Authors

Discussion

Introduction

Sustained malaria control relies on accurate diagnosis and effective antimalarial treatment. However, the emergence and spread of Plasmodium falciparum parasites with Histidine-rich protein 2 and 3 (pfhrp2/pfhrp3) deletions, compromising HRP2-based rapid diagnostic tests (RDTs), and mutations such as ketch13 (pfk13) associated with resistance to artemisinin and partner drugs threaten recent gains. Fragmented surveillance systems and limited genomic capacity in endemic regions hinder timely detection and response. This body of work establishes and integrates molecular and genomic surveillance platforms across multiple transmission settings in Africa and Asia to investigate diagnostic and drug resistance dynamics.

Methods Cross-sectional and longitudinal studies were conducted in collaboration with national malaria control programmes and academic partners in Eritrea, Somalia, Yemen, Cameroon, Nigeria, and Indonesia. Dried blood spots and whole blood samples were collected from health facilities and community surveys. Molecular assays including qPCR were used to confirm infection and quantify parasitaemia as well as to detect pfhrp2 and pfhrp3 gene deletions. Amplicon deep sequencing using next-generation sequencing platforms were deployed to characterise mutations in pfk13 and key drug resistance loci including pfcrt, pfmdr1, pfdhfr, and pfdhps. Bioinformatic pipelines were developed to assess allele frequencies, haplotypes, and transmission patterns, alongside structured capacity strengthening and in-country training.

Findings Across diverse epidemiological contexts, from high transmission settings in West and Central Africa to lower transmission and elimination-focused regions in the Horn of Africa and Southeast Asia, this work identified heterogeneous patterns of diagnostic and therapeutic resistance markers. pfhrp2/3 deletions were detected in multiple settings, with implications for HRP2-based RDT performance. Variability in the prevalence and distribution of pfk13 mutations and partner drug resistance markers was observed, reflecting local selection pressures and drug use histories. In several regions, evolving resistance landscapes underscored the need for continuous molecular surveillance. Sustainable in-country genomic capacity was established or strengthened, enabling near real-time data generation and interpretation.

Interpretation