Periodic Reporting for period 1 - REACT (Respiratory Host-Pathogen Interaction)
Okres sprawozdawczy: 2022-08-01 do 2024-01-31
Respiratory tract infections caused by seasonal epidemics and pandemics are among the leading causes of death worldwide, with influenza viruses, paramyxoviruses and coronaviruses being the predominant aetiological agents. Treatment options are scarce or only supportive, therefore it is important to identify new targets for prophylactic interventions and models for early prediction of disease progression to improve treatments and response within the healthcare system.
The REACT (Respiratory Host-Pathogen Interaction) project aims to define and further investigate which mechanisms and variants may affect the course and development of lower respiratory viral diseases, focusing on the predominant viruses; respiratory syncytial virus (RSV), influenza virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This will be done by analysing patient and virus characteristics, patient-pathogen interactions, and by the immunological characterization of the response in ethnically diverse retrospective and prospective cohorts. By this, we aim to provide further knowledge on critical factors and key variants for disease predisposition and progression, symptom expression and clinical outcomes, helping to improve personalised treatments and future vaccine development.
The REACT (Respiratory Host-Pathogen Interaction) project aims to define and further investigate which mechanisms and variants may affect the course and development of lower respiratory viral diseases, focusing on the predominant viruses; respiratory syncytial virus (RSV), influenza virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). This will be done by analysing patient and virus characteristics, patient-pathogen interactions, and by the immunological characterization of the response in ethnically diverse retrospective and prospective cohorts. By this, we aim to provide further knowledge on critical factors and key variants for disease predisposition and progression, symptom expression and clinical outcomes, helping to improve personalised treatments and future vaccine development.
To meet the project aims, both retrospective and prospective cohort samples will be analyzed. Among the partners are multiple biobanks, providing large and diverse cohort samples, which together with prospective samples collected at general practitioners and hospitals will provide a large sample pool comprising of patients with varying disease severity and outcomes, as well as sociodemographics and ethnicity.
In the first reporting period, major efforts have therefore been directed at the creation of patient cohorts. For the retrospective samples, extensive work to identify relevant cohorts has been carried out, focusing on the different types of infections, degrees of severity, types of disparate samples and relevant associated data. For the prospective sample collection, the conditions and requirements of respiratory samples and live cells from virus-infected patients have been identified. For prospective cohorts, patients with positive diagnosis of SARS-Cov-2, influenza and RSV will be asked to join the project, allowing via an informed consent the use of their samples and associated data. Furthermore, logistics for both the collection and sharing of samples within the consortium have been put in place. This has obviously demanded ensuring the scientific, legal and ethical approvals, as well as GDPR compliance across partner institutions for the effective collection, storing and transferring of data between project partners.
In Spain, the REACT consortium has succeeded in establishing a network for the creation of the relevant cohorts for the project, obtaining more than 500 retrospective samples from patient cases and controls, and the implementation of varied and delocalised connections with 8 biobanks of the ISCIII Platform for Biobanks and Biomodels, facilitating access to patients with different disease severities and contexts. In Denmark, ethical and legal approvals have been obtained and the collection of prospective samples at general practitioners and hospitals have begun. Blood and airway secretion samples from both adults and children with diverse symptoms have been collected at the hospital, and samples from adults at the general practitioners, and thus given a diverse sample pool. For the study of COVID-19 disease in the context of an African population, a longitudinal cohort of black African adults was recruited at Chris Hani Baragwanath Hospital (CHBH) in Soweto, Johannesburg, South Africa. Samples were processed for storage at the National Institute for Communicable Diseases (NICD) with a total of 123 South African SARS-CoV-2 hospitalized patients, living with and without HIV-1 (GIVOCA cohort (Genetics, Immunology, and Virology of COVID-19 in Africa)).
Part of the aim in REACT is characterising virus characteristics, and for this, currently 12 positive SARS-CoV-2 and influenza samples have been received, all of which have been sequenced and characterized according to existing protocols. Furthermore, a study has been conducted investigating the most suitable cell lines for the cultivation of SARS-CoV-2 variants. Here, 11 different variants have been grown on 6 different cell lines, and growth kinetics have been analysed by qPCR. Moreover, cell-line-specific adaptations are currently being investigated by whole genome sequencing.
For the immunological characterization, studies of both the adaptive and innate immune response have begun. For the experimental evaluation of T and B-cell immunity, validation and implementation of the experimental strategies has been conducted and are hence ready for application on the above outlined sample collections. Furthermore, interactions between partners have led to the identification of a set of viral proteins and variants (based on the seasonal variants) of focus for the T cell enumeration and HLA ligandomes has been identified for such protein. Single-cell RNA transcriptomic technologies have been established to study the innate immune response in relation to changes in adaptive immune cells to determine protective/deleterious immune events that predispose SARS-CoV-2 infected hospitalised patients to different disease outcomes. These are ready to apply to the already described GIVOCA cohort, where quantitation of plasma cytokines and soluble proteases has been completed. HLA and KIR genotyping will commence using next generation sequencing and in-house established assays, respectively. Moreover, work to generate organoid model systems for analysing viral infection is ongoing.
Lastly, a continuous engagement with a broad range of stakeholders, including European project cohort networks, is done in aim to fulfil the project objectives. The REACT partners have identified and presented a roadmap of synergies with other projects and networks that could serve as a basis for the implementation and further development of the project results as the project advances.
In the first reporting period, major efforts have therefore been directed at the creation of patient cohorts. For the retrospective samples, extensive work to identify relevant cohorts has been carried out, focusing on the different types of infections, degrees of severity, types of disparate samples and relevant associated data. For the prospective sample collection, the conditions and requirements of respiratory samples and live cells from virus-infected patients have been identified. For prospective cohorts, patients with positive diagnosis of SARS-Cov-2, influenza and RSV will be asked to join the project, allowing via an informed consent the use of their samples and associated data. Furthermore, logistics for both the collection and sharing of samples within the consortium have been put in place. This has obviously demanded ensuring the scientific, legal and ethical approvals, as well as GDPR compliance across partner institutions for the effective collection, storing and transferring of data between project partners.
In Spain, the REACT consortium has succeeded in establishing a network for the creation of the relevant cohorts for the project, obtaining more than 500 retrospective samples from patient cases and controls, and the implementation of varied and delocalised connections with 8 biobanks of the ISCIII Platform for Biobanks and Biomodels, facilitating access to patients with different disease severities and contexts. In Denmark, ethical and legal approvals have been obtained and the collection of prospective samples at general practitioners and hospitals have begun. Blood and airway secretion samples from both adults and children with diverse symptoms have been collected at the hospital, and samples from adults at the general practitioners, and thus given a diverse sample pool. For the study of COVID-19 disease in the context of an African population, a longitudinal cohort of black African adults was recruited at Chris Hani Baragwanath Hospital (CHBH) in Soweto, Johannesburg, South Africa. Samples were processed for storage at the National Institute for Communicable Diseases (NICD) with a total of 123 South African SARS-CoV-2 hospitalized patients, living with and without HIV-1 (GIVOCA cohort (Genetics, Immunology, and Virology of COVID-19 in Africa)).
Part of the aim in REACT is characterising virus characteristics, and for this, currently 12 positive SARS-CoV-2 and influenza samples have been received, all of which have been sequenced and characterized according to existing protocols. Furthermore, a study has been conducted investigating the most suitable cell lines for the cultivation of SARS-CoV-2 variants. Here, 11 different variants have been grown on 6 different cell lines, and growth kinetics have been analysed by qPCR. Moreover, cell-line-specific adaptations are currently being investigated by whole genome sequencing.
For the immunological characterization, studies of both the adaptive and innate immune response have begun. For the experimental evaluation of T and B-cell immunity, validation and implementation of the experimental strategies has been conducted and are hence ready for application on the above outlined sample collections. Furthermore, interactions between partners have led to the identification of a set of viral proteins and variants (based on the seasonal variants) of focus for the T cell enumeration and HLA ligandomes has been identified for such protein. Single-cell RNA transcriptomic technologies have been established to study the innate immune response in relation to changes in adaptive immune cells to determine protective/deleterious immune events that predispose SARS-CoV-2 infected hospitalised patients to different disease outcomes. These are ready to apply to the already described GIVOCA cohort, where quantitation of plasma cytokines and soluble proteases has been completed. HLA and KIR genotyping will commence using next generation sequencing and in-house established assays, respectively. Moreover, work to generate organoid model systems for analysing viral infection is ongoing.
Lastly, a continuous engagement with a broad range of stakeholders, including European project cohort networks, is done in aim to fulfil the project objectives. The REACT partners have identified and presented a roadmap of synergies with other projects and networks that could serve as a basis for the implementation and further development of the project results as the project advances.
Through the retrospective and prospective cohorts, biological samples and associated clinical and demographical data from patients with SARS-CoV-2, influenza and RSV will be collected and analysed. The REACT consortium will be able to evaluate and analyse different genotypic, immunophenotypic, demographic and clinical variables and factors, and their effect in the disease course. This will help in personalised treatment strategies, the identification of therapeutic targets, as well as defining and refining vaccination efforts, improving our understanding of respiratory infectious diseases from different methodological perspectives.