BackgroundA multicomponent vaccine is increasingly recognized as a necessary tool to control and eliminate malaria globally. However, genetic diversity in Plasmodium falciparum poses a significant challenge, particularly for blood-stage antigens associated with protective immunity. Individuals in endemic regions acquire clinical immunity without exposure to all antigenic variants, suggesting that a deeper understanding of antigen diversity could inform more effective vaccine strategies.MethodsThe genetic diversity of the polymorphic gene locus for merozoite surface protein 2 was assessed with nested PCR and capillary electrophoresis fragment sizing in P. falciparum isolates from 34 countries across Sub-Saharan Africa. High fidelity long-read sequencing was used to investigate sequence diversity within msp2 variants.ResultsWe successfully genotyped msp2 from 2761 P. falciparum-positive samples using capillary electrophoresis, identifying 412 distinct msp2 size variants. Several msp2 size variants were consistently overrepresented across geographical regions, transmission intensities, and time points. These variants comprised multiple unique sequences, of which several were geographically and temporally widespread. Nucleotide and amino acid sequences showed high diversity without geographical clustering.ConclusionsThis study provides a comprehensive assessment of msp2 diversity across Sub-Saharan Africa. The widespread prevalence of certain variants of this highly polymorphic antigen suggests possible structural constraints or selective advantages for the parasite. Maintenance of specific gene lengths and sequences across diverse settings highlights their potential as targets for next-generation, multicomponent malaria vaccines.