Part 2
Landscape analysis

ESFRI RIs in Response to Emergencies

EXAMPLES FROM THE COVID-19 CRISIS

ESFRI RIs demonstrated an enormous capacity to respond to the emergency represented by COVID-19 pandemics, by rapidly revising/adapting their access programmes operations and delivering their services, including ad hoc new services to support research related to COVID-19.

RIs in the health domain were at the forefront and immediately acted, being able to offer all the necessary services in the whole pipeline of vaccine and therapeutics development, for the research on diagnostic tools and the analysis of the direct and indirect impact of the crisis. To facilitate COVID-19 related research, fast-track access calls were issued and publicized through the RIs websites, which were continuously updated. The information was also promptly collected on the Life Sciences Research Infrastructures (LS RIs) websiteLife Sciences Research Infrastructures (LS RIs)
https://lifescience-ri.eu/ls-ri-response-to-Covid-19.html
providing the users community with a comprehensive set of available services and resources. ESFRI also gathered information on COVID-19 related activities on its websiteRIs against COVID-19 pandemic
www.esfri.eu/Covid-19
.

Open Science data were at the base of success stories since the current pandemic started – the genome of the SARS-CoV-2 virus was sequenced much quicker than for previous similar pathogens (such as MERS-CoV and Ebola) and deposited in the public domain. This allowed other scientists to start studying the virus and tracking its spread. Likewise, research data on the COVID-19 disease has been readily made available in the public domain, thereby helping our clinical understanding of its effects, and informing the development of treatments and tracking new variants of the virus through genomic sequencing and coordinated data-sharing efforts. ELIXIR has played a key role in mobilizing public data infrastructure to enable research data-sharing via the COVID-19 Data PortalCOVID-19 Data Portal
https://www.Covid19dataportal.org/
, a single entry point that provides free and open access to viral sequence data and other relevant data including proteins, imaging, expression data and literature relating to COVID-19 and SARS-CoV-2. The establishment of the effort and connections across Europe to national-level initiatives has been supported through uplifts to the Horizon 2020 ELIXIR-CONVERGE and EOSC-Life projects result ing in the development of a set of services that include databases, analysis tools and workflows, resources to make COVID-19 data ‘FAIR’ and significant computing resources. At the European policy level, both the ERA Versus Corona Action PlanERA Versus Corona Action Plan
https://ec.europa.eu/info/sites/default/files/covid-firsteravscorona_actions.pdf
, and the HERA IncubatorHERA Incubator
https://ec.europa.eu/info/news/eu-invest-eu150-million-research-counter-coronavirusvariants-2021-feb-17_en
programme have placed the European COVID-19 Data Platform at the centre of research data sharing efforts. The new HERA Incubator programme will indeed support the expansion of the COVID-19 Data Platform enabling Europe and scientists globally to respond better to other future pandemics and outbreaks of infectious disease as and when they occur.

Imaging technologies provided by Euro-BioImaging ERIC are powerful tools to study any infectious disease agent that might cause emergencies such as COVID-19 did. They are of key importance for studies on the structure and function of pathogens at the cellular level, to understand virus infection, binding, intracellular trafficking, replication, assembly, etc. They are also crucial in revealing how viruses affect the host cell physiology and how the virus-mediated disease condition may be targeted by drugs or other interventions. Imaging-related services are also needed in the discovery and development of new vaccines and virus-targeted drugs, e.g. imaging of immune cells to reveal binding of antibody components to viruses or viral replication inside the host cell. In the clinical field, PET-CT technologies allow imaging of the biodistribution of vaccines after administration. Image data services built on artificial intelligence and machine learning applications address the complexity of virus-mediated disease analysis, especially when combining advanced imaging data with cohort data and other large biomolecular datasets.

Structural biology technologies provided by INSTRUCT ERIC are central to the pharmaceutical field, in particular to determine the 3D structures of druggable proteins – and thus determine sites where small molecules might bind – or to characterize viral protein antigens or specific parts of them to unravel their interactions with human antibodies. Indeed, these technologies properly integrated produced the structural characterization of key proteins only weeks after the SARS-CoV-2 sequence was released. INSTRUCT ERIC X-ray, Cryo-EM and NMR centres have brought these technologies centre-stage in drug discovery and since then there is a strong commitment to prioritizing COVID-19 researches. INSTRUCT ERIC established also a Resource Centre with tools and information to assist research relating to SARS-CoV-2 and COVID-19.

INFRAFRONTIER rapidly evolved a broad portfolio of services to evaluate the potential of new anti-COVID-19 compounds and therapeutics on suitable humanized models as well as BSL3 laboratories for in vivo testing, through which the compounds can proceed to clinical testing. INFRAFRONTIER has also launched a new service call to provide researchers access to test their innovative and novel COVID-19 therapeutics in a standardized infection pipeline that uses preclinical models developed to study COVID-19 infection and its pathophysiological consequences, including the complete characterization of genes critically involved in the infection and the effect of the new anti-viral compounds.

Drug repurposing activities and high-throughput screening assays services made available by EU-OPENSCREEN ERIC are key to identify candidate molecules for COVID-19 therapeutics and, to this end, a collection of about 2,500 bioactive molecules from EU-OPENSCREEN was tested. All chemical and biological data are made available in EU-OPENSCREEN open access European Chemical Biology DatabaseEuropean Chemical Biology Database
https://ecbd.eu
and the European COVID-19 Data PlatformCOVID-19 Data Portal
https://www.Covid19dataportal.org/
. The EU-OPENSCREEN ERIC collection of about 1,000 fragments was used to identify novel binders to Nsp3, an essential component of the replication complex of the virus. Data for 24 compounds from the collection provided alternative starting points for the development of anti-COVID-19 therapeutics.

EATRIS ERIC provided to COVID-19 vaccine developers the EATRIS COVID-19 Research Forum, quickly made publicly available and updated weekly, developed a self-test, which reached wide media coverageGargling test: Czech Republic trials faster & cheaper way to check for coronavirus
https://www.youtube.com/watch?v=oOn3sQP92lg
and is working to develop and introduce to the market a nasal spray vaccine against COVID-19University of Eastern Finland researchers introduce a nasal COVID-19 vaccine – Science Business, March 2021
https://sciencebusiness.net/network-updates/university-eastern-finland-researchers-introduce-nasal-Covid-19-vaccine
.

ECRIN ERIC rapidly provided informatics services to harvest information on any COVID-19 actions in the biomedical fields. Within the EOSC-Life project, ECRIN developed a secure and GDPR-compliant patient-level data pilot repository linked to the EU COVID-19 data portal, enabling COVID-19 trial data sharing, while participating in the VACCELERATE projectVACCELERATE project
https://www.vaccelerate.eu
is contributing to the activities for future pandemic preparedness (HERA Incubator).

Specific role in the infection threads plays ERINHA, a pan-European Research Infrastructure dedicated to the study of high-consequence emerging and re-emerging pathogens. ERINHA offers access to a large range of high containment in vitro and in vivo capacities to facilitate a wide variety of studies on SARS-CoV-2/ COVID-19 and coordinates joint RI European activities regarding the service to vanquish COVID-19 pandemics.Besides  RIs in Life Sciences, also other RIs provided specific services during the COVID-19 crisis.

According to UNESCOCOVID-19: the ocean, an ally against the virus
https://en.unesco.org/news/covid-19-ocean-ally-against-virus
, the ocean can be an ally against COVID-19. Bacteria found in the deep sea are used to carry out rapid testing to detect the presence of COVID-19. Species found in the ocean offer an excellent promising future for pharmaceuticals. Years ago, research from the Woods Hole Oceanographic Institute identified microbes living in deep-sea hydrothermal vents harbour whose enzymes can be used in diagnostic tests, like those to detect the pandemics of AIDS and SARS. Their role has been revisited for COVID-19; they have been used to carry out rapid tests to detect the virus’s presence. EMSO ERIC ecology and biodiversity services include developing samplers with other ERICs – EMBRC ERIC, LifeWatch ERIC – for DNA monitoring.

ACTRIS supported the authorities by securing the full documentation of atmospheric composition changes due to lockdowns in the various parts of Europe. The main goals were: i) to provide reliable estimates of effects of reduced emissions; ii) to open some atmospheric simulation chambers for testing protection gears such as face masks; iii) to support authorities by providing science-based analysis of current knowledge and finally; iv) to illustrate the complex interplay between emission restrictions and human behaviour, and the necessity for structural changes to reach the WHO air quality standards in Europe.

FAIR at GSI efforts have been providing new insights and new technologies that may help to fight the SARS-CoV-2 virus: i) ion radiation for vaccine development; ii) therapeutic effect of low-dose radiation in SARS-CoV-2 induced pneumonia; iii) Improved and fast virus detection with single nanopore membranes.

The biology laboratories of European XFEL joined DESY and its partners in the screening effort to find novel binding partners to inhibit two important SARS-CoV-2 proteins (main protease and papain-like protease) using drugs that are either already on the market for other diseases or in late clinical trials. In parallel, EuXFEL contributed to the international effort on COVID-19 research by preparing and supporting a variety of Covid-related experiments, utilizing liquid jet serial femtosecond X-ray crystallography (SFX) to investigate new structures and time-resolved SFX of COVID-19 proteins.

The particular contrast provided by neutron techniques by ILL helps scientists to determine how protein complexes function, as well as the specificity of protein interactions with membranes. Finally, neutron spectroscopy provides insight into the dynamics of the biological components, which may constitute the ultimate key to understanding their functionality.

SKAO played an active role in the COVID-19 pandemic response, with contributions spanning from managing the design and production of respiratory ventilators and 3D printing of Personal Protective Equipment to the development of educational online tools to support home-schooling or contributing to a public information campaign to combat misinformation, just to mention a few.

Feasibility studies in the ESRF Extremely Brilliant Source, the world’s first high-energy fourth-generation synchrotron, have already demonstrated it can resolve unprecedented detail revealing the damage caused by COVID-19 on human lungs, linking from the major airways all the way down to the finest micro-vasculature in an intact lung. promises to develop a transformational X-ray tomography technology that will enable the scanning of a whole human body with resolution of 25 microns, thinner than a human hair – tens of times the resolution of a CT scanner. Further, it can then zoom into local areas with cellular-level imaging, or one micron – over 100x better resolution than a CT scanner.

PRACE has made computing time available at short notice throughout Europe for projects in connection with COVID-19PRACE Versus COVID-19: Actions & Activities
https://prace-ri.eu/hpc-access/hpcvsvirus/
. Thirty different projects ranging from molecular biology to epidemiology were computed.

Also, RIs in the Social Sciences domain acted promptly to assess the impact of the pandemic on the society at large. A special Corona questionnaire included in the SHARE ERIC targeted telephone interviews (Computer-Assisted-Telephone-Interview, CATI) from June to August 2020, brought to release the Wave 8 COVID-19 data in December 2020, available for researchers all over the world to examine the health, social, economic and environmental situation of European citizens and beyond against the background of the pandemic. A further wave of telephone interviews of the SHARE Corona survey has been conducted in 2021. This study is the ideal database to study the non-intended socio-economic and health consequences of the epidemiological containment decisions and the long-term effects of the COVID-19 pandemic.

In its 2020-2021 round, the European Social Survey ERIC added a dedicated COVID-19 module to its longitudinal questionnaire including a number of health indicators. Combined with its core questionnaire, the dataset will enable ample opportunities for pre-post analyses of the wider social, economic and political consequences of the SARS-CoV-2 pandemic, for examining the medium and long term effects of the pandemic across countries and social groups, and for comparing policy responses and their outcomes in terms of social inequalities and social cohesion. At the same time the pandemic highlighted the fragility of relying on face to face fieldwork for RIs like the ESS. An alternative method has been developed to ensure data collection in 2021 can proceed. The need for a permanent panel infrastructure, reaching respondents by web and other non in-person methods, was underlined.

In June 2020 DARIAH ERIC launched a call under its bi-annual DARIAH Theme funding scheme entitled ‘Arts, Humanities and COVID-19’. Projects being submitted to this call are being asked to explore how DARIAH ERIC will collect, curate, preserve and interpret the heterogeneous record of the experience of life and work in early 2020. DARIAH will also look for innovative projects exploring humanities contributions to understanding the virus and its impacts, and what the study of culture, the arts, values, practices and language can contribute to our response to this global challenge.

Through extending the collection of parliamentary datasets with curated collections of recent parliamentary debates about the corona dynamics, the European Research Infrastructure for language resources CLARIN ERIC set the basis for comparative research into how public bodies have responded to the crisis across countries.

The COVID-19 pandemic has demonstrated the capacity of the ESFRI RIs to respond to emergencies providing specific services to support the science-led response to the COVID-19 outbreak and also the capacity in many cases to rapidly react and return to operate even during the lockdown period. The Covid crisis has massively accelerated some pre-existing trends, in particular digitalization. It has shaken the world, setting in motion a wide range of possible trajectories.

Perhaps the most important lesson learnt is that the ESFRI RIs ensure that research across all topics and areas can continue even during a big crisis. Not knowing where the next crisis may hit, the ESFRI RIs are preparing their research programme along all fronts including fundamental research trying to be ready to provide the necessary services to society.