Genomic surveillance in Morocco tracks SARS-CoV-2 variant shift from Alpha to Omicron sublineage JN1

The persistent evolution of SARS-CoV-2 highlights the crucial role of genomic surveillance in tracking emerging variants and guiding public health interventions. We performed whole-genome sequencing on 235 SARS-CoV-2-positive samples collected across Morocco between 2021 and 2024 to characterize viral evolution and variant dynamics. Our analysis revealed a temporal shift in variant prevalence that paralleled global trends: initial co-circulation of Alpha and Delta variants, followed by complete replacement by Omicron and its sub-lineages in 2022. Phylogenetic reconstruction identified key mutations associated with enhanced immune evasion and transmissibility, demonstrating the virus's adaptive capacity. These findings underscore the critical importance of sustained genomic surveillance for monitoring viral evolution, informing vaccine and therapeutic strategies, and guiding public health responses. Our results advocate for expanded collaborative surveillance networks to proactively address threats from SARS-CoV-2 and other betacoronaviruses.