title: Next generation sequencing to detect variation in the Plasmodium falciparum circumsporozoite protein.
abstract: The malaria vaccine RTS,S/AS01, based on immunogenic regions of the Plasmodium falciparum circumsporozoite protein (CSP), has partial efficacy against clinical malaria in African children. Understanding how sequence diversity in CSP T- and B-cell epitopes relates to naturally acquired and vaccine-induced immunity may be useful in efforts to improve the efficacy of CSP-based vaccines. However, limitations in sequencing technology have precluded thorough evaluation of diversity in the immunogenic regions of this protein. In this study, 454, a next generation sequencing technology, was evaluated as a method for assessing diversity in these regions. Portions of the circumsporozoite gene (cs) were sequenced both by 454 and Sanger sequencing from samples collected in a study in Bandiagara, Mali. 454 detected more single nucleotide polymorphisms and haplotypes in the T-cell epitopes than Sanger sequencing, and it was better able to resolve genetic diversity in samples with multiple infections; however, it failed to generate sequence for the B-cell epitopes.
authors.affiliation: Center for Vaccine Development, University of Maryland School of Medicine, Baltimore, Maryland 21201, USA. Kavita.Gandhi@som.umaryland.edu
authors.forename: Kavita
authors.initials: K
authors.lastname: Gandhi
authors.forename: Mahamadou A
authors.initials: MA
authors.lastname: Thera
authors.forename: Drissa
authors.initials: D
authors.lastname: Coulibaly
authors.forename: Karim
authors.initials: K
authors.lastname: Traoré
authors.forename: Ando B
authors.initials: AB
authors.lastname: Guindo
authors.forename: Ogobara K
authors.initials: OK
authors.lastname: Doumbo
authors.forename: Shannon
authors.initials: S
authors.lastname: Takala-Harrison
authors.forename: Christopher V
authors.initials: CV
authors.lastname: Plowe
mesh_terms: D000913:Antibodies, Protozoan / Q000235:genetics; D001483:Base Sequence; D016054:DNA, Protozoan / Q000235:genetics / Q000302:isolation & purification; D018985:Epitopes, B-Lymphocyte / Q000235:genetics / Q000276:immunology; D018984:Epitopes, T-Lymphocyte / Q000235:genetics / Q000276:immunology; D005787:Gene Frequency; D006239:Haplotypes; D017780:Malaria Vaccines / Q000235:genetics / Q000276:immunology; D016778:Malaria, Falciparum / Q000517:prevention & control; D008302:Mali; D008969:Molecular Sequence Data; D010963:Plasmodium falciparum / Q000235:genetics* / Q000276:immunology / Q000472:pathogenicity; D020641:Polymorphism, Single Nucleotide; D015800:Protozoan Proteins / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA
chemical_list: D000913:Antibodies, Protozoan; D016054:DNA, Protozoan; D018985:Epitopes, B-Lymphocyte; D018984:Epitopes, T-Lymphocyte; D017780:Malaria Vaccines; D015800:Protozoan Proteins; C041595:circumsporozoite protein, Protozoan