Contribution of genomic surveillance to the detection and monitoring of SARS-CoV-2 variants during the 6 pandemic waves in the Central African Republic from 2020 to 2023

Abstract

Abstract Objective: The COVID-19 pandemic has highlighted the need to strengthen diagnostic and genomic surveillance capacities. The Central African Republic was able to manage 5 waves of disease during health monitoring and integrated genomic surveillance as a surveillance tool in 2021. The aim of this study was to report surveillance data from the National Laboratory of Clinical Biology and Public Health and describe the landscape of circulation of SARS-CoV-2 variants. Materials and methods: This retrospective, descriptive observational study over a period of 3 years (ranging from April 2020 to November 2023) was carried out on a population of consenting volunteers from throughout the CAR and tested by RT‒PCR on nasopharyngeal samples with sufficient information in the LNBCSP database. Sequencing is largely carried out at the INRB in KINSHASA and from May 2023 at the LNBCSP. Results and discussion: Out of 97,864 RT‒PCR tests carried out, 9,764 were positive, which corresponds to a prevalence of 9.98%. The average age of the patients was 39.97 ± 13.76 years, and the sex ratio (M/F) was 2.12. RT‒PCR positivity was significantly associated with age (p=0.001), sex (p=0.013) and clinical manifestations. Ten variants circulated during the 5 waves recorded. The landscape of circulating variants was dominated by the Omicron (B.1.1.529) and Delta (B.1.617.2) variants and especially by B.1.620 and B.640, which marked the second wave in CAR-T cells. Conclusion: This retrospective series provides key information for understanding the history of the COVID-19 pandemic in the CAR. Risk factors were identified, and the variant circulation landscape was described. Strengthening national genomic surveillance capacities would help the country adopt a better response against this pandemic.