Working…
ClinicalTrials.gov
ClinicalTrials.gov Menu

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

The safety and scientific validity of this study is the responsibility of the study sponsor and investigators. Listing a study does not mean it has been evaluated by the U.S. Federal Government. Know the risks and potential benefits of clinical studies and talk to your health care provider before participating. Read our disclaimer for details.
 
ClinicalTrials.gov Identifier: NCT04351503
Recruitment Status : Recruiting
First Posted : April 17, 2020
Last Update Posted : June 17, 2021
Sponsor:
Collaborators:
sciCORE University of Basel
Leonhard Med IT ETH Zurich
Swiss Institute of Bioinformatics
Information provided by (Responsible Party):
University Hospital, Basel, Switzerland

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

Condition or disease Intervention/treatment
SARS Coronavirus (SARS-CoV-2) Infection Other: Study A Other: Study B Other: Study C Other: Study D

Detailed Description:

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.

Layout table for study information
Study Type : Observational
Estimated Enrollment : 10000 participants
Observational Model: Other
Time Perspective: Retrospective
Official Title: A Systems Approach to Predict the Outcome of SARS-CoV-2 in the Population of a City
Actual Study Start Date : April 9, 2020
Estimated Primary Completion Date : April 2022
Estimated Study Completion Date : April 2022

Group/Cohort Intervention/treatment
SARSCoV-infected patients (cases) 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:

  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).

non-SARS-CoV-2 infected patients (control)
non-SARS-CoV-2 infected patients with or without other respiratory viruses (control).
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.




Primary Outcome Measures :
  1. Identification of factors associated with (i) infection (binary, yes/no), (ii) hospitalization (binary, yes/no), (iii) requirement for ICU treatment (binary, yes/no) [ Time Frame: at baseline ]
    Identification of factors associated with (i) infection (binary, yes/no), (ii) hospitalization (binary, yes/no), (iii) requirement for ICU treatment (binary, yes/no)

  2. duration of hospitalization (in days) [ Time Frame: at baseline ]
    duration of hospitalization (in days)

  3. duration of Intensive Care Unit (ICU) stay (in days) [ Time Frame: at baseline ]
    duration of ICU stay (in days)

  4. in-hospital mortality (binary, yes/no) [ Time Frame: at baseline ]
    in-hospital mortality (binary, yes/no)

  5. Number of infected cases within the city of Basel [ Time Frame: at baseline ]
    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

  6. whole genome sequencing to study pathogen evolution (number, type, and complexity of viral genome) [ Time Frame: at baseline ]
    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.

  7. Identification which treatment modality is associated with adverse events (binary, yes/no) [ Time Frame: at baseline ]
    Identification which treatment modality is associated with adverse events (binary, yes/no)

  8. Identification which treatment modality is associated with pulmonary recovery (binary, yes/no) [ Time Frame: after 30 and 90 days ]
    Identification which treatment modality is associated with pulmonary recovery(binary, yes/no)



Information from the National Library of Medicine

Choosing to participate in a study is an important personal decision. Talk with your doctor and family members or friends about deciding to join a study. To learn more about this study, you or your doctor may contact the study research staff using the contacts provided below. For general information, Learn About Clinical Studies.


Layout table for eligibility information
Ages Eligible for Study:   Child, Adult, Older Adult
Sexes Eligible for Study:   All
Accepts Healthy Volunteers:   Yes
Sampling Method:   Probability Sample
Study Population
SARSCoV- 2 infected patients and non-SARS-CoV-2 infected patients with or without other respiratory viruses with residency in Basel (Basel-Stadt, Riehen, and Bettingen)
Criteria

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)

Information from the National Library of Medicine

To learn more about this study, you or your doctor may contact the study research staff using the contact information provided by the sponsor.

Please refer to this study by its ClinicalTrials.gov identifier (NCT number): NCT04351503


Contacts
Layout table for location contacts
Contact: Adrian Egli, Prof. Dr. med. +41 61 556 57 49 adrian.egli@usb.ch

Locations
Layout table for location information
Switzerland
Viollier AG Recruiting
Allschwil, Switzerland, 4123
Contact: Diana Ciardo, Dr. med    +41 61 486 11 11    diana.ciardo@viollier.ch   
University Hospital Basel Recruiting
Basel, Switzerland, 4031
Contact: Adrian Egli, Prof. Dr. med    +41 61 556 57 49    adrian.egli@usb.ch   
Sub-Investigator: Stefano Bassetti, Prof. Dr. med.         
Sub-Investigator: Roland Bingisser, Prof. Dr. med         
Sub-Investigator: Andreas Buser, Prof. Dr. med         
Sub-Investigator: Hans Hirsch, Prof. Dr. med.         
Sub-Investigator: Hans Pargger, Prof. Dr. med         
Sub-Investigator: Bram Stieltjes, Dr. med         
Sub-Investigator: Sarah Tschudin- Sutter, Prof. Dr. med.         
Biozentrum University of Basel Recruiting
Basel, Switzerland, 4056
Contact: Richard Neher, Prof. Dr. med    +41 61 207 58 34    richard.neher@unibas.ch   
sciCore University of Basel Recruiting
Basel, Switzerland, 4056
Contact: Thierry Sengstag, Dr.    +41 61 207 18 53    thierry.sengstag@unibas.ch   
Department of Biosystems Science and Engineering ETH Zurich Recruiting
Basel, Switzerland, 4058
Contact: Karsten Borgwardt, Prof.Dr. med    +41 61 387 34 20    karsten.borgwardt@bsse.ethz.ch   
Swiss Institute of Bioinformatics Recruiting
Geneva, Switzerland, 1202
Contact: Valérie Barbié, Dr. med    +41 22 379 02 65    valerie.barbie@sib.swiss   
Contact: Aitana Lebrand, Dr. med.    +41 22 379 02 67    aitana.lebrand@sib.swiss   
Sub-Investigator: Aitana Lebrand, Dr. med.         
Sub-Investigator: Valérie Barbié, Dr. med.         
Sponsors and Collaborators
University Hospital, Basel, Switzerland
sciCORE University of Basel
Leonhard Med IT ETH Zurich
Swiss Institute of Bioinformatics
Investigators
Layout table for investigator information
Principal Investigator: Adrian Egli, Prof. Dr. med. Division of Clinical Bacteriology & Mycology, University Hospital Basel
Publications automatically indexed to this study by ClinicalTrials.gov Identifier (NCT Number):
Layout table for additonal information
Responsible Party: University Hospital, Basel, Switzerland
ClinicalTrials.gov Identifier: NCT04351503    
Other Study ID Numbers: 2020-00769; qu20Egli2
First Posted: April 17, 2020    Key Record Dates
Last Update Posted: June 17, 2021
Last Verified: June 2021

Layout table for additional information
Studies a U.S. FDA-regulated Drug Product: No
Studies a U.S. FDA-regulated Device Product: No
Keywords provided by University Hospital, Basel, Switzerland:
Coronavirus Disease 2019 (COVID19)
SARS-CoV-2 re-infection
Additional relevant MeSH terms:
Layout table for MeSH terms
Coronavirus Infections
Coronaviridae Infections
Nidovirales Infections
RNA Virus Infections
Virus Diseases