Kelch13 mutations in Africa

Summary

K13 (Pfk13) mutations in Africa are widespread but usually low-frequency and heterogeneous; a few validated or candidate artemisinin partial-resistance markers (notably R561H, A675V, P574L, P441L, P553L, C469Y) have been detected regionally with emerging focal increases and uncertain but concerning clinical impact. 

Enhanced genomic and phenotypic surveillance plus partner‑drug monitoring are the main public‑health responses described in the literature.

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Geographic distribution

The geographic pattern of Pfk13 variation in Africa is heterogeneous: most countries report low-frequency, diverse non-synonymous variants, while a small number of East African locales show higher frequencies of specific candidate or validated markers. Large systematic sequencing efforts across sub‑Saharan Africa found non-synonymous Pfk13 mutations in ~2.7% of isolates overall, with resistance‑linked alleles concentrated mainly in eastern Africa, and isolated detections elsewhere [1]. Regional genomic surveys in Zambia, Namibia, Tanzania/Zanzibar, Kenya, Ethiopia, Rwanda, Uganda and a few other countries report variable presence and focal clustering of particular K13 alleles, including pockets where candidate/validated markers reach measurable prevalence [4], [5], [6], [3], [2].

• West and central Africa: generally low overall prevalence of Pfk13 non‑synonymous variants and few WHO‑validated resistance alleles reported in large surveys [1], [9].

• East Africa and the Great Lakes: disproportionate detection of mutations linked to artemisinin partial resistance (for example R561H, P441L, C469Y, A675V, P574L), with some local increases documented in Rwanda, Tanzania, Uganda, Eritrea and neighbouring areas [2], [6], [4].

• Southern Africa and Zambia/Namibia: recent genomic screens identified candidate/validated markers at varied facility‑level prevalences (heterogeneous hotspots), including P441L and P574L and A675V in some districts [4], [5].

Mutations and resistance

The Pfk13 landscape in Africa is characterized by many distinct low‑frequency alleles; a minority match WHO‑validated or candidate resistance markers identified from Southeast Asia or shown to associate with delayed clearance in African settings [1], [2]. Key mutations reported in Africa include R561H, A675V, P574L, P553L, C469Y, P441L and occasional C580Y detections, with differing levels of evidence for association to artemisinin partial resistance.

Mutation	African locations reported	Evidence/status	Reference(s)
R561H	Rwanda, Tanzania, Uganda, parts of East Africa	Associated with delayed parasite clearance and clinical concern in Rwanda; considered an artemisinin partial‑resistance marker where expanding clonally in Rwanda [2], [6]	[2], [6]
A675V	Detected in Kenya and other East African sites	Reported as WHO‑listed/validated in some studies but generally low frequency; potential AR association in specific foci [3], [2]	[3], [2]
P574L	Seen in a few African countries at low frequency	Candidate/validated in some genomic surveys; low national prevalence but present in focal sites [4], [5]	[4], [5]
P553L	Rare detections in limited African reports	Observed at very low frequency; clinical relevance not broadly demonstrated in Africa [2]	[2]
C469Y / C469F	Detected in Rwanda, Uganda and parts of East Africa	Emerging in East Africa; some selection signals reported though full clinical validation pending [2], [7]	[2], [7]
P441L	Reported in Tanzania, Namibia and other surveys	Candidate marker with high local prevalence in some studies (e.g., Namibia) but clinical impact requires phenotyping/efficacy correlation [6], [5]	[6], [5]
C580Y	Very rare detections in Africa; dominant in Southeast Asia	When present in Africa it is uncommon and usually isolated; high‑frequency C580Y epidemics like SE Asia have not been reported continent‑wide [1], [2]	[1], [2]

Notes: WHO validation and clinical linkage vary by allele and location; many African Pfk13 variants remain of unknown significance and require phenotypic confirmation and in vivo efficacy correlation [1], [3].

Clinical implications

Documented clinical impact from K13 alleles in Africa remains limited but concerning where studied: the R561H allele showed an association with delayed parasite clearance and clonal expansion in Rwanda, constituting the clearest African example of a K13 mutation linked to a clinical artemisinin partial‑resistance phenotype [2]. In most surveyed African settings ACTs retain clinical efficacy despite low‑frequency K13 variation, and many detected non‑synonymous alleles have no demonstrated treatment failure linkage to date [3], [9], [4]. Several recent genomic surveillance studies report co‑occurrence of K13 variants with changes in partner‑drug susceptibility signals (for example decreasing lumefantrine susceptibility associated with other loci), raising the public‑health concern that combined resistance could undermine ACT effectiveness [7], [4].

• Treatment efficacy: Routine therapeutic efficacy studies cited in the literature generally report preserved ACT efficacy in the studied sites, but focal delayed clearance and phenotypic signals warrant vigilance [3], [2], [4].

• Partner‑drug interactions: Genomic analyses have identified selection at non‑K13 loci (e.g., PX1) and multidrug resistance markers that correlate with reduced susceptibility to lumefantrine and other partner drugs, potentially compounding any K13‑mediated artemisinin tolerance [7], [4].

• Clinical guidance evidence: Published African data call for local clinical efficacy studies and phenotypic assays to interpret molecular signals; routine K13 detection alone has limited immediate policy implications without correlated efficacy/phenotype data [1], [8], [3].

Where clinical treatment failures or delayed clearance have been reported in Africa, the literature points to targeted investigation and rapid sentinel monitoring rather than continent‑wide policy shifts solely on the basis of low‑frequency molecular findings [2], [4].

Surveillance and public health responses

Surveillance programs in Africa combine molecular genotyping, targeted amplicon sequencing, genomic surveillance and phenotypic assays; authors urge re‑establishing sentinel networks and integrating partner‑drug monitoring. Papers emphasize routine Pfk13 sequencing within national surveillance, the use of high‑throughput amplicon approaches and whole‑genome sequencing to detect focal increases, and deployment of improved phenotypic assays such as extended recovery/GRRA formats to link genotype to drug‑response phenotypes [8], [4], [5], [3].

• Current activities: National and multi‑country genomic surveys, facility‑level amplicon panels and cross‑sectional monitoring have been implemented in Zambia, Namibia, Kenya, Ethiopia, Tanzania, Rwanda and elsewhere to detect candidate/validated K13 alleles [4], [5], [3], [6].

• Phenotyping linkage: Extended Recovery Ring‑stage Survival Assays and the Growth, Resistance and Recovery Assay (GRRA) are recommended to validate molecular signals with in vitro resistance phenotypes and better correlate with clinical clearance half‑life [8].

• Public health recommendations in the literature: re‑establish sentinel therapeutic efficacy testing, perform routine K13 and partner‑drug marker surveillance, and investigate clusters of mutations with targeted clinical and in vitro follow‑up; several papers call for urgent, coordinated monitoring rather than immediate mass treatment policy changes [2], [1], [4].

• Gaps: Authors note uneven geographic sampling, variable genomic capacity, and the need to link molecular findings to therapeutic efficacy before changing national first‑line regimens [1], [3], [5].

Differences and trends

African K13 variation differs from Southeast Asia in that Africa shows many distinct low‑frequency alleles, limited continent‑wide high‑frequency sweeps, and multiple independent emergences rather than large, region‑wide clonal expansions seen historically in the Greater Mekong Subregion; however, focal clonal expansion (R561H in Rwanda) demonstrates Africa can also experience local selection events with clinical impact [1], [2]. Recent trend reports and 2023–2025 genomic surveys document rising detection of several candidate or validated markers in East Africa and heterogeneous but sometimes high facility‑level prevalences in Southern Africa (Zambia, Namibia) and Tanzania/Zanzibar, triggering concern about regional spread and co‑selection with partner‑drug resistance loci [6], [4], [5], [7].

• Key contrasts with SE Asia: SE Asia experienced high‑frequency validated K13 sweeps (e.g., C580Y) tied to marked treatment failures; Africa so far shows low‑frequency diversity with isolated validated/candidate markers and occasional local expansion events rather than continent‑wide sweeps [1], [2].

• Recent emerging concerns: expansion of R561H in Rwanda and detection of P441L, P574L, A675V in multiple East and Southern African surveys; concurrent signals of declining partner‑drug susceptibility (e.g., lumefantrine) in Uganda and elsewhere raise risks of multi‑drug compromise [2], [6], [7], [4].

• Public‑health implication: the combination of focal K13 increases plus partner‑drug selection pressures supports urgent scaling of integrated genomic‑phenotypic surveillance to detect and respond to actionable resistance patterns [2], [8], [4].

Treatment recommendations and evidence gaps

Published African studies and reviews call for strengthened surveillance and therapeutic efficacy testing, but they do not uniformly recommend continent‑wide changes to first‑line ACTs based solely on current molecular findings. While some localized investigations have prompted intensified monitoring, broad guideline changes require correlated clinical efficacy loss and phenotypic confirmation. The literature therefore emphasizes rapid detection, localized response (enhanced efficacy trials and containment), and partner‑drug monitoring rather than preemptive nationwide treatment switches [2], [1], [4], [3].

• Practical steps reported: enhanced surveillance, therapeutic efficacy studies, targeted phenotyping, and partner‑drug resistance monitoring are the recurring programmatic recommendations in the cited literature [2], [8], [4].

• Formal treatment policy: the reviewed studies do not present unified new national treatment recommendations; where authors discuss policy they advocate evidence‑based changes following demonstrated clinical failures and partner‑drug compromise rather than molecular detection alone [1], [3].

• If asked for immediate action: literature supports rapid local response (investigate clusters, expand sampling and efficacy testing) and reinforce case management and drug‑quality controls until robust evidence for treatment failure accumulates [2], [4].

References

[1] D. M. Mvumbi, "Spatial and molecular mapping of Pfkelch13 gene polymorphism in Africa in the era of emerging Plasmodium falciparum resistance to artemisinin: a systematic review," Lancet Infectious Diseases, 2020.

[2] A. M. Dondorp, J. Raman, R. W. Snow and P. Bejon, "A review of the frequencies of Plasmodium falciparum Kelch 13 artemisinin resistance mutations in Africa," 2021.

[3] D. Zhong, M. C. Lee, D. Yewhalaw et al., "Molecular surveillance of Kelch 13 polymorphisms in Plasmodium falciparum isolates from Kenya and Ethiopia," Malaria Journal, 2023. doi: 10.1186/s12936-023-04812-y

[4] A. Aranda‑Díaz, T. I. Makhanthisa et al., "Plasmodium falciparum Genomic Surveillance Reveals a Diversity of Kelch 13 Mutations in Zambia," Am. J. Trop. Med. Hyg., 2025. doi: 10.4269/ajtmh.25-0110

[5] E. Eloff, A. Aranda‑Díaz et al., "High Prevalence of Molecular Markers Associated with Artemisinin, Sulfadoxine, and Pyrimethamine Resistance in Northern Namibia," Am. J. Trop. Med. Hyg., 2025. doi: 10.4269/ajtmh.24-0870

[6] S. V. Connelly, M. Muller et al., "Artemisinin Partial Resistance Mutations in Zanzibar and Tanzania Suggest Regional Spread and African Origins, 2023," J. Infect. Dis., 2025. doi: 10.1093/infdis/jiaf431

[7] K. Niaré, E. Tafesse et al., "A novel locus associated with decreased susceptibility of Plasmodium falciparum to lumefantrine and dihydroartemisinin has emerged and spread in Uganda," bioRxiv, 2025. doi: 10.1101/2025.07.30.667738

[8] S. Sievert et al., "Measuring growth, resistance, and recovery after artemisinin treatment of Plasmodium falciparum in a single semi-high-throughput assay," Malaria Journal, 2025. doi: 10.1186/s12936-025-05481-9

[9] F. V. Ajogbasile, P. E. Oluniyi et al., "Molecular profiling of the artemisinin resistance Kelch 13 gene in Plasmodium falciparum from Nigeria," PLoS One, 2022. doi: 10.1371/journal.pone.0264548

September 08, 2025

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