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SARS-CoV-2 variants of concern (VOC) should not escape molecular surveillance. We investigated if SARS-CoV-2 rapid antigen tests (RATs) could detect B.1.1.7 and B.1.351 VOCs in certain laboratory conditions. Infectious cell culture supernatants containing B.1.1.7, B.1.351 or non-VOC SARS-CoV-2 were respectively diluted both in DMEM and saliva. Dilutions were analysed with Roche, Siemens, Abbott, nal von minden and RapiGEN RATs. While further studies with appropriate real-life clinical samples are warranted, all RATs detected B.1.1.7 and B.1.351, generally comparable to non-VOC strain.

The digital Polymerase Chain Reaction (dPCR), for the detection and absolute quantification of DNA, is a relatively new technique but its application in analytical laboratories is steadily increasing. In contrast to quantitative real-time PCR, DNA (fragments) can be quantified without the need for standard curves. Using dPCR, the PCR mix containing the (target) DNA is partitioned – depending on the device used – currently into a maximum of 10,000,000 small compartments with a volume as low as a few picoliters. These can be either physically distinct compartments on a chip (referred to as chamber-based digital PCR [cdPCR]), or these compartments correspond to water-in-oil droplets (referred to as droplet digital [ddPCR]). Common to both approaches, once PCR has been carried out simultaneously in all compartments/droplets, the number of positive and negative signals for each partition is counted by fluorescence measurement. With this technique, an absolute quantification of DNA copy numbers can be performed with high precision and trueness, even for very low DNA copy numbers. Furthermore, dPCR is considered less susceptible than qPCR to PCR inhibitory substances that can be co-extracted during DNA extraction from different sources. Digital PCR has already been applied in various fields, for example for the detection and quantification of GMOs, species (animals, plants), human diseases, food viruses and bacteria including pathogens. When establishing dPCR in a laboratory, different aspects have to be considered. These include, but are not limited to, the adjustment of the type of the PCR master mix used, optimised primer and probe concentrations and signal separation of positive and negative compartments. This document addresses these and other aspects and provides recommendations for the transfer of existing real-time PCR methods into a dPCR format., JRC.F.5-Food and Feed Compliance

Unauthorised GMOs (UGM) and derived materials are not uncommon in products found on the European market. At present there is zero tolerance for UGM in the EU. In most documented cases, the UGM concentration relative to the product in which the UGM material is found, was low. Low level presence will always represent a challenge to analytically based detection, in particular if the UGM is obscured by other GM material. Analytical ad hoc implementation of the zero tolerance for particular UGMs in feed is described in Regulation (EU) No 619/2011. In Europe, GM detection is predominantly achieved with polymerase chain reaction (PCR) derived methods targeting the transgenic construct and insertion site DNA sequences. The increase in number and divergence of GMOs developed and commercialised has gradually forced the GM detection laboratories to rationalise their analytical work, and most laboratories now apply initial PCR based screenings followed by (when appropriate) more specific PCR based identification and quantification. The detection of any GM is dependent on availability of suitable detection method(s) and control materials to verify the performance of the method(s). Other information, e.g. describing the novel trait, introduced genetic elements, etc. may also facilitate detection, verification and identification of the GM. For UGM, this is a major challenge, and the GMOs are therefore classified into four knowledge groups in the present document. This classification may facilitate stakeholder communication and decision making in analytical laboratories. A decision tree is presented, summarising the recommended principles of GM and UGM detection. Notably, the state-of-the-art of GMO analysis is not static, and it is expected that the guidelines and recommendations presented in this document will have to be modified on a regular basis. Finally, the document highlights a number of R&D priorities and points out the need for reinforced information sharing at the global level.

Unauthorised GMOs (UGM) and derived materials are not uncommon in products found on the European market. At present there is zero tolerance for UGM in the EU. In most documented cases, the UGM concentration relative to the product in which the UGM material is found, was low. Low level presence will always represent a challenge to analytically based detection, in particular if the UGM is obscured by other GM material. Analytical ad hoc implementation of the zero tolerance for particular UGMs in feed is described in Regulation (EU) No 619/2011. In Europe, GM detection is predominantly achieved with polymerase chain reaction (PCR) derived methods targeting the transgenic construct and insertion site DNA sequences. The increase in number and divergence of GMOs developed and commercialised has gradually forced the GM detection laboratories to rationalise their analytical work, and most laboratories now apply initial PCR based screenings followed by (when appropriate) more specific PCR based identification and quantification. The detection of any GM is dependent on availability of suitable detection method(s) and control materials to verify the performance of the method(s). Other information, e.g. describing the novel trait, introduced genetic elements, etc. may also facilitate detection, verification and identification of the GM. For UGM, this is a major challenge, and the GMOs are therefore classified into four knowledge groups in the present document. This classification may facilitate stakeholder communication and decision making in analytical laboratories. A decision tree is presented, summarising the recommended principles of GM and UGM detection. Notably, the state-of-the-art of GMO analysis is not static, and it is expected that the guidelines and recommendations presented in this document will have to be modified on a regular basis. Finally, the document highlights a number of R&D priorities and points out the need for reinforced information sharing at the global level., JRC.I.3-Molecular Biology and Genomics

Unauthorised GMOs (UGM) and derived materials are not uncommon in products found on the European market. At present there is zero tolerance for UGM in the EU. In most documented cases, the UGM concentration relative to the product in which the UGM material is found, was low. Low level presence will always represent a challenge to analytically based detection, in particular if the UGM is obscured by other GM material. Analytical ad hoc implementation of the zero tolerance for particular UGMs in feed is described in Regulation (EU) No 619/2011. In Europe, GM detection is predominantly achieved with polymerase chain reaction (PCR) derived methods targeting the transgenic construct and insertion site DNA sequences. The increase in number and divergence of GMOs developed and commercialised has gradually forced the GM detection laboratories to rationalise their analytical work, and most laboratories now apply initial PCR based screenings followed by (when appropriate) more specific PCR based identification and quantification. The detection of any GM is dependent on availability of suitable detection method(s) and control materials to verify the performance of the method(s). Other information, e.g. describing the novel trait, introduced genetic elements, etc. may also facilitate detection, verification and identification of the GM. For UGM, this is a major challenge, and the GMOs are therefore classified into four knowledge groups in the present document. This classification may facilitate stakeholder communication and decision making in analytical laboratories. A decision tree is presented, summarising the recommended principles of GM and UGM detection. Notably, the state-of-the-art of GMO analysis is not static, and it is expected that the guidelines and recommendations presented in this document will have to be modified on a regular basis. Finally, the document highlights a number of R&D priorities and points out the need for reinforced information sharing at the global level.