Convergent evolution of artemisinin and chloroquine resistance in Ethiopian Plasmodium falciparum parasites

The emergence of antimalarial drug resistance has threatened the control and elimination of malaria in Africa. Ethiopia, once a success story in case reduction, is now facing resurgence. This study examined the key drug resistance genes (Pfmdr1, Pfcrt, Pfk13, Pfdhfr, and Pfdhps) and mitochondrial genomes of 605 Plasmodium falciparum isolates from 15 districts across Ethiopia, varying in transmission intensity and P. vivax co-endemicity. A dominant PfMDR1 NFSND haplotype, associated with reduced lumefantrine susceptibility, was identified alongside near-fixation of the PfCRT CVIET chloroquine-resistant haplotype in specific areas. Concerningly, PfK13 variants associated with partial artemisinin resistance – R622I (10%), A675V (1.7%), and P441L (1.1%) – were expanding. Drug resistance markers were primarily found in settings with low transmission of P. falciparum and high levels of P. vivax coendemicity. Along with a distinct parasite lineage and limited gene flow, these findings suggest ..., Surveillance sites and sample collection
Fifteen sites across Ethiopia's administrative districts were selected for genomic surveillance of antimalarial resistance (Fig. 1A). Site selection prioritized settings that reported malaria outbreaks [31,68,69], markers of drug-resistant parasites [34],high pfhrp2/3 deletion rates [34], representation of the transmission strata of the country (ranging from low and unstable to high, Fig. 1B), varying P. vivax co-endemicity with P. falciparum (Fig. 1C), and areas prone to importation of parasites from neighboring countries.
A total of 605 blood samples were collected from symptomatic P. falciparum between October 2019 and January 2023. Finger-prick blood samples (0.5 mL) collected in EDTA microtainer tubes were used for malaria diagnosis by microscopy and to prepare dried blood spots (DBS) on Whatman 3MM filter paper.
Ethical Consideration
The study protocol was approved by the Armauer Hansen Research Institute and ALERT Hospital E..., # Convergent evolution of artemisinin and chloroquine resistance in Ethiopian Plasmodium falciparum parasites

We have submitted our raw sequence data (available at ENA, see section 7), a detailed laboratory Drug resistance Tagets genes amplification protocol (**Supplementary_Information.doc**), extended data figures (**Extended_Data.doc**), and a comprehensive data file (**Supplementary_Tables.xlsx**) containing all prevalence data, statistical analyses, and sample metadata. Custom R and Python scripts used for the analyses are available on GitHub (see section 6).

# Dataset for: Genomic Surveillance of Antimalarial Drug Resistance in Ethiopian Plasmodium falciparum

## 1. General Information

This dataset provides comprehensive genetic data on antimalarial drug resistance in Plasmodium falciparum, the deadliest malaria parasite. The data were generated from targeted deep-amplicon sequencing of 605 P. falciparum samples collected from 15 geographically diverse districts in Ethiopia bet..., Written informed consent was obtained from all study participants and their parents or guardians before recruitment. All personally identifiable information was removed in the dataset.