Genomic characterization of SARS-CoV-2 variants circulating in the population of Bangui, Central African Republic (CAR) in 2022.

Introduction : With the ongoing global resurgence of COVID-19, it is crucial to better understand past transmission dynamics to strengthen national preparedness for future surges. Since its emergence in Wuhan, China, in December 2019, SARS-CoV-2 has caused multiple waves of infection worldwide. The World Health Organization (WHO) has identified several variants of concern, including Alpha, Beta, Gamma, and Delta. At the end of 2021, the Omicron variant emerged in South Africa and rapidly spread across the globe. While many studies have explored the evolution and transmission of these variants, data from the Central African Republic remain limited. This study aimed to identify and characterize the SARS-CoV-2 variants circulating in Bangui to provide critical insights for healthcare professionals and support rapid, effective surveillance in anticipation of future COVID-19 waves. Methodology : We conducted a retrospective, descriptive study in Bangui, CAR, from January to August 2022. A total of 102 nasopharyngeal samples positive for SARS-CoV-2 (Ct ≤ 30), selected from the biobank of the Pasteur Institute in Bangui, were reanalyzed using multiplex qPCR to confirm their Ct. These eligible samples were then sequenced using the MinIon MK1C nanopore platform at the Pasteur Institute Paris (CIBU). Genomic sequences were obtained and analyzed using bioinformatics to obtain complete genomes. The different variants were described using the Nexstrain web application. Results : The results revealed that 68 genomes out of the 102 sequenced samples, or 67%, had complete genomic coverage (80-99%), all belonging to the Omicron variant. Four sub-lineages were identified according to the Pangolin classification: BA.1 (14.7%), BA.2 (35.3%), BA.4.1 (4.4%), and BA.5.1 (45.6%). These variants were present in all eight districts, with a predominance in the eighth district, and were most frequently diagnosed in June (fourth wave of the epidemic). Conclusion : This study highlights the circulation of a single SARS-CoV-2 variant in the Central African Republic, namely Omicron, with a diversity of sub-lineages. It is crucial to establish continuous surveillance of SARS-CoV-2 to detect any emerging variants in real time, while strengthening sequencing capabilities at the national level. This is essential for better surveillance of potential SARS-CoV-2 epidemics.