Group | Genotyping

Malaria molecular surveillance (MMS) is increasingly being implemented in malaria endemic countries, and provides useful information complementing traditional epidemiological data. Indeed, using adequate and highly sensitive techniques for PCR correction, monitoring of drug and insecticide resistance markers, or histidine-rich protein 2 and 3 deletions are key for effective malaria interventions. In low transmission settings, the detection of asymptomatic carriers, and characterization of transmission chains are crucial for reactive case interventions aiming at malaria elimination.

Research: The genotyping group is developing and implementing molecular assays for malaria molecular surveillance. This include Next Generation Sequencing (NGS) assays for targeted amplicon deep sequencing (TADS) and whole genome sequencing (WGS). Current projects include investigation into alternative genotyping methods including microsatellites and amplicon sequencing, to improve our understanding of parasite populations dynamics and current methods to distinguish recrudescence from new infection, as well as identification of new molecular markers of drug resistance. We are working closely with National Malaria Control Programs (NMCPs) and research institutes in malaria endemic countries to implement those new assays in routine surveillance, and provide critical evidence for malaria monitoring, especially mitigation of antimalarial drug resistance. Together with other groups at Swiss TPH, we are supporting elimination efforts by using genomic and serological techniques to understand parasite reservoirs and guide the implementation of targeted elimination activities.

Services provision: Genotyping services are provided to drug developers performing regulatory clinical trials. Indeed our laboratory is ISO 17025:2017 accredited, and is increasingly implementing a GxP compliant quality management system. The services provided include: distinguishing recrudescence from new infection, identification of antimalarial drug resistance markers, quantitative PCRs for low parasite density and gametocyte detection and quantification.

SPREAD - Assessment of the Factors Affecting Emergence and Spread of Artemisinin Resistance in Rwanda

Artemisinin resistance has been reported and confirmed in Rwanda and other countries in East and Horn of Africa; calling for a thorough investigation to understand the factors affecting the emergence of resistance and spread in the African context. In this project, NMCP staff will be trained on molecular techniques and ex vivo assays, to better understand the factors affecting the emergence and spread of artemisinin resistance in Rwanda. This project is aiming at strengthening the capacity for antimalarial drug resistance surveillance in Rwanda, providing robust data to the national health authorities to monitor the spread of artemisinin and partner dug resistance. Read more

Genome-wide Analysis of Variations in Plasmodium falciparum Parasite Populations from Different Regions of Tanzania

The objective of the project is to develop a whole genome sequencing (WGS) assay based on long-reads with Oxford Nanopore technology (ONT - Minion), through exploring different DNA extraction and DNA enrichment methods prior to ONT sequencing. The study is aiming at identifying the ideal laboratory assay for sufficient DNA yield required for WGS, and optimizing the recommended method for generation of long-reads data. This project is part of a large consortium; the Molecular Surveillance of Malaria in Tanzania (MSMT) Project led by the National Institute of Medical Research (NIMR) in Tanzania. The assay developed will be transferred to NIMR laboratory in Tanzania. Through this study, new variants may be discovered, which could be used in surveillance and monitoring the emergence and spread of drug resistance and hrp2/3 gene deletions. Read more

Evaluation of the Community-based Malaria Surveillance and Response in Rwanda

Malaria incidence has considerably reduced in Rwanda in the last 5 years through combined malaria control interventions. Further decreasing and reducing transmissions to zero in our communities including high-risk or vulnerable populations is essential to achieving and sustaining malaria elimination. To achieve this, the research project proposes to (1) evaluate the impact of malaria control interventions in Rwanda over the last 5 years, (2) evaluate the contribution of integrated interventions approach through reactive Community-based Malaria Surveillance and Response in accelerating malaria elimination in Rwanda and (3) identify malaria infection characteristics and risk factors in Rwanda to inform tailored interventions. Read more

Bakari C et al. Trends of Plasmodium falciparum molecular markers associated with resistance to artemisinins and reduced susceptibility to lumefantrine in Mainland Tanzania from 2016 to 2021. Malar J. 2024;23:71. DOI: 10.1186/s12936-024-04896-0

Holzschuh A et al. Using a mobile nanopore sequencing lab for end-to-end genomic surveillance of Plasmodium falciparum: a feasibility study. PLOS Glob Public Health. 2024;4(2):e0002743. DOI: 10.1371/journal.pgph.0002743

Hosch S et al. PHARE: a bioinformatics pipeline for compositional profiling of multiclonal Plasmodium falciparum infections from long-read Nanopore sequencing data. J Antimicrob Chemother. 2024;79(5):987-996. DOI: 10.1093/jac/dkae060

Mwanga E.P et al. Reagent-free detection of Plasmodium falciparum malaria infections in field-collected mosquitoes using mid-infrared spectroscopy and machine learning. Sci Rep. 2024;14:12100. DOI: 10.1038/s41598-024-63082-z

Bechtold P et al. Development and evaluation of PlasmoPod: a cartridge-based nucleic acid amplification test for rapid malaria diagnosis and surveillance. PLOS Glob Public Health. 2023;3(9):e0001516. DOI: 10.1371/journal.pgph.0001516

Fakih B.S et al. Risk of imported malaria infections in Zanzibar: a cross-sectional study. Infect Dis Poverty. 2023;12:80. DOI: 10.1186/s40249-023-01129-5