Objectives: In this study, we assessed the genetic variation in CSP sequences from Kalifabougou, Mali, by evaluating the diversity of haplotypes in the N- and C- Terminal region, the repeat regions, and the T- and B-cell epitopes.

Methods: Sequences used for the study were generated from 59 sequences collected during a malaria transmission season conducted in Kalifabougou, Mali. Generated using the PacBio SMRT platform.

Results: Results showed that the central repeat and C-terminal Th2R/Th3R epitope regions were highly polymorphic in this study, whereas the N-terminal non-repeat region was less variable. Furthermore findings highlighted CSP polymorphism and suggested that the repeat and B-cell epitope of our samples is similar to those of 7G8 PfCSP, whereas the C-terminal is similar to that of the 3D7 PfCSP strain. Finally, findings the CSP sequences from the Kalifabougou site are more similar to those from Navrongo than to those from Cape Coast.