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

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 remained limited. This study aimed to identify and characterize SARS-CoV-2 variants circulating in Bangui to support genomic surveillance and COVID-19 prevention strategies. Characterizing circulating variants provides essential information for the early detection of emerging lineages, the anticipation of potential epidemic waves, and the adaptation of public health strategies. We conducted a retrospective, descriptive study in Bangui, Central African Republic (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 values. Eligible samples were then sequenced using the MinION MK1C (Oxford Nanopore Technologies) platform, following the ARTIC Network protocol at the Institut Pasteur, Paris (CIBU). Bioinformatics processing using reads mapping to a reference genome, followed by consensus sequence generation, included standard steps of basecalling, demultiplexing, quality filtering, genome alignment, primer trimming, consensus generation, and variant calling. The different variants were described using the Nexstrain web application. The results revealed that 66.7% of sequenced genomes (n = 68) had high coverage ≥ 80%, 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 sub-lineages 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). Omicron was the only variant detected among successfully sequenced samples, although limited sampling and sequencing success restrict broader generalisation. 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. Continuous genomic surveillance is crucial to anticipate potential future COVID-19 waves and to enable timely public health responses.