Resolving the evolutionary origins of artemisinin resistance in african p. Falciparum malaria using long-read sequencing - proposal summary malaria remains a critical global health challenge,…

The National Institute of Allergy and Infectious Diseases awarded Brown University $100,228 on February 17, 2027, to support pre-doctoral research training under the Allergy and Infectious Diseases Research program (CFDA 93.855).

The award funds development and application of long-read sequencing technologies to resolve the evolutionary origins and dissemination of artemisinin resistance in African Plasmodium falciparum malaria. The fellow will develop a validated multiplex long-range PCR and Nanopore sequencing assay to resolve 15-kilobase haplotypes across the short tandem repeat-rich sequence flanking the Kelch13 locus, determining whether multiple observed haplotypes carrying the same Kelch13 mutation arose from a single rare event obscured by gene conversion or multiple independent origins. The fellow will also develop and apply a high-throughput Nanopore panel targeting haplotype-tagging variation utilizing Bayesian deconvolution to resolve regional resistance patterns. This work addresses whether artemisinin resistance in Northeast Africa is driven by ubiquitous independent de novo events or by rare, high-fitness lineages; if the latter, geographically focused containment remains viable public health strategy.

Place of performance is Providence, Rhode Island. The period of performance runs through August 31, 2028.

Resolving the evolutionary origins of artemisinin resistance in african p. Falciparum malaria using long-read sequencing - proposal summary malaria remains a critical global health challenge, causing an estimated 610,000 deaths annually, primarily in sub-saharan africa. The emergence of plasmodium falciparum partial resistance to artemisinin (art-r) threatens to undermine frontline artemisinin-based combination therapies (acts). This resistance is conferred by mutations in the KELCH13 (K13) gene which are spreading rapidly across northeast africa. Current genomic models suggest these mutations arose through ubiquitous, independent DE novo events, implying that containment is futile. However, these models rely on short-read sequencing, which fails to resolve the hyper- variable, at-rich intergenic regions flanking K13. Consequently, current data cannot distinguish between independent emergence and the alternative hypothesis proposed here: that key mutations arose from rare events followed by rapid local haplotype diversification via mechanisms such as gene conversion. Distinguishing these models is urgent; if resistance is driven by rare, high-fitness lineages, geographically focused containment remains a viable public health strategy. This project aims to support the training of a pre-doctoral fellow in developing and applying novel long- read sequencing technologies to resolve the evolutionary origins and dissemination of art-r. In aim 1, the applicant will develop a validated multiplex long-range PCR and nanopore sequencing assay. This tool will resolve 15KB haplotypes across the STR-rich sequence flanking the K13 locus to definitively determine if multiple observed haplotypes carrying the same K13 mutation arose from a single rare event obscured by gene conversion or multiple independent origins. In aim 2, the applicant will develop and apply a high-throughput nanopore panel targeting haplotype tagging variation (HTV) utilizing bayesian deconvolution to resolve relative proportions of lineage-defining markers to current and ongoing sample collections as well as a longitudinal archive of malaria field samples from uganda, rwanda, ethiopia, tanzania, and the democratic republic of congo. By integrating this genomic data with phylodynamic modeling, the project will track the spatiotemporal spread of specific high-fitness lineages and quantify their expansion advantage. This research aligns with public health efforts to preserve act efficacy by delivering a scalable surveillance framework and critical data to distinguish between containment policies. Furthermore, the fellowship will support the candidate's cross-disciplinary training at the intersection of wet-lab genomics, bioinformatics, and evolutionary modeling. This unique combination of skills will prepare the trainee for a promising career as an independent investigator capable of leveraging advanced genomic approaches to inform infectious disease control.