Abstract
<title>Abstract</title> <p> <bold>Background</bold> In South Sudan, Artesunate-amodiaquine (ASAQ) is the first-line regimen, and Artemether-Lumefantrine (AL) is the second-line regimen for treating uncomplicated Plasmodium falciparum malaria. However, no therapeutic efficacy study (TES) has been conducted in South Sudan since the introduction of ASAQ and AL. Our TES aimed to assess the efficacy of ASAQ and AL across four sites in South Sudan. <bold>Methods</bold> This study was conducted in Juba, Bor, Wau, and Yambio. Children aged 6 months to 59 months with microscopically confirmed uncomplicated P. falciparum monoinfection were assigned to ASAQ (at all sites except Yambio) or AL (at Juba and Yambio) and followed for 28 days to assess treatment response. The primary endpoint was the Kaplan-Meier PCR-corrected adequate clinical and parasitological response (ACPR) on Day 28. Day 3 parasite positivity was used as a measure of early treatment response. Dried blood spots were collected to distinguish recrudescence from new infections. All enrolled participants who received treatment were included in the primary outcome analysis. <bold>Results</bold> Between 3 <sup>rd</sup> January 2024 and 29 <sup>th</sup> January 2025, 390 children were enrolled across all arms, of whom 40 (10.3%) were lost to follow-up, and 350 (89.7%) were included in the per-protocol analysis. Kaplan-Meier uncorrected ACPR was 96.5% (95% CI: 92.6 – 100.0) in Juba-AL, 95.6% (95% CI: 90.8 – 100.0) in Juba-ASAQ, 97.7% (95% CI: 94.6 – 100.0) in Bor, 100.0% (95% CI: 100.0 – 100.0) in Wau, and 93.0% (95% CI: 87.8 – 98.6) in Yambio. Kaplan-Meier PCR-corrected ACPR exceeded 90% in all arms: Juba-AL 98.9% (95% CI: 96.6 – 100.0), Juba-ASAQ 100.0% (95% CI: 100.0 – 100.0), Bor 100.0% (95% CI: 100.0 – 100.0), Wau 100.0% (95% CI: 100.0 – 100.0), and Yambio 98.9% (95% CI: 96.8 – 100.0). Day 3 parasite positivity was notably elevated at Bor (13.8%), exceeding the WHO 10% threshold used as an indicator of suspected artemisinin partial resistance. <bold>Conclusions</bold> ASAQ and AL remain highly efficacious against uncomplicated P. falciparum malaria in South Sudan, supporting the continuation of the current treatment policy. The high Day 3 positivity rate at Bor warrants enhanced molecular surveillance and repeat efficacy monitoring. This study establishes a baseline for systematic national TES surveillance. </p>