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The 500-ns CG-MD simulation trajectory towards SARS-CoV-2 virus.

This model has been invalidated.

Supplementary Tables of Scientific Paper

Deliverable report 3.2 describes the findings on the analysis of the Science-Policy-Society (SPS) collaboration system on specific casesthrough a Net-Map analysis. Net-Map is an interview-based mapping tool to visualize implicit knowledge and understand the interplay of complex formal and informal networks, power relations, and actors/stakeholders’ goals; uncover sources of conflicts as well as potentials for cooperation; facilitate knowledge exchange and learning processes; and develop visions and strategies to achieve common goals. The development of the Net-Map analysis tool is described. Due to the Covid-19 pandemic, the interviewbased mapping tool was adapted to fit in an online setting. Online meeting applications such as Microsoft Teams® and MIRO® were implemented to map the stakeholders and their relations in the society-policyscience (SPS) collaboration system in risk analysis of emerging food safety issues and to identify constraints in relations, resources, and capabilities. Food safety scenarios based on gobal challenges were selected based on the in-depth expert interviews (Deliverable 3.1). These were food safety concerns regarding emerging mycotoxins and recycled food contact materials (FCM). Several steps in mycotoxin risk analysis are incomplete due to e.g. lack of occurrence or toxicokinetic/toxicity data, lack of analytical techniques and lack of scientific knowledge. Therefore, this case of emerging mycotoxins was used to perform a Net-Map analysis to identify stakeholders involved in this risk analysis and how they interact. For the FCMs, the focus was put on packaging consisting of recycled paper or cardboard, as they have become increasingly important in the light of sustainability and circular economy. However, food safety challenges are related to these materials, making it a good model case to apply the Net-Map tool on. A Net-Map guidance protocol, including a standardized data reporting format, was distributed among the food safety hub (HUB) leaders. Pilot workshops with FS4EU consortium partners were held, enabling further refinement of the protocol. The final protocol has been made publicly available through the FS4EU website and can be applied in many other contexts. Next, four Net-Map workshops were carried out in the respective home countries of the HUB leaders. In Belgium (West HUB) and Finland (North HUB) the case of FCMs was implemented, while participants of Italy (South HUB) and the Czech Republic (East HUB) worked on the emerging mycotoxins case. First, stakeholders and their main goals in mycotoxin/FCM risk analysis were identified. The next step was to characterise how the stakeholders were linked in the system, followed by an assessment on how influential the stakeholders were. Finally a discussion took place on constraints compromising the risk analysis. The workshops resulted in complex Net-Maps, visualizing how the SPS collaboration system regarding risk analysis of the aforementioned food safety issues is set up in each country. The most prominent stakeholders who take up a central role in the risk analysis process were identified. Many linkages between stakeholders were revealed, going from information sharing (legally required or voluntary), data requesting or communicating to the public. Moreover, in every country, constraints related to these linkages could be identified. These constraints, such as lack of resources or communication issues can be used to define needs for improvements in the current SPS collaboration system. While the initial results are already very interesting to discuss, further validation and verification of the obtained conclusions is needed.

Il titolo originale del testo, “Il mutuo appoggio” è una citazione esplicita del testo del naturalista e filosofo russo Peter Kropotkin “Il mutuo appoggio, un fattore dell'evoluzione” del 1902 e vuole rappresentare, al tempo stesso, un’adesione a questa corrente di pensiero. Se le teorie evoluzionistiche occidentali sono state segnate dal pensiero dell’evoluzione competitiva darwiniana, basata su un individualismo spinto, Kropotkin, il cui pensiero è molto diffuso nella penisola iberica e nei paesi mediterranei e sud americani, sostiene che il mutuo appoggio fornisca vantaggi pratici per la sopravvivenza delle comunità, sia di quella umana che di altre specie, e che, tanto quanto la coscienza morale, sia stata premiata dalla selezione naturale. La pandemia da Covid-19 ha evidenziato le molteplici vulnerabilità di cui soffre l’umanità contemporanea. L’espansione del virus ha provocato, in soli due anni, più di 418 milioni di contagi e circa 6 milioni di decessi in tutto il mondo fino a febbraio 2022. Tuttavia, la pandemia ha evidenziato, al tempo stesso, la forza delle nostre società. L'iniziativa SOLIVID è nata proprio per dare supporto, dall’ambito universitario, alle pratiche solidali della cittadinanza. Il presente volume riassume i risultati di questo impegno e integrato con i contributi dei gruppi di ricerca che hanno partecipato all’iniziativa. In questa introduzione si espongono le sue origini, la diffusione, il funzionamento della rete, la metodologia seguita e i principali risultati ottenuti. Infine, si presentano i contributi che costituiscono i capitoli del libro.

These files include the survey questions for data collection as well as the 6 messaging appeals used in this research project.

Background Early reports on the pandemic nature of coronavirus disease 2019 (COVID-19) directed the nephrology community to develop infection prevention and control (IPC) guidance. We aimed to make an inventory of strategies that dialysis centres followed to prevent infection with COVID-19 in the first pandemic wave. Methods We analyzed IPC measures taken by hemodialysis centres treating patients presenting with COVID-19 between 1 March 2020 and 31 July 2020 and that completed the European Renal Association COVID-19 Database centre questionnaire. Additionally, we made an inventory of guidelines published in European countries to prevent spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in dialysis centres. Results Data from 73 dialysis units located in and bordering Europe were analyzed. All participating centres implemented IPC measures to mitigate the impact of SARS-CoV-2 during the first pandemic wave. Measures mentioned most often included triage with questions before entering the dialysis ward, measuring body temperature, hand disinfection, masking for all patients and staff, and personal protective equipment for staff members. These measures were also recommended in most of the 14 guidelines that were identified in the inventory of national guidelines and were also scored as being among the most important measures by the authors of this paper. Heterogeneity existed between centres and national guidelines regarding the minimal distance between dialysis chairs and recommendations regarding isolation and cohorting. Conclusions Although variation existed, measures to prevent transmission of SARS-CoV-2 were relatively similar across centres and national guidelines. Further research is needed to assess causal relationships between measures taken and spread of SARS-CoV-2.

Prispevek predstavlja izhodišča za razpravo o jezikovnih smernicah in učnih ciljih v vrtcih in šolah s slovenskim učnim jezikom v Tržaški in Goriški pokrajini ter v večstopenjski šoli s slovensko-italijanskim dvojezičnim poukom v Špetru. Izhaja iz rezultatov kvantitativne raziskave o poteku pouka na daljavo med epidemijo covid-19, izvedene med pedagoškim kadrom, dijaki in starši otrok, ki obiskujejo vrtce in šole s slovenskim učnim jezikom in dvojezičnim slovensko-italijanskim poukom v Italiji. Izsledke dopolnjuje analiza petnajstih polstrukturiranih globinskih intevjujev z učitelji o didaktično-metodičnih izzivih pri poučevanju učencev, katerih prvi ali primarni jezik ni slovenski, slovenščina pa tudi ni jezik okolja, v katerem živijo.

SARS-CoV-2 viruses engage ACE2 as a functional receptor with their spike protein. The S1 domain of the spike protein contains a C-terminal receptor-binding domain (RBD) and an N-terminal domain (NTD). The NTD of other coronaviruses includes a glycan-binding cleft. However, for the SARS-CoV-2 NTD protein-glycan binding was only observed weakly for sialic acids with highly sensitive methods. Amino acid changes in the NTD of Variants of Concern (VoC) shows antigenic pressure, which can be an indication of NTD-mediated receptor binding. Trimeric NTD proteins of SARS-CoV-2, Alpha, Beta, Delta, and Omicron did not reveal a receptor binding capability. Unexpectedly, the SARS-CoV-2 Beta subvariant strain (501Y.V2-1) NTD binding to Vero E6 cells was sensitive to sialidase pretreatment. Glycan microarray analyses identified a putative 9- O -acetylated sialic acid as a ligand, which was confirmed by catch-and-release ESI-MS, STD-NMR analyses, and a graphene-based electrochemical sensor. The Beta (501Y.V2-1) variant attained an enhanced glycan binding modality in the NTD with specificity towards 9- O -acetylated structures, suggesting a dual-receptor functionality of the SARS-CoV-2 S1 domain, which was quickly selected against. These results indicate that SARS-CoV-2 can probe additional evolutionary space, allowing binding to glycan receptors on the surface of target cells. Graphical abstract: Synopsis: Coronaviruses utilize their N-terminal domain (NTD) for initial reversible low-affinity interaction to (sialylated) glycans. This initial low-affinity/high-avidity engagement enables viral surfing on the target membrane, potentially followed by a stronger secondary receptor interaction. Several coronaviruses, such as HKU1 and OC43, possess a hemagglutinin-esterase for viral release after sialic acid interaction, thus allowing viral dissemination. Other coronaviruses, such as MERS-CoV, do not possess a hemagglutinin-esterase, but interact reversibly to sialic acids allowing for viral surfing and dissemination. The early 501Y.V2-1 subvariant of the Beta SARS-CoV-2 Variant of Concern has attained a receptor-binding functionality towards 9- O -acetylated sialic acid using its NTD. This binding functionality was selected against rapidly, most likely due to poor dissemination. Ablation of sialic acid binding in more recent SARS-CoV-2 Variants of Concern suggests a fine balance of sialic acid interaction of SARS-CoV-2 is required for infection and/or transmission.