Caractérisation moléculaire et phylogénétique des séquences génomiques du Coronavirus du syndrome respiratoire aigu sévère 2 : Diversité, profil des mutations associés au tableau clinique et réseau de transmission de la COVID-19 au Burkina Faso

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19). It is an emerging and progressive infection whose first cases were reported in December 2019 in Wuhan, China. SARSCoV-2 is the cause of numerous transmissions and thousands of deaths around the world, including Burkina Faso. The SARS-CoV-2 genome is 29,903 base pairs in size. It includes: a polyprotein called orf1ab (open Reading frame or cadre reading) which covers 2/3 of the viral genome (21290 nt) orientation 5 'and also 4 genes which code for structural proteins. Structural proteins cover 1/3 of the genome, 3 'orientation and include: 1) surface proteins (S), 2) envelope proteins (E), 3) membrane proteins (M) and 4 ) the proteins of the nucleocapsid (N) (29). The SARS-CoV-2 genome also contains 6 accessory proteins which are encoded by the genes ORF3a, ORF6, ORF7a, ORF7b, ORF8 and ORF10. Each of these structural and accessory proteins of SARS-CoV-2 play a specific role in the pathophysiology and pathogenesis of COVID-19. Protein S, for example, is responsible for binding the virus to membrane receptors and to entry into the host cell. The M, E and N proteins are constituents of the nucleocapsid of viral particles. Like any coronavirus, the S and N genes of SARSCoV-2 are constantly mutating (positive selection). These mutations and adaptations could affect the stability and pathogenicity / transmissibility of SARS-CoV-2. For example, mutations in the S or spike gene can alter viral pathogenicity or its increased affinity with the angiotensin converting enzyme receptor (ACE2). More recently, mutations in the S gene are the origin of many so-called British (20I / 501Y.V1, VOC 202012/01, or B.1.1.7), South African (20H / 501Y.V2 or B. 1.351), Brazilian (P.1)). These variants are highly infectious and transmissible and could escape many vaccines developed or in development. Protein S, for example, is the target of vaccines from Pfizer / BioNTech and Moderna. They may also affect the effectiveness of diagnostic tests and the establishment of effective treatments for COVID-19. To do this, genomic monitoring of mutations and variants of SARS-CoV-2 will make it possible to identify which ones are likely to lead to vaccine, therapeutic or diagnostic test failures. It will make it possible to adapt response strategies against COVID-19 and the identification of foci of transmission of the disease through phylogenetic analyzes combining socio-demographic and clinical data in Burkina Faso, in the West African sub-region. and in the world Expected Outputs 1.The genetic diversity or variants of circulating SARS-CoV-2 in patients infected with COVID-19 in Burkina Faso and their clinical meanings are determined. 2. The profile of the genetic mutations of the sequences of the SARS-CoV-2 genome according to the course of the disease in patients infected with COVID-19 in Burkina Faso is determined. 3. COVID-19 transmission networks and risk factors associated with its spread among infected individuals in Burkina Faso are identified