This study is to gain critical knowledge to understand the factors influencing the outcome of a pandemic virus within the city of Basel.
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.
Other: Study A
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.
Other: Study B
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.
Other: Study C
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.
Other: Study D
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).
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)
Viollier AG
Allschwil, Switzerland
University Hospital Basel
Basel, Switzerland
Biozentrum University of Basel
Basel, Switzerland
sciCore University of Basel
Basel, Switzerland
Department of Biosystems Science and Engineering ETH Zurich
Basel, Switzerland
Swiss Institute of Bioinformatics
Geneva, Switzerland
Adrian Egli, Prof. Dr. med.
+41 61 556 57 49
adrian.egli@usb.ch
Adrian Egli, Prof. Dr. med., Principal Investigator
Division of Clinical Bacteriology & Mycology, University Hospital Basel