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

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.

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.

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.

"Study D: collection of safety and efficacy data of different treatment modalities. Currently the following treatments are considered as part of the treatment:~1. Lopinavir/Ritonavir~2. Hydroxychloroquine~3. Tocilizumab~4. Eculizumab~5. Ruxolitinib~6. Remdesivir~7. Treatment with convalescent plasma blood count, blood chemistry and pulmonary function test (collected on a routine basis during hospitalization and in the outpatient setting)."