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

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.