USING NEXT-GENERATION SEQUENCING (NGS) TO PREDICT AND MONITOR THE EVOLUTION OF SARS-COV-2 VARIANTS IN BENIN

The purposes of this investigation were identifying, describing and characterizing SARS-CoV-2 variants circulating in Benin (Delta, Omicron, Beta and B.1.640), using next generation sequencing NGS. The phylogenetic tree show evidence of rapid expansion of Delta variant compared and apart from its introductions and prevalence, pointed out comprehensively some specific mutations, such as L452R and T478K that promote infectivity and immune escape. Vaccinated participants showed significantly higher levels of neutralizing antibodies compared to those who were unvaccinated, regardless of the variant causing the infection. However, individuals infected with the Delta variant and those who tested PCR-negative appeared to have lower protection levels compared to those infected with Omicron, Beta, and B.1.640. Our results highlight the critical role of combining genomic surveillance with immunological assessments to gain a deeper understanding of variant evolution, immune responses, and their impact on public health strategies. This study provides essential tools to guide vaccine selection, develop effective immunization strategies, and improve epidemic control measures. Moving forward, we plan to analyze a larger sample size to create a more precise genetic map of SARS-CoV-2. This will further enhance genomic surveillance efforts, particularly in resource-limited settings, and contribute to regional and global pandemic preparedness.