt the concept of networks of laboratories, and effectively use the limited resources.

Please share some capacity building opportunities for detection and identification of SB products that we can tap into.

Barbara

Thank you once again Shakirat for chairing this second discussion topic.
I will follow your guiding questions to contribute to the discussion.

- Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
The tools available in developed countries are related to PCR detection (qPCR in the EU) following mostly labelling requirements. In developing countries, either PCR or immunostrips.

- 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?
Yes, the novelty of some new GMOs require the development of additional tools. The tools I think of are not related to analytical techniques but rather the methodological approach. The majority of current approaches use trasngenic sequences or junction regions and transgenic sequences as targets for PCR amplification. New GMOs might not have transgenes inserted in their genomes so that strategy is no longer viable. In addition, new GMOs might have genome changes that could be found, in terms of DNA sequences, also in non-GM organisms. In such cases, detection will be still possible but no identification based on a single target will be able to differentiate GM and non-GM products.

- Could the current analytical techniques be used to distinguish between products of synthetic biology and their naturally occurring or chemically synthesized counterparts?
Yes. The analytical techniques can be used to distinguish new GM and non-GM organisms but the approaches need to be updated. The strategy of a single target focused on the transgene and trasgene junction sequence might be no longer suitable. But, as said, qPCR and PCR might be still valid.

Thank you

Sarah

Dear Colleagues

- Which tools are currently available for detecting, identifying and monitoring organisms, components and products of synthetic biology?
Current GMOs are developed using traditional genetic engineering principles, and standard PCR or immunological detection methods are used. For GM plants this is relatively straightforward, as almost every GM plant uses the P35S and T-NOS sequences and can be quickly screened. Identification can then be attempted using appropriate primers.

- 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?
Existing tools are adequate for detection. The advent of GM plants with multiple stacked events, and construction of entire biochemical pathways using synthetic biology principles raise the challenges of identification substantially. Combining tools such as multiplex PCR and digital PCR may provide better means for identifying multiple events.

While not entirely novel, the coming out of age of GM animals may also pose significant challenge, as unlike GM plants, there are no P35S and T-NOS equivalents in animals. Each animal taxon requires and will contain specific promoters and regulatory elements. This can quickly overwhelm a laboratory not equipped for large volumes of testing.

If identification and traceability are the required regulatory outcomes, a PCR array covering a large variety of known transgenes will be very useful.

The advent of gene editing techniques has allowed the creation of modified organisms carrying a change of only one nucleotide without leaving any other genetic footprints.  Provided that the exact genetic modification is known, it is technically possible to detect gene edited GMOs using a combination of PCR and classical sanger sequencing. If information on the genetic change is not available, it is still possible to detect a one nucleotide change using next generation sequencing. The major difficulty, as pointed out by most colleagues, is to prove that the modification is engineered and did not happened naturally. Thus detection of such gene-edited organisms will depend more on the disclosure of information and appropriate regulatory arrangements rather than new tools. 

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

This depends on the nature of the products, and if they are designed to mimic their natural counterparts accurately. For proteins, peptides and other biologics, current technology such as mass spectroscopy and glycan profiling may allow us to detect subtle molecular differences and differentiate between ‘natural’ products from those created using synthetic biology, and even between different platforms of synthetic bio. For metabolites or chemical compounds, attempts to determine their origins generally involve scrutinizing co-purified contaminants. This may not work well for highly purified products.

Dear Participants,

Thank you for your valuable input for the detection and identification of the organisms, components and products of synthetic biology.

At this time, the Secretariat would like to extend the forum to 1:00 GMT on Monday 11 November. We would like to strongly encourage all participants to share their experiences with the detection and identification of the organisms, components and products of synthetic biology. These discussions will be informative for the parallel processes under Synthetic Biology.

We look forward to receiving further input under Topic 2.

Best regards,

Austein McLoughlin

Thanks to all contributors to Topic 2 - Stephen (#9981), Judith (#10017) and for the reference link shared, Barbara ((#10019), Sarah (#10022) and Lelde (#10041)

We invite more forum participants to contribute and share their knowledge and experiences on this topic.



Shakirat

Dear colleagues,
We do not have any experience in this field.

Best ragards,
Lelde Grantina-Ievina, Dr. biol.
Senior Researcher,
Department of Risk Asessment and Epidemiology,
Institute of Food Safety, Animal Health and Environment “BIOR”,
Lejupes Street 3,
Riga, LV1076,
Latvia

Dear colleagues,

To my understanding, so far all organisms that might be assigned to synthetic biology are LMO. Therefore, the detection and identification of organisms of synthetic biology follows the same approaches used for LMO detection and identification. However, new analytical methods might be required, if foreign DNA is not present.

Within the EU, marketing of authorized food and feed products derived from genetically modified organisms demands traceability (EU Regulation (EC) 1830/2003), i.e. these products are accompanied by documents providing the information on the specific LMO event and their genetically modified origin. In cases, where a discrimination between products of synthetic biology and their naturally occurring or chemically synthesized counterparts might not be feasible, this can help to solve challenges if no analytical tools are available to distinguish them. For example, it is a clearly impossible to identify a LMO if no DNA is present in the product, e.g. sugar products.

Thank you very much to Shakirat for preparing this topic. I am grateful for the opportunity to contribute to the discussion!

Best regards,
Lutz

Dear Participants,
As commented several times previously in the participation in the CBD synthetic biology programme of work, the Global Industry Coalition agrees that most organisms “assigned to synthetic biology” are LMOs – with the exception of organisms developed using genome editing. I have addressed the challenges of detecting certain organisms developed using genome editing in my post # under Topic 1.

Dear Forum Participants,

Thank you very much for all your contributions in the past 2 weeks under Topic 2. It has been very engaging and interactive. And I hope that all participants will find the information shared here useful.

Kind regards

Shakirat

Dear Participants,

Thank you all for your vibrant discussions and insightful input.

The forum is now closed for comment.

Thank you very much and kind regards,

The Secretariat