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Updated: Feb 18, 2026
A Multi-detection Assay for Malaria Transmitting Mosquitoes
Published on: February 28, 2015
Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria
Anita Lerch1,2,3, Cristian Koepfli3,4, Natalie E Hofmann1,2
1Swiss Tropical and Public Health Institute, Basel, Switzerland.
Background:
Amplicon deep sequencing permits sensitive detection of minority clones and improves discriminatory power for genotyping multi-clone Plasmodium falciparum infections. New amplicon sequencing and data analysis protocols are needed for genotyping in epidemiological studies and drug efficacy trials of P. falciparum.
Methods:
Targeted sequencing of molecular marker csp and novel marker cpmp was conducted in duplicate on mixtures of parasite culture strains and 37 field samples. A protocol allowing to multiplex up to 384 samples in a single sequencing run was applied. Software "HaplotypR" was developed for data analysis.
Results:
Cpmp was highly diverse (He = 0.96) in contrast to csp (He = 0.57). Minority clones were robustly detected if their frequency was >1%. False haplotype calls owing to sequencing errors were observed below that threshold.
Conclusions:
To reliably detect haplotypes at very low frequencies, experiments are best performed in duplicate and should aim for coverage of >10'000 reads/amplicon. When compared to length polymorphic marker msp2, highly multiplexed amplicon sequencing displayed greater sensitivity in detecting minority clones.
