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Personalised medicine and infectious diseases: understanding the individual host response to viruses (e.g. SARS-CoV-2)

Proposals are expected to characterize the host response and host-pathogen interaction to a virus (or viruses) at the level of genetic patterns, physiological mechanisms and molecular pathways involving different organs and systems to identify factors that predispose to different clinical symptoms, different progression of the viral disease and different clinical outcomes. The study should include patient follow-up to identify conditions (including long-term ones) that may appear after the patient has recovered from the viral disease.

In all cases, actions should cover deep immunological phenotyping of the host response, including the use of animal models or in-vitro models if relevant. The latter should cover the dynamics of the innate and adaptive immune responses to the chosen virus(es) (comprising immunity duration, the effect of potential subsequent infections, etc.) including, if relevant, the association of HLA assets of patients with protective or harmful immune responses. Ultimately, this research should inform disease progression and the development of personalised prophylactic and therapeutic strategies.

The analysis should address the effect of differences in age, sex, gender, ethnicity, chronic conditions, co-morbidities, treatments offered and other relevant characteristics. The sample should be geographically representative for Europe. Where relevant, the sample could also include the data of subjects from outside Europe.

The data used should be standardized following the best available international practices and standards. Equally, sample collection and processing should be done following recognised standard operating procedures. All data should be treated in accordance with GDPR and ethical principles.

Proposals that focus on COVID-19 are strongly encouraged to build links with the EU-funded project ORCHESTRA[[]]. Proposals should pay special attention and link to the newly established European COVID-19 data sharing platform[[]] and collaborate with the existing network of COVID-19 projects[[]] funded under Horizon 2020.

Proposals could consider the involvement of the European Commission's Joint Research Centre (JRC) on modelling the pathogenesis of COVID-19 using Adverse Outcome Pathways.

Collaboration with other relevant initiatives, such as the International Consortium for Personalised Medicine (ICPerMed)[[]], the 1+ Million Genomes initiative[[]] and the EBrains[[ ]] research infrastructure is encouraged, where relevant. Whenever the proposed data sources or fields of application include genomics, the proposals should consider the data standards, and legal, ethical and technical interoperability requirements and guidelines agreed within the 1+ Million Genomes initiative where relevant.