A Systems Approach to Predict the Outcome of SARS-CoV-2 in the Population of a City; COVID-19

Study Overview
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Brief Summary
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This study is to gain critical knowledge to understand the factors influencing the outcome of a pandemic virus within the city of Basel.

Detailed Description
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In order to evaluate the impact of the new SARS-CoV-2 this study analyzes the clinical outcomes of patients with a confirmed SARS-CoV-2 infection using a systems approach. The objective is to integrate various datasets covering clinical and non-clinical variables. Beside host factors such as age, gender, comorbidities and treatments, microbiological factors, such as SARS-CoV-2 viral loads using a (semi)-quantitative nucleic acid test (QNAT), genome sequences, and virus-specific immune responses are included. In addition, epidemiological aspects within the city, such as case numbers in specific areas and resulting saturation of the healthcare system (e.g. patients being hospitalized, and ICU occupancy), will be analyzed. Further epidemiological data will be generated from biological measurements from all available serum and respiratory samples (leftover material) collected from February 2020 to November 2021 over two seasons as it is likely that a second wave will be circulating in the following winter 2020/2021. In this project, three retrospective studies will be conducted: Study A: retrospective observational case-control study to predict the clinical outcomes and features of SARS-CoV-2 infection. The clinical outcomes of SARSCoV-2 infected patients (cases) and non-SARS-CoV-2 infected patients with or without other respiratory viruses (control) will be explored. Study B: retrospective observational epidemiological surveillance study to describe the epidemiology of the SARS-CoV-2 outbreak; description of the epidemiological spread of the new SARS-CoV-2 virus in people living in Basel. Study C: retrospective observational viral evolution study whereby respiratory materials and matching blood and tissue materials will be used to perform whole genome sequencing to study pathogen evolution between hosts as well as in-host evolution. No additional material will be collected. Virus genomes obtained during the expanding, peak, and contracting phase of the pandemic will be compared to identify predictors of viral evolution, viral loads, majority species, immune escape variants, and the implications for clinical outcome, diagnostic detection, treatment, and vaccine design. Correlating specifically the occurrence and rate and variants of SARS-CoV-2 re-infections in city blocks of high activity and exposure risk will be of interest. Study D: retrospective observational treatment outcome study whereby clinical outcome, laboratory, radiological, pulmonary function and virological data as well as data on immune responses will be used to study safety and efficacy of different treatment modalities. All data and material will be collected on a routine basis during hospitalization and in the outpatient setting to assess the safety and effect of different treatment modalities on outcome.

Official Title
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A Systems Approach to Predict the Outcome of SARS-CoV-2 in the Population of a City

Conditions
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SARS Coronavirus (SARS-CoV-2) Infection

Intervention / Treatment
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* Other: Study A
* Other: Study B
* Other: Study C
* Other: Study D


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Study A: All patients being tested for SARS-CoV-2 at the University Hospital Basel (USB) and with residency in Basel (Basel-Stadt, Riehen, and Bettingen) will be included for clinical outcome evaluation. All age groups will be included. In addition, non-clinical data such as epidemiological and hospital associated data of all people living in Basel but not necessarily tested at the University Hospital Basel will be included Study B: Epidemiological data and serum and respiratory samples across all Age groups from people with residency in Basel (Basel-Stadt, Riehen, and Bettingen) with and without confirmed SARS-CoV-2 infection will be included Study C: SARS-CoV-2 viral genome analysis will be conducted from all patients tested positive for SARS-CoV-2 genome by NAT at the University Hospital Basel and living in Basel (Basel-Stadt, Riehen, and Bettingen). In addition, viral genome analysis will be conducted from all people tested positive for SARS-CoV-2 genome by NAT living in Basel by the mentioned study partners. All Age groups will be included. Patients with cleared SARS-CoV-2 infection coming for plasma donation will be included to describe immunological response after successfully cleared infection. Exclusion Criteria: documented refusal of the general consent or an available/known written or oral statement against Research People, who are tested at the USB, with residency outside of Basel (Basel-Stadt, Riehen, and Bettingen)
Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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Accepts Healthy Volunteers

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| SARSCoV-infected patients (cases)<br> | Other: Study A<br>* Study A: collection of data of clinical outcomes and features of SARS-CoV-2 infection. Demographical, clinical, microbiological, laboratory, epidemiological and hospital-associated data will be analyzed. For this study part, only patients with a visit at the University Hospital Basel will be included in order to access patient charts.<br>Other: Study B<br>* Study B: collection of epidemiological surveillance data to describe the epidemiology of the SARS-CoV-2 outbreak. The epidemic transmission of Influenza viruses in the City of Basel serves as an important reference to identify similarities and differences to the pandemic SARS-CoV-2 situation. In addition data collected during the Influenza projects - in particular data on statistical blocks of the city, e.g. population density, income and living space will be re-used. Already collected and stored samples such as serum and respiratory material (leftover material) will be (re-) used.<br>Other: Study C<br>* Study C: data collection for viral evolution. Respiratory materials and matching blood and tissue materials will be used to perform whole genome sequencing to study pathogen evolution between hosts as well as in-host evolution. No additional material will be collected.<br>Other: Study D<br>* Study D: collection of safety and efficacy data of different treatment modalities. Currently the following treatments are considered as part of the treatment: Lopinavir/Ritonavir Hydroxychloroquine Tocilizumab Eculizumab Ruxolitinib Remdesivir Treatment with convalescent plasma blood count, blood chemistry and pulmonary function test (collected on a routine basis during hospitalization and in the outpatient setting).<br>|
| non-SARS-CoV-2 infected patients (control)<br>non-SARS-CoV-2 infected patients with or without other respiratory viruses (control). | Other: Study A<br>* Study A: collection of data of clinical outcomes and features of SARS-CoV-2 infection. Demographical, clinical, microbiological, laboratory, epidemiological and hospital-associated data will be analyzed. For this study part, only patients with a visit at the University Hospital Basel will be included in order to access patient charts.<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Identification of factors associated with (i) infection (binary, yes/no), (ii) hospitalization (binary, yes/no), (iii) requirement for ICU treatment (binary, yes/no) | Identification of factors associated with (i) infection (binary, yes/no), (ii) hospitalization (binary, yes/no), (iii) requirement for ICU treatment (binary, yes/no) | at baseline | 
| duration of hospitalization (in days) | duration of hospitalization (in days) | at baseline | 
| duration of Intensive Care Unit (ICU) stay (in days) | duration of ICU stay (in days) | at baseline | 
| in-hospital mortality (binary, yes/no) | in-hospital mortality (binary, yes/no) | at baseline | 
| Number of infected cases within the city of Basel | Number of infected cases confirmed either by nucleic acid test (NAT) or by positive serology within the city of Basel expressed as incidence per statistical block | at baseline | 
| whole genome sequencing to study pathogen evolution (number, type, and complexity of viral genome) | Number, type, and complexity of viral genome variants and quasispecies identified by deep-sequencing during rise, peak, and contraction of the pandemic in patients and geographic areas. | at baseline | 
| Identification which treatment modality is associated with adverse events (binary, yes/no) | Identification which treatment modality is associated with adverse events (binary, yes/no) | at baseline | 
| Identification which treatment modality is associated with pulmonary recovery (binary, yes/no) | Identification which treatment modality is associated with pulmonary recovery(binary, yes/no) | after 30 and 90 days | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Coronavirus Disease 2019 (COVID19), SARS-CoV-2 re-infection