Variants of SARS-CoV-2 Causing COVID-19 in Africa

Study Overview
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Brief Summary
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The main objective of this research is to identify and characterize the different molecular variants of SARS-CoV-2, emerging and / or circulating in several countries of Sub-Saharan Africa (Burkina Faso, Côte d'Ivoire, Gabon, Mali, Chad and Republic of Congo) and determine their role in the evolution of the pandemic.

Detailed Description
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The main objective of this research is to identify and characterize the different molecular variants of SARS-CoV-2, emerging and / or circulating in several countries of Sub-Saharan Africa (Burkina Faso, Côte d'Ivoire, Gabon, Mali, Chad and Republic of Congo) and determine their role in the evolution of the pandemic. The research will combine retrospective and prospective approaches to determine the evolutionary dynamics of the virus since the start of the pandemic. It is planned to sequence the entire Spike protein gene for 1550 viruses and make 300 entire genomes. This work will be supplemented by antibody seroneutralization and respiratory transcriptomics tests, in order to estimate the immuno-virological response of the COVID-19 disease associated with the identified SARS-CoV-2 variants.

Official Title
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Variants of SARS-CoV-2 in Central and West Africa: Frequency of Circulating Viruses and Implications for the Management and Control of the Pandemic

Conditions
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COVID-19

Intervention / Treatment
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* Diagnostic Test: RT PCR


Participation Criteria
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Eligibility Criteria
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Inclusion Criteria: Major subject (cf. country) Presenting for a SARS-COV-2 diagnosis, whether symptomatic or not Not objecting to participating in the research Exclusion Criteria: NA

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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Accepts Healthy Volunteers

Study Plan
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How is the study designed?
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Arms and Interventions

| Participant Group/Arm | Intervention/Treatment |
| --- | --- |
| Retrospective<br>12000 participants positive for SARS-COV-2 | Diagnostic Test: RT PCR<br>* Characterize the different molecular variants of SARS-CoV-2, determine the escape potential of the new variants from neutralization by monoclonal antibodies and currently available vaccines and characterization of the mRNAs expressed in infected persons<br>* Other names: Respiratory transcriptomics;|
| Prospective<br>600 participants positive for SARS-COV-2 | Diagnostic Test: RT PCR<br>* Characterize the different molecular variants of SARS-CoV-2, determine the escape potential of the new variants from neutralization by monoclonal antibodies and currently available vaccines and characterization of the mRNAs expressed in infected persons<br>* Other names: Respiratory transcriptomics;|

What is the study measuring?
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Primary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Number of SARS-CoV-2 sequences generated partially and in whole genome | This outcome represent our main gaol and will include sequences that were partially generated in the Spike proteine and full genomes as well. Our current target is 1550 sequences. | Through study completion, an average of 1 year. | 

Secondary Outcome Measures

| Outcome Measure | Measure Description | Time Frame |
| --- | --- | --- |
| Number of individuals tested positive for COVID-19 | This outcome will be focused on the number of persons that will be tested positive for COVID-19 throughout the study, using SARS-CoV-2 rapid antigen tests. We planned to screen 12000 individuals overall in the six participating countries. | Up to six months | 
| Number of new SARS-CoV-2 variants identify | This outcome represents the number of new viruses that are identified at the end of the study and have not been reported previously. | Through study completion, an average of 1 year. |