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On 26 November 2021, the World Health Organization (WHO) classified variant B.1.1.529, reported earlier by the South African authorities as “Variant of Concern” with the name Omicron. The decision was taken because Omicron is bearing a number of mutations with a potential impact on its transmissibility, severity of disease following infection, as well as on the effectiveness of immune protection resulting from both vaccines and natural infection. In this paper, we present an in silico developed RT-PCR based detection method (named OmMet) that was designed to be highly specific for the detection of the Omicron variant. Bioinformatic prediction tests demonstrate that the sequences in the primer sets are highly accurate, and do not match with genetic sequences of other viruses, including other coronaviruses or SARS-CoV-2 variants. The methodology presented does not rely on S-gene target failure (SGTF) of existing RT-PCR assays, widely used currently, but allows the direct specific identification of the variant B.1.1.529 (Omicron).

SUMMARY The frequent association between COVID-19 disease and different extrapulmonary clinical manifestations in symptomatic patients was reported recently. The data reported here suggest an association between COVID-19 disease and the release in the body of (oligo-)peptides almost identical to toxic components of venoms from animals. The presence of these peptides opens new scenarios on the aetiology of the COVID-19 clinical symptoms observed up to now, including neurological manifestations.

RATIONALE: SARS-CoV-2 virus that causes COVID-19 disease and led to the pandemic currently affecting the world has been broadly investigated. Different studies have been performed to understand the infection mechanism and the involved human genes, transcripts and proteins. In parallel, numerous clinical extra-pulmonary manifestations co-occurring with COVID-19 disease have been reported and evidence of their severity and persistence is increasing. Whether these manifestations are linked to other disorders co-occurring with SARS-CoV-2 infection, is under discussion. In this work, we report the identification of toxin-like peptides in COVID-19 patients by application of the SANIST-Cloud Ion Mobility Mass Spectrometry (SANIST-CIMS) technology. METHODS: Plasma, urine and faecal samples from COVID-19 patients and control individuals were analysed to study toxins profiles. SANIST-CIMS instrumental parameters were selected to discriminate the ion cloud containing low and high molecular weight compounds. SANIST-Disc module was employed to investigate the differentially expressed molecules. RESULTS: Toxin-like peptides, almost identical to toxic components of venoms from animals like conotoxins, phospholipase A2, phospholipase A1, activating prothrombotic factors, phosphodiesterases, zinc metal proteinases, and bradykinins, have been identified. As they were found only in samples from COVID-19 patients, their presence is considered somehow connected to SARS-CoV-2 infection. The presence of these peptides can potentially explain a large set of heterogeneous extra-pulmonary COVID-19 clinical manifestations, like myalgia, headache, encephalopathy, dizziness, dysgeusia, and anosmia. Even if the presence of each individual symptom is not selective of the disease, their combination could be related to COVID-19 in the presence of the panel of detected toxin-like peptides. CONCLUSIONS: The data reported here suggest an association between COVID-19 disease and the release in the body of (oligo-)peptides almost identical to toxic components of venoms from animals. The presence of these peptides opens new scenarios on the aetiology of the COVID-19 clinical symptoms observed up to now, including neurological manifestations., DECLARATION The scientific output expressed does not imply a policy position of the European Commission. Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use that might be made of this publication.

Recent developments in genetics are opening unprecedented possibilities to understand the physical and mental health of individuals. Moreover, with the advent of genome editing techniques it has become possible to introduce subtle changes in the DNA and thus to intervene in the combined sets of traits of an individual, including the curing of certain diseases. In this report we focus on the first part, namely on the understanding and interpretation of the genetic information and its connection with the functionality in the host organism, and we will zoom in on the great wealth of information the reading, analysing and comprehension of the complete DNA sequence across organisms, including humans may provide. However, since this technology is not based on agreed standard methodologies including validated algorithms, a warning is raised with respect to the possibility of misinterpretation and this in turn may have scientific, ethical and thus policy implications. This report analyses how these developments are impacting not only on health through personalised medicine, but also on social aspects of individuals and of human well-being. In particular, among these new applications, it highlights the possible policy implications of genome wide association studies (GWAS), polygenic scores (PGS) and social science genetics, an interdisciplinary research field that studies if and how human behaviour and socio-economic outcomes are influenced by genetic factors. Due to the fact that these developments have the potential to affect many areas of public interest including public health, privacy rights, data security, threats of discrimination, new technologies for forensics, the emergence of new industries and the functioning of markets, schooling, and even direct changes to the human gene pool that can be passed on to future generations, they need to be observed, evaluated and scrutinised. They also raise ethical questions that touch the core of what type of society we want to live in. The purpose of the current report is not to deliver final, definite answers as to which consequences genetics and genomics might have on the society, but to provide unbiased knowledge on the possible policy implications of recent developments in these fields, with a specific focus on GWAS, PGS and social science genetics. Rather, the purpose is: ● to provide an accessible entry point for policy makers and the wider public to understand the goals and tools of these developments, ● to track the progress of the field until now, ● to identify areas that are potentially relevant from a public policy perspective, ● to open a dialogue between scientists, policy makers, and the general public about how to move forward. It is also not intended with this report to extensively discuss in detail the possible applications of the technology. In the medical field, there is still some resistance to act on the basis of the results of genome analysis through the polygenic risk score (PRS), even in cases of "high risk" patients, and there is an ongoing debate with respect to the level of evidence required prior to a routine introduction of the approach for personalised care. Here, we will exclude these discussions from the scope of the report. This report links, more generally, to the ongoing activities within the European Commission Joint Research Centre (JRC) on eHealth and Big Data, both related to the implementation of the EC Digital Single Market strategy. It is complementary to the 2018 JRC Science for Policy Report Overview of EU National Legislation on Genomics , a mapping of existing national legislations linked to genomics aimed to be used as a baseline for the analyses of possible consequences for EU policies already in place, and to forecast policy gaps and eventual interventions., JRC.F.7-Knowledge for Health and Consumer Safety

The JRC as European Union Reference Laboratory for GM Food and Feed (EURL-GMFF), established by Regulation (EC) No 1829/2003, in collaboration with the European Network of GMO Laboratories (ENGL), has carried out a collaborative study to assess the performance of a quantitative event-specific method to detect and quantify the MON 88017 transformation event in maize DNA (unique identifier MON-88Ø17-3). The collaborative trial was conducted according to internationally accepted guidelines (1, 2). In accordance with Regulation (EC) No 1829/2003 of 22 September 2003 on genetically modified food and feed and with Regulation (EC) No 641/2004 of 6 April 2004 on detailed rules for the implementation of Regulation (EC) No 1829/2003, Monsanto provided the detection method and the samples (maize seeds containing the transformation event and conventional maize seeds). The JRC prepared the validation samples (calibration samples and blind samples at unknown GM percentage [DNA/DNA]). The collaborative trial involved twelve laboratories from nine European countries. The results of the international collaborative trial met the ENGL performance requirements. The method is therefore considered applicable to the control samples provided, in accordance with the requirements of Annex I-2.C.2 to Commission Regulation (EC) No 641/2004, JRC.I.3-Molecular Biology and Genomics

The JRC as European Union Reference Laboratory for GM Food and Feed (EURL-GMFF), established by Regulation (EC) No 1829/2003, in collaboration with the European Network of GMO Laboratories (ENGL), has carried out a collaborative study to assess the performance of a quantitative event-specific method to detect and quantify the MON 88017 transformation event in maize DNA (unique identifier MON-88Ø17-3). The collaborative trial was conducted according to internationally accepted guidelines (1, 2). In accordance with Regulation (EC) No 1829/2003 of 22 September 2003 on genetically modified food and feed and with Regulation (EC) No 641/2004 of 6 April 2004 on detailed rules for the implementation of Regulation (EC) No 1829/2003, Monsanto provided the detection method and the samples (maize seeds containing the transformation event and conventional maize seeds). The JRC prepared the validation samples (calibration samples and blind samples at unknown GM percentage [DNA/DNA]). The collaborative trial involved twelve laboratories from nine European countries. The results of the international collaborative trial met the ENGL performance requirements. The method is therefore considered applicable to the control samples provided, in accordance with the requirements of Annex I-2.C.2 to Commission Regulation (EC) No 641/2004, JRC.I.3-Molecular Biology and Genomics