Study of COVID-19 Outbreak in Hospital Departments of Bamako, Mali

Study Overview
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Brief Summary
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The new coronavirus known as SARS-Cov-2 (severe acute respiratory syndrome -coronavirus 2) was first reported in December 2019 and rapidly became a public health emergency. The COVID-19 pandemic is now affecting sensitive regions with fragile health care systems, such as South America and Africa. Caregivers, in the front line of Covid19 patient management, may accidentally become infected and a source of infection during the incubation phase or in case of asymptomatic infection. The objectives of this project are thus i) to assess SARS-Cov-2 spread over the hospital departments of Bamako by carrying out a systematic molecular screening of patients and caregivers, ii) to evaluate the feasibility of Point-Of-Care molecular assays in Mali and iii) to estimate the immunity acquired from SARS-Cov-2 among health workers through serological testing, allowing also the assessment of asymptomatic caregiver rate and absence of re-infection among the immunized caregivers. Finally, iv) variability of the virus over time and spread of different variants around the world will be studied by sequencing the viral genome.

Official Title
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Étude de l'épidémie de SARS-CoV-2 Dans Les Services Hospitaliers de Bamako, Mali

Conditions
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Covid19

Intervention / Treatment
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* Diagnostic Test: SARS-CoV-2 screening by molecular biology
* Diagnostic Test: Serological screening


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Free and informed consent accepted in writing Patient: patient hospitalized in one of the four hospitals of Bamako, with clinical signs of infection of the upper or lower respiratory tracts (sore throat, cough/sputum, nasal congestion and rhinorrhea, odynophagia, thoracic oppression, dyspnea, desaturation) with fever or feeling of fever or any other signs of SARS-Cov-2 infection (that is to say the following clinical manifestations, of sudden onset: unexplained asthenia, unexplained myalgia, headache without a known migraine disease, anosmia or hyposmia without associated rhinitis, dysgueusia, diarrhea, heart rhythm disorders, acute myocardial injury, severe thromboembolic event) or who have been in close contact with a SARS-CoV-2 infected person without effective protective measures (FFP2/surgical masks or physical separation) and defined as follows: having shared the same place of life as the confirmed case, for example: family, same room or having a direct contact in face to face with less than 1 meter from the confirmed case during a talk; intimate friends; class or office neighbours; adjacent to the index case in a plane or a train; or having provided or received hygiene or care acts from a confirmed case. Caregivers: caregivers of one of the four hospitals of Bamako Exclusion Criteria: Persons subject to legal protection or not able to give a free and informed consent. Caregivers: caregivers not able to follow the project schedule

Ages Eligible for Study
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Minimum Age: 18 Years

Sexes Eligible for Study
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All

Accepts Healthy Volunteers
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No

Study Plan
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How is the study designed?
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Design Details

Primary Purpose: Screening
Allocation: Non-Randomized
Intervention Model: Parallel Assignment
Interventional Model Description: Interventions Serological screening of caregivers at D0, M1, M2, M3. Screening of patients by molecular biology: a nasopharyngeal swab will be performed to symptomatic hospitalized patients or who have been in close contact with a SARS-CoV-2 infected person without effective protective measures to search for SARS-CoV-2 genome. Positive clinical isolates will be sequenced. Screening of caregivers by molecular biology: a nasopharyngeal swab will be performed to symptomatic caregivers or who have seroconverted to SARS-CoV-2 or who have been in close contact with a SARS-CoV-2 infected person without effective protective measures to search for SARS-CoV-2 genome. Positive clinical isolates will be sequenced.
Masking: None (Open Label)


Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Experimental: Patients<br>- Hospitalized patients in one of the four centers in Bamako, with clinical signs of infection of the upper or lower respiratory tracts with fever or feeling of fever or any other signs of SARS-Cov-2 infection or who have been in close contact with a SARS-CoV-2 infected person without effective protective measures | Diagnostic Test: SARS-CoV-2 screening by molecular biology<br>* SARS-CoV-2 RT-PCR in nasopharyngeal swab targeting 2 regions of the viral genome<br>|
| Experimental: Caregivers<br>Caregivers of one of the four centers in Bamako. Serological screening: all. Molecular screening: with clinical signs of infection of the upper or lower respiratory tracts with fever or feeling of fever or any other signs of SARS-Cov-2 infection or who have seroconverted to SARS-CoV-2 or who have been in close contact with a SARS-CoV-2 infected person without effective protective measures | Diagnostic Test: SARS-CoV-2 screening by molecular biology<br>* SARS-CoV-2 RT-PCR in nasopharyngeal swab targeting 2 regions of the viral genome<br>Diagnostic Test: Serological screening<br>* Serological screening of caregivers at D0, M1, M2, M3 (anti-nucleocapsid antibodies).<br>|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Incidence rate of positive SARS-Cov-2 RT-PCR in Bamako hospital departments during the study | Positive SARS-Cov-2 RT-PCRs are defined by the detection of SARS-Cov-2 genome after amplification using a test targeting 2 regions of the genome. | Through the completion of subject participation (up to 15 months after study start date). | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Number of Cepheid Xpert® Xpress SARS-Cov-2 cartridges available for 19.8 USD/number required for the project |  | Through the completion of subject participation (up to 15 months after study start date). | 
| Percentage of positive serological tests among the caregivers of the hospital departments of Bamako. |  | Assessed on the fourth serological assay performed (at Month 3). | 
| Percentage of caregivers asymptomatic but immunized to SARS-CoV-2 |  | Assessed on the fourth serological assay performed (at Month 3). | 
| Percentage of caregivers immunized and re-infected with SARS-CoV-2 |  | Through the completion of caregiver participation (up to 15 months after study start date). | 
| Number of SARS-CoV-2 mutations/variants detected during the study |  | Through the completion of subject participation (up to 15 months after study start date). | 
| Percentage of SARS-CoV-2 mutations/variants detected during the study |  | Through the completion of subject participation (up to 15 months after study start date). | 

 Terms related to the study
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Keywords Provided by Centre Hospitalier Valida
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Covid-19, SARS-CoV-2, Mali, Africa, Hospital