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

NCT04351503 | Completed

• 1 other identifier: 2020-00769; qu20Egli2
• Study Type: observational
• Target: 126,586
• Locations: 1 country
• Sites: 6

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.

Conditions

SARS Coronavirus (SARS-CoV-2) Infection

Keywords

Coronavirus Disease 2019 (COVID19); SARS-CoV-2 re-infection

Outcome Measures

Primary Outcomes (8)

• 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

Study Arms (2)

SARSCoV-infected patients (cases)

Other: Study A; Other: Study B; Other: Study C; Other: Study D

non-SARS-CoV-2 infected patients (control)

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

Other: Study A

Interventions

Study A OTHER

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.

SARSCoV-infected patients (cases); non-SARS-CoV-2 infected patients (control)

Study B OTHER

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.

SARSCoV-infected patients (cases)

Study C OTHER

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.

SARSCoV-infected patients (cases)

Study D OTHER

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).

SARSCoV-infected patients (cases)

Eligibility Criteria

• Sex: all
• Healthy Volunteers: Yes
• Age Groups: Child (0-17), Adult (18-64), Older Adult (65+)
• 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)

You may qualify if:

• 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.

You may not qualify if:

• 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)

Sponsors & Collaborators

• University Hospital, Basel, Switzerland: lead
• sciCORE University of Basel: collaborator
• Leonhard Med IT ETH Zurich: collaborator
• Swiss Institute of Bioinformatics: collaborator

Study Sites (6)

Viollier AG

Allschwil, 4123, Switzerland

Location

University Hospital Basel

Basel, 4031, Switzerland

Location

Biozentrum University of Basel

Basel, 4056, Switzerland

Location

sciCore University of Basel

Basel, 4056, Switzerland

Location

Department of Biosystems Science and Engineering ETH Zurich

Basel, 4058, Switzerland

Location

Swiss Institute of Bioinformatics

Geneva, 1202, Switzerland

Location

Related Publications (5)

• Sava M, Sommer G, Daikeler T, Woischnig AK, Martinez AE, Leuzinger K, Hirsch HH, Erlanger T, Wiencierz A, Bassetti S, Tamm M, Tschudin-Sutter S, Stoeckle M, Pargger H, Siegemund M, Boss R, Zimmer G, Vu DL, Kaiser L, Dell-Kuster S, Weisser M, Battegay M, Hostettler K, Khanna N. Ninety-day outcome of patients with severe COVID-19 treated with tocilizumab - a single centre cohort study. Swiss Med Wkly. 2021 Aug 10;151:w20550. doi: 10.4414/smw.2021.20550. eCollection 2021 Aug 2.

  PMID: 34375986 RESULT

• Seth-Smith H, Vesenbeckh S, Egli A, Ott S. SARS-CoV-2 in an immunocompromised host: convalescent plasma therapy and viral evolution elucidated by whole genome sequencing. BMJ Case Rep. 2023 Dec 9;16(12):e255255. doi: 10.1136/bcr-2023-255255.

  PMID: 38087481 RESULT

• Peter JK, Wegner F, Gsponer S, Helfenstein F, Roloff T, Tarnutzer R, Grosheintz K, Back M, Schaubhut C, Wagner S, Seth-Smith HMB, Scotton P, Redondo M, Beckmann C, Stadler T, Salzmann A, Kurth H, Leuzinger K, Bassetti S, Bingisser R, Siegemund M, Weisser M, Battegay M, Sutter ST, Lebrand A, Hirsch HH, Fuchs S, Egli A. SARS-CoV-2 Vaccine Alpha and Delta Variant Breakthrough Infections Are Rare and Mild but Can Happen Relatively Early after Vaccination. Microorganisms. 2022 Apr 21;10(5):857. doi: 10.3390/microorganisms10050857.

  PMID: 35630302 RESULT

• Bruningk SC, Klatt J, Stange M, Mari A, Brunner M, Roloff TC, Seth-Smith HMB, Schweitzer M, Leuzinger K, Sogaard KK, Albertos Torres D, Gensch A, Schlotterbeck AK, Nickel CH, Ritz N, Heininger U, Bielicki J, Rentsch K, Fuchs S, Bingisser R, Siegemund M, Pargger H, Ciardo D, Dubuis O, Buser A, Tschudin-Sutter S, Battegay M, Schneider-Sliwa R, Borgwardt KM, Hirsch HH, Egli A. Determinants of SARS-CoV-2 transmission to guide vaccination strategy in an urban area. Virus Evol. 2022 Mar 17;8(1):veac002. doi: 10.1093/ve/veac002. eCollection 2022.

  PMID: 35310621 RESULT

• Stange M, Mari A, Roloff T, Seth-Smith HM, Schweitzer M, Brunner M, Leuzinger K, Sogaard KK, Gensch A, Tschudin-Sutter S, Fuchs S, Bielicki J, Pargger H, Siegemund M, Nickel CH, Bingisser R, Osthoff M, Bassetti S, Schneider-Sliwa R, Battegay M, Hirsch HH, Egli A. SARS-CoV-2 outbreak in a tri-national urban area is dominated by a B.1 lineage variant linked to a mass gathering event. PLoS Pathog. 2021 Mar 19;17(3):e1009374. doi: 10.1371/journal.ppat.1009374. eCollection 2021 Mar.

  PMID: 33740028 DERIVED

MeSH Terms

Conditions

Severe Acute Respiratory Syndrome; Infections; COVID-19

Condition Hierarchy (Ancestors)

Respiratory Tract Infections; Coronavirus Infections; Coronaviridae Infections; Nidovirales Infections; RNA Virus Infections; Virus Diseases; Respiratory Tract Diseases; Pneumonia, Viral; Pneumonia; Lung Diseases

Study Officials

• Adrian Egli, Prof. Dr. med.

  Division of Clinical Bacteriology & Mycology, University Hospital Basel

  PRINCIPAL INVESTIGATOR

Study Design

• Study Type: observational
• Observational Model: OTHER
• Time Perspective: RETROSPECTIVE
• Sponsor Type: OTHER
• Responsible Party: SPONSOR

Study Record Dates

• First Submitted: April 15, 2020
• First Posted: April 17, 2020
• Study Start: April 9, 2020
• Primary Completion: July 31, 2022
• Study Completion: July 31, 2022
• Last Updated: May 9, 2024

Record last verified: 2024-05

Locations

CH (6)