Evidence of artemisinin partial resistance in northwestern Tanzania: clinical and molecular markers of resistance

High Prevalence of Artemisinin-Resistant Plasmodium falciparum, Southeastern Sudan

We conducted a hospital-based cross-sectional study of Plasmodium falciparum in 2017 in southeastern Sudan. Among 257 P. falciparum samples, we found 22% harbored the pfkelch13 R622I mutation and 10.7% showed hrp2/3 gene deletions. Our findings highlight the urgent need for enhanced surveillance of drug- and diagnostic-resistant parasites in the Horn of Africa.

Assessment of the in vitro activity and selectivity of Artemisia afra and Artemisia annua aqueous extracts against artemisinin-resistant Plasmodium falciparum

BACKGROUND

The recent emergence of artemisinin resistance in Africa is drawing scrutiny toward the use of alternative anti-malarial therapy based on Artemisia annua and Artemisia afra phytotherapies. This study aimed to determine if either A. annua and A. afra extracts are active against artemisinin-resistant Plasmodium falciparum isolates and determine the selectivity of inhibitory phytotherapies.

METHODS

Artemisia extracts were tested in vitro to mimic parasites exposure to extracts in population drinking Artemisia sp. teas. Artemisia extracts were tested in Ring Stage Survival Assays (RSA0-3 h) against Cambodian clinical isolates previously genetically and phenotypically characterized as artemisinin resistant or sensitive. Primary human hepatocytes and a human hepatoblastoma cell line (HepG2 cells) were used to assess the cytotoxicity of Artemisia extracts.

RESULTS

The study revealed a substantially decreased in vitro activity of A. annua extracts when tested on artemisinin-resistant parasites mutated in the Pfkelch13 gene (RSA50 0.137-2.56 g.L-1) compared to artemisinin-sensitive parasites (RSA50 0.080 g.L-1). Conversely, the A. afra extracts have a similar activity on the isolates tested whether they are sensitive or resistant to artemisinin (RSA50 0.537-0.758 g.L-1) However, the selectivity index for A. afra extracts was much lower than for A. annua extracts (A. afra: 4.628, 4.305 and 6.076 vs A. annua: 387.625, 226.350 and 12.099, respectively for WT, C580Y and R539T).

CONCLUSIONS

Artemisia annua activity is driven by artemisinin, implicating the same resistance profiles and concerns associated with semisynthetic artemisinin derivatives. Artemisia afra showed artemisinin-independent antiplasmodial activity. However, the molecular basis of this activity is unknown and may not present a sufficient selectivity, thus further characterization of A. afra is essential.

Novel Plasmodium falciparum Kelch13 polymorphisms in Cameroon with structural and physicochemical impact

The recent emergence of Plasmodium falciparum (Pf) parasites resistant to artemisinin-based combination therapies (ACT) in Africa has outlined the need for continuous molecular surveillance of artemisinin partial resistance. Here, the genetic polymorphism in the Kelch 13 gene (pfk13) and its structural impact were analyzed. PfDNA was extracted from dried blood spots of symptomatic and asymptomatic individuals living in different epidemiological facets of Cameroon. The pfk13 gene was amplified by nested polymerase chain reaction, and amplicons were sequenced to detect single nucleotide polymorphisms (SNPs). The evolutionary history and the impact of the polymorphisms on physicochemical properties, structure, and function of the pfK13 protein were appraised using various in silico models. A total of ten SNPs were identified in this study, of which five non-synonymous SNPs have not been previously reported (L647F, D648V, N657S, K658R, and L663P). The genetic diversity of pfk13 sequences was low, and the pfk13 gene evolved under the neutral model. Some mutations, especially L663P, appeared to affect the function and structure of the pfK13 protein. Analysis of the physicochemical properties of the Cameroonian pfK13 protein sequences revealed slight changes in the solvent-accessible surface area, isoelectric point, and hydrophobicity. The results support the ongoing use of ACTs in the study areas, given the absence of validated SNPs associated with artemisinin partial resistance. Computational findings suggest a possible deleterious effect of some novel SNPs on the pfK13 structure and/or function.

Development of Next-Generation Antimalarial Acridones with Radical Cure Potential

Building from our previous lead compound T111 (1) possessing activity against both Plasmodium falciparum asexual blood-stage (ABS) and Plasmodium berghei liver-stage (LS) parasites, next-generation antimalarial acridones were systematically designed and synthesized. A large number of newly generated acridones displayed excellent antimalarial activities against both ABS and LS parasites, with feasible safety and metabolic profiles. In a high-throughput hypnozoitocidal assay using Plasmodium cynomolgi, a number of these acridones significantly inhibited schizont and hypnozoite formation in both prophylactic and radical cure-dosing modes. Notably, newer generation acridones substantially mitigated cross-resistance with atovaquone. Representative compound 28 (T229) provided full LS protection and a sustained blood-stage cure for murine P. berghei infection dosed at both 10 and 40 mg/kg/day orally. Furthermore, compound 28 demonstrated a low risk of both genotoxicity and cardiotoxicity and was highly effective against ART-resistant parasites. This study demonstrated the first and robust antirelapse LS activity from a novel acridone family.

Investigating Pfk13 mutations in Plasmodium falciparum natural populations from two malaria-endemic areas of Cameroon

BACKGROUND

The emergence of Plasmodium falciparum resistance to artemisinin is a huge concern in Africa. We investigated and characterized mutations of Pfk13 propeller sequences from P. falciparum isolates across two endemic areas with different eco-geographical settings in Cameroon.

METHODS

A total of 259 dried blood spot samples were collected through a cross-sectional survey in two health facilities located in Bimengue (rural area) and the Efoulan District Hospital in Yaoundé (urban area). The molecular analysis of Pfk13 was performed using nested polymerase chain reaction followed by Sanger sequencing.

RESULTS

Our findings highlight that of the 23 mutations found, most of the genetic variants were observed in Yaoundé, suggesting a possible higher drug pressure in this locality. Three Pfk13 mutations (F446S, C469W and A681D) were found in polymorphic sites known to be associated with artemisinin resistance, but with different amino acid substitutions. In addition, three other mutations have already been reported to circulate in other African countries, with an unknown impact on delayed response to artemisinin therapy (P475L, S477F and F628L).

CONCLUSIONS

Although there is an absence of validated artemisinin resistance-associated polymorphisms in the study, the results highlight the need for further studies to quantify the frequency of these and other Pfk13 gene polymorphisms over time.

Geographical Heterogeneity in Antimalarial Resistance Markers Revealed by Genomic Surveillance in Angola, 2023

Plasmodium falciparum malaria remains a leading cause of mortality in Angola, with emerging antimalarial resistance threatening treatment and prevention strategies. Efficacy of artemether-lumefantrine, one of the country's preferred malaria treatments, has been reported below 90% in two provinces, underscoring the need for routine resistance surveillance and efficacy monitoring to guide policy decisions. Between March and July 2023, dried blood spots and demographic data were collected from P. falciparum-positive participants at 16 health facilities across 8 provinces. Multiplexed amplicon deep sequencing was used to characterize single nucleotide polymorphisms in 12 genes linked with resistance, estimate allele frequencies, and detect co-infecting non-falciparum Plasmodium species. Sequence data from 817 samples revealed significant geographic variation in resistance markers. In the southeast, artemisinin partial resistance markers (k13 P574L, P441L), were detected at very low prevalence (<0.1%), while the quintuple dhps/dhfr haplotype, linked to sulfadoxine-pyrimethamine (SP) resistance, was very prevalent (>40% of samples). In the northwest, the sextuple dhps/dhfr haplotype, a marker of higher SP resistance, was most prevalent in Zaire (14.2%). The crt CVIET haplotype, associated with chloroquine resistance, had a national prevalence of 15.9%, detected in over 48% of samples from Zaire and Uíge. The mdr1 N86 genotype, linked to reduced lumefantrine susceptibility, was widespread, detected in 99.3% of samples. Co-infections of P. falciparum and non-falciparum species were rare with no clear geographic distribution. No P. vivax co-infections were detected. These findings highlight the need for continued monitoring to safeguard treatment efficacy, reinforcing the importance of molecular surveillance in malaria control strategies.

Performance of rapid diagnostic tests, microscopy, and qPCR for detection of Plasmodium parasites among community members with or without symptoms of malaria in villages located in North-western Tanzania

BACKGROUND

Despite the implementation of different control interventions, Plasmodium parasite infections in the communities (among asymptomatic and symptomatic individuals) still play a crucial role in sustaining malaria transmission. This study evaluated the performance of rapid diagnostic tests (RDTs), microscopy, and quantitative PCR (qPCR) in detecting Plasmodium parasites among community members in five villages of Kyerwa district, Kagera region in north-western Tanzania.

METHODS

The study used samples and data collected during a community cross-sectional survey of asymptomatic and symptomatic participants (n = 4454) aged ≥ 6 months which was conducted in July and August 2023. Plasmodium parasites were detected using RDTs, microscopy, and qPCR (targeting 18S rRNA gene). The performance of RDTs and microscopy was assessed by sensitivity, specificity, and predictive values, using qPCR as the reference method. Factors affecting the accuracy of these methods were determined using a multivariate logistic regression model.

RESULTS

The prevalence of Plasmodium parasite infections among 4454 participants was 44.4%, 32.1%, and 39.8% by RDTs, microscopy, and qPCR, respectively. The prevalence of Plasmodium falciparum, Plasmodium malariae and Plasmodium ovale mono-infection by microscopy was 28.7%, 0.2%, and 0.3%, while by qPCR it was 35.3%, 0.4% and 0.5%, respectively. The geometric mean parasite densities (GMPDs) by microscopy were 642 (95% confidence intervals (CI) = 570-723), 126 (95% CI = 98-162), and 124 (95% CI = 82-160) asexual parasites/µL for P. falciparum, P. ovale spp., and P. malariae, respectively. By qPCR, the GMPDs were 1180 (95% CI = 1032-1349) parasites/µL for P. falciparum, 44 (95% CI = 32-61) for P. ovale spp., and 50 (95% CI = 29-89) for P. malariae. The sensitivity and specificity of RDTs were 94.0% (95% CI = 92.8-95.1%) and 87.5% (95% CI = 86.2-88.7%), respectively, whereas those of microscopy were 74.6% (95% CI = 72.5-76.6%) and 95.2% (95% CI = 94.3-96.0%), respectively. The sensitivity of RDTs, and microscopy was low at very low parasitaemia (< 100 parasites/μL) but increased significantly with increasing parasitaemia, reaching ≥ 99.6% at > 10,000 parasites/μL (p < 0.001).

CONCLUSION

High prevalence of Plasmodium parasites was detected, and the performance of RDTs and qPCR was comparable, but microscopy had lower performance. Higher sensitivity of RDTs compared to microscopy indicates that RDTs are effective for detection of infections caused by Plasmodium parasites in routine case management and surveillance in this area with confirmed artemisinin partial resistance (ART-R) and can be utilized in the ongoing plans to develop a response to ART-R.

High Frequency of Artemisinin Partial Resistance Mutations in the Great Lakes Region Revealed Through Rapid Pooled Deep Sequencing

BACKGROUND

In Africa, the first Plasmodium falciparum artemisinin partial resistance mutation was Kelch13 (K13) 561H, detected and validated at appreciable frequency in Rwanda in 2014. Surveillance to better define the extent of the emergence in Rwanda and neighboring countries is critical.

METHODS

We used novel liquid blood drop preservation with pooled sequencing to provide cost-effective rapid assessment of resistance mutation frequencies at multiple collection sites across Rwanda and neighboring regions in Uganda, Tanzania, and the Democratic Republic of the Congo. Malaria-positive samples (N = 5465) from 39 health facilities collected between May 2022 and March 2023 were sequenced in 199 pools.

RESULTS

In Rwanda, K13 561H and 675V were detected in 90% and 65% of sites, with an average frequency of 19.0% (range, 0%-54.5%) and 5.0% (0%-35.5%), respectively. In Tanzania, 561H had high frequency in multiple sites. 561H appeared at 1.6% in Uganda. 561H was absent from the Democratic Republic of the Congo, although 675V was seen at low frequency. Concerningly, candidate mutations were observed: 441L, 449A, and 469F co-occurred with validated mutations, suggesting that they are arising under the same pressures. Other markers for decreased susceptibility to artemether-lumefantrine are common: P falciparum multidrug resistance protein 1 N86 at 98.0% (range, 63.3%-100%) and 184F at 47.0% (0%-94.3%) and P falciparum chloroquine resistance transporter 76T at 14.7% (0%-58.6%). Additionally, sulfadoxine-pyrimethamine-associated mutations show high frequencies.

CONCLUSIONS

K13 mutations are rapidly expanding in the region, further endangering control efforts with the potential of engendering partner drug resistance.

Genetic diversity of Plasmodium falciparum reticulocyte binding protein homologue-5, which is a potential malaria vaccine candidate: baseline data from areas of varying malaria endemicity in Mainland Tanzania

BACKGROUND

The limited efficacy of the two recently approved malaria vaccines, RTS,S/AS01 and R21/Matrix- M™, highlights the need for alternative vaccine candidate genes. Plasmodium falciparum Reticulocyte Binding Protein Homologue 5 (Pfrh5) is a promising malaria vaccine candidate, given its limited polymorphism, its essential role in parasite survival, a lack of immune selection pressure and higher efficacy against multiple parasites strains. This study evaluated the genetic diversity of Pfrh5 gene among parasites from regions with varying malaria transmission intensities in Mainland Tanzania, to generate baseline data for this potential malaria vaccine candidate.

METHODS

This study utilized secondary data of 697 whole-genome sequences which were generated by the MalariaGEN Community Network. The samples which were sequenced to generated the data were collected between 2010 and 2015 from five districts within five regions of Mainland Tanzania, with varying endemicities (Morogoro-urban district in Morogoro region, Muheza in Tanga, Kigoma-Ujiji in Kigoma, Muleba in Kagera, and Nachingwea district in Lindi region). Wright's fixation index (FST), Wright's inbreeding coefficient (Fws), Principal component analysis (PCA), nucleotide diversity (π), haplotype network, haplotype diversity (Hd), Tajima's D, and Linkage disequilibrium (LD) were used to assess the diversity of the gene.

RESULTS

Of the sequences used in this study, 84.5% (n = 589/697) passed quality control and 313 (53.1%) were monoclonal (contained infections from a single strain of P. falciparum) and were used for haplotype diversity and haplotype network analysis. High within-host diversity (Fws < 0.95) was reported in Kigoma-Ujiji (60.7%), Morogoro-urban (53.1%), and Nachingwea (50.8%), while Muleba (53.9%) and Muheza (61.6%) had low within-host diversity (Fws ≥ 0.95). PCA did not show any population structure and the mean FST value was 0.015. Low nucleotide diversity values were observed across the study sites (mean π = 0.00056). A total of 27 haplotypes were observed among the 313 monoclonal samples and under-fives exhibited higher haplotype counts. The Pf3D7 was detected as Hap_1, which occurred in 16/313 (5.1%) monoclonal sequences. Negative Tajima's D values were observed among the parasite populations in all the study sites.

CONCLUSION

Low levels of polymorphism in the pfrh5 gene were observed based on low nucleotide and haplotype diversity, a lack of population structure and negative Tajima's D values. This study provides essential data on the diversity of the Pfrh5 gene indicating that it can be considered in the development of the next generation malaria vaccines. Robust and intensive studies of this and other candidate genes are crucial to support the prioritization of the Pfrh5 gene for potential inclusion in a broadly cross-protective malaria vaccine.

The extended recovery ring-stage survival assay is a scalable alternative for artemisinin susceptibility phenotyping of fresh Plasmodium falciparum isolates

Artemisinin partial resistance (ART-R) has emerged in eastern Africa, necessitating regular surveillance of susceptibility of Plasmodium falciparum to artemisinins. The microscopy-based ring-stage survival assay (RSA) provides a laboratory correlate of ART-R but is limited by low throughput and subjectivity of microscopic counts of viable parasites. The extended recovery ring-stage survival assay (eRRSA) replaces microscopy with efficient quantitative PCR (qPCR) readouts but has been studied only with culture-adapted P. falciparum clones. We measured susceptibility to dihydroartemisinin (DHA) after a 6-h incubation with 700-nM DHA, followed by culture without drug, by comparing survival with that of untreated controls by microscopy (the RSA) or qPCR (the eRRSA) and also performed standard growth inhibition (half-maximal inhibitory concentration [IC50]) assays for 122 P. falciparum isolates freshly collected in eastern and northern Uganda from March to July 2022. The median values for RSA survival, eRRSA fold change, and DHA IC50 were 3.0%, 46.2, and 3.2 nM, respectively. RSA percent survival and eRRSA fold changes correlated strongly (Spearman correlation coefficient [rs] = -0.7411, P < 0.0001), with modest associations between the presence of validated P. falciparum Kelch13 ART-R mutations (C469Y or A675V) and RSA (median survival 2.6% for wild type [WT] vs 4.1% for mutant, P = 0.01), or eRRSA (median fold change 63.4 for WT vs 30.9 for mutant, P = 0.003) results. Significant correlations were also observed between DHA IC50 values and both RSA percent survival (rs = 0.4235, P < 0.0001) and eRRSA fold changes (rs = -0.4116, P < 0.0001). The eRRSA is a scalable alternative for phenotyping fresh P. falciparum isolates, providing similar results with improved throughput.

Optimization of B-Ring-Functionalized Antimalarial Tambjamines and Prodiginines

Malaria has been a deadly enemy of mankind throughout history, affecting over 200 million people annually, along with approximately half a million deaths. Resistance to current therapies is of great concern, and there is a dire need for novel and well-tolerated antimalarials that operate by clinically unexploited mechanisms. We have previously reported that both tambjamines and prodiginines are highly potent novel antiplasmodial agents, but they required rigor optimizations to enhance the oral efficacy, safety, and physicochemical properties. Here, we launched a comprehensive structure-activity relationship study for B-ring-functionalized tambjamines and prodiginines with 54 novel analogues systematically designed and synthesized. A number of compounds exhibited remarkable antiplasmodial activities against asexual erythrocytic Plasmodium parasites, with improved safety and metabolic profiles. Notably, several prodiginines cured erythrocytic Plasmodium yoelii infections after oral 25 mg/kg × 4 days in a murine model and provided partial protection against liver stage Plasmodium berghei sporozoite-induced infection in mice.

Geospatial Analysis of Malaria Burden in Kagera Region, Northwestern Tanzania Using Health Facility and Community Survey Data

Background

Malaria transmission in Tanzania has declined significantly over the last 2 decades due to scaled-up control interventions. However, recent confirmation of artemisinin partial resistance (ART-R) in Kagera region in northwest Tanzania threatens the ongoing efforts to eliminate malaria in the country. This study was conducted according to the World Health Organization recommendation to generate evidence of malaria burden in areas with confirmed ART-R as the first step before developing a response strategy to the resistance.

Methods

We assessed the local burden of malaria in Kagera region by geospatial analysis, using data collected retrospectively from health facilities and community surveys from 2015 to 2023 to identify malaria hot spots.

Results

From 2017 to 2023, a total of 8 124 363 suspected malaria cases were reported by health facilities, and 2 983 717 (36.7% [95% range across wards, 22.7%-50.7%]) tested positive by rapid diagnostic tests. Test positivity rates were similar among patients aged <5 years (33.1% [95% range, 19.7%-46.5%]) and those aged ≥5 years (33.7% [21.0%-46.5%]). The malaria prevalence was 10.0% (95% range across wards, 5.1%-14.9% [n = 84 999 of 853 761]) in pregnant women and 26.1% (11.7%-40.6% [n = 3409 of 13 065]) in schoolchildren. Despite high temporal variations, we identified hot spots and cold spots, including persistently high burden in 69 of 192 wards (35.9%).

Conclusions

The malaria burden in Kagera exhibited high temporal and spatial heterogeneity, with schoolchildren showing the highest prevalence. This demographic pattern underlines the need for targeted interventions and provides evidence for developing an ART-R response for the region.