COVID-19 Genomic Surveillance in Bangui (Central African Republic) Reveals a Landscape of Circulating Variants Linked to Validated Antiviral Targets of SARS-CoV-2 Proteome.

Since its outbreak, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) spread rapidly, causing the Coronavirus Disease 19 (COVID-19) pandemic. Even with the vaccines' administration, the virus continued to circulate due to inequal access to prevention and therapeutic measures in African countries. Information about COVID-19 in Africa has been limited and contradictory, and thus regional studies are important. On this premise, we conducted a genomic surveillance study about COVID-19 lineages circulating in Bangui, Central African Republic (CAR). We collected 2687 nasopharyngeal samples at four checkpoints in Bangui from 2 to 22 July 2021. Fifty-three samples tested positive for SARS-CoV-2, and viral genomes were sequenced to look for the presence of different viral strains. We performed phylogenetic analysis and described the lineage landscape of SARS-CoV-2 circulating in the CAR along 15 months of pandemics and in Africa during the study period, finding the Delta variant as the predominant Variant of Concern (VoC). The deduced aminoacidic sequences of structural and non-structural genes were determined and compared to reference and reported isolates from Africa. Despite the limited number of positive samples obtained, this study provides valuable information about COVID-19 evolution at the regional level and allows for a better understanding of SARS-CoV-2 circulation in the CAR.

Five successive waves of SARS-CoV-2 infection in the Central African Republic: a prospective observational study from 2020-2022.

Introduction: the National Laboratory of Clinical Biology and Public Health (NLBPH) in Bangui in the Central African Republic (CAR) carries out the vast majority of molecular screening tests for SARS-CoV-2 infection nationwide. This study aimed to show the contribution of molecular diagnosis and genomic surveillance in monitoring the evolution of longitudinal variations of the SARS-CoV-2 infection epidemic in CAR between 2020 and the end of 2022. Methods: this is an observational study on the variations in the prevalence of detection of SARS-CoV-2 by RT-PCR at the NLCBPH from nasopharyngeal samples taken prospectively over a period of 3 years since the beginning of the COVID-19 epidemic. A subgroup of SARS-CoV-2 positive samples was selected for molecular sequencing performed by Illumina® and MinIon® at the National Institute for Biomedical Research in Kinshasa, Democratic Republic of the Congo. Results: from March 2020 to December 31th, 2022, 88,442 RT-PCR tests were carried out (4/5 of the country) and detected 9,156 cases of SARS-CoV-2 infection in 5 successive waves. The average age of the patients was 39.8 years (extremes ranging from to 92 years). Age(P=0.001), sex(P=0.001) and symptom presentation(P=0.001) were significantly associated with RT-PCR test positivity. Among the different variants identified during successive waves, the Omicron variant predominated during the last two waves. Conclusion: this prospective study over a period of 3 years, marked by 5 successive waves, made it possible to report that age, sex and the presence of clinical symptoms are associated with RT-PCR positivity. Among the different variants identified during successive waves, the Omicron variant predominated during the last two waves.