PHARE

PHARE identifies and profiles Plasmodium falciparum haplotypes carrying resistance mutations within polyclonal infections using Oxford Nanopore Technologies MinION long-read sequencing for compositional profiling.

Key Features:

• Haplotype identification: Identifies and characterizes haplotypes carrying resistance mutations within polyclonal P. falciparum samples.
• Long-read sequencing (MinION): Developed for data generated by Oxford Nanopore Technologies MinION long-read sequencing.
• Integration of tools and scripts: Combines established bioinformatics tools with bespoke Python scripts for computational analysis.
• High recall and accuracy: Demonstrated high recall and accuracy across control datasets, including mixtures of four laboratory strains at varying ratios.
• Versatility across genes: Applicable to any gene and validated with amplicons of pfdhps, pfdhfr, and pfK13.
• Clinical validation: Validated on clinical samples from children in the Central African Republic.

Scientific Applications:

• Detection and tracking of drug-resistant clones: Enables detection and tracking of drug-resistant P. falciparum clones within multiclonal infections in endemic areas.
• Informing treatment recommendations: Provides haplotype-level resistance profiles that can inform treatment decision-making.
• Surveillance of multiclonal infections: Supports surveillance and monitoring of resistance allele frequencies and compositional changes in clinical and field samples.

Methodology:

Sequencing was performed using Oxford Nanopore Technologies MinION long-read sequencing followed by computational analysis that combines established bioinformatics tools and bespoke Python scripts to identify and compositionally profile multiple parasite clones and their resistance haplotypes.