Plasmodium Falciparum Haplotype Diversity Prior to Malaria Vaccine Rollout

35% of 100 collected P. falciparum samples were successfully genotyped for the circumsporozoite protein gene, revealing 22 distinct haplotypes. Innocent M. Ali published this dataset in 2026, providing a molecular baseline from the Kaelé Health District, Cameroon, for 2022–2023.

Use Cases

• Analyze haplotype diversity metrics like heterozygosity (He) and nucleotide diversity (π) for the csp gene to assess pre-vaccine genetic variation.
• Correlate the presence of the vaccine-matched csp haplotype (found in 20% of genotyped infections) with future vaccine effectiveness studies.
• Compare genotyping success rates and within-participant haplotype counts across the four targeted genes (csp, ama1, sera2, trap).
• Investigate signs of balancing selection in the csp gene's T cell epitopes (TH2 and TH3) using provided statistics like Tajima's D.
• Use the baseline ama1 and sera2 haplotype data to monitor post-vaccine antigenic shifts and strain replacement.

Strengths

• Provides a precise pre-vaccine baseline with 100 P. falciparum samples collected over a defined 2-year period (2022–2023).
• Reports specific diversity metrics for four genes, including heterozygosity (He=0.908) and nucleotide diversity (π=0.021) for csp.
• Identifies 22 distinct csp haplotypes and quantifies the vaccine-matched strain frequency at 20%.

Limitations

• Small sample size with only 100 collected dried blood spots and a low genotyping success rate of 35% for the primary csp gene.
• Geographic scope is limited to a single health district (Kaelé) in Cameroon, limiting generalizability.
• Dataset is tiny (25.8 KB), indicating it contains summary statistics and likely not the raw sequencing data.

Provenance

Source

Innocent M. Ali via figshare.

Collection Method

Genetic analysis of 100 P. falciparum-positive dried blood spots using the 4CAST amplicon sequencing assay and SeekDeep for haplotype identification.

Time Range

2022–2023

Freshness

Data covers 2022–2023 and was last updated on the platform in April 2026.

Geography

Mapoussere, Kaelé Health District, Cameroon.