Country wide surveillance reveals prevalent artemisinin partial resistance mutations with evidence for multiple origins and expansion of sulphadoxine-pyrimethamine resistance mutations in northwest Tanzania

BackgroundEmergence of artemisinin partial resistance (ART-R) in Plasmodium falciparum is a growing threat to the efficacy of artemisinin combination therapies (ACT) and the efforts for malaria elimination. The emergence of Plasmodium falciparum Kelch13 (K13) R561H in Rwanda raised concern about the impact in neighboring Tanzania. In addition, regional concern over resistance affecting sulfadoxine-pyrimethamine (SP), which is used for chemoprevention strategies, is high. MethodsTo enhance longitudinal monitoring, the Molecular Surveillance of Malaria in Tanzania (MSMT) project was launched in 2020 with the goal of assessing and mapping antimalarial resistance. Community and clinic samples were assessed for resistance polymorphisms using a molecular inversion probe platform. FindingsGenotyping of 6,278 samples collected countrywide in 2021 revealed a focus of K13 561H mutants in northwestern Tanzania (Kagera) with prevalence of 7.7% (50/649). A small number of 561H mutants (about 1%) were found as far as 800 km away in Tabora, Manyara, and Njombe. Genomic analysis suggests some of these parasites are highly related to isolates collected in Rwanda in 2015, supporting regional spread of 561H. However, a novel haplotype was also observed, likely indicating a second origin in the region. Other validated resistance polymorphisms (622I and 675V) were also identified. A focus of high sulfadoxine-pyrimethamine drug resistance was also identified in Kagera with a prevalence of dihydrofolate reductase 164L of 15% (80/526). InterpretationThese findings demonstrate the K13 561H mutation is entrenched in the region and that multiple origins of ART-R, similar as to what was seen in Southeast Asia, have occurred. Mutations associated with high levels of SP resistance are increasing. These results raise concerns about the long-term efficacy of artemisinin and chemoprevention antimalarials in the region. FundingThis study was funded by the Bill and Melinda Gates Foundation and the National Institutes of Health. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe did a literature search via PubMed for research articles published from January 2014 to October 2023 using the search term "Africa" and "Artemisinin resistance" linked to "R561H" or "A675V" or "R622I", returning 32 studies. The published literature shows the emergence and establishment of these three validated Plasmodium falciparum kelch13 (K13) mutations associated with artemisinin partial resistance (ART-R) in Africa. Large molecular studies of 675V in Uganda and 622I in Ethiopia have defined the regional spread of these mutations. However, limited data is available from recent studies about the spread and origins of the 561H mutation in the Great Lakes region of East Africa. In particular, detailed studies of the regions of Tanzania that border Rwanda have not been carried out since the mutation was detected in Rwanda. These data are needed for malaria control programs to define and implement strategies for controlling the spread of ART-R in Africa, a potential global public health disaster and the potential obstacle to the ongoing elimination strategies. Added value of this studyThis analysis reports the first large-scale analysis of antimalarial resistance in Tanzania, with a focus on the regions bordering Rwanda since the 561H mutation reached high frequency in the area. Using 6,278 P. falciparum positive samples sequenced using molecular inversion probes (MIPs), we show that the mutation has become frequent in the districts of Kagera bordering Rwanda. Importantly, we provide evidence for the separate emergence of a different extended haplotype around 561H in Tanzania. This is the first evidence that multiple independent emergences of the 561H ART-R have occurred in Africa, as was seen within the last two decades in Southeast Asia. Implications of all the available evidenceThese findings highlight that, similar to 622I and 675V in other parts of Africa, we can expect the 561H mutation to continue to spread in the region. In addition, it highlights that we need to be watchful for new origins of mutations beyond the spread of existing resistant parasite lineages. ART-R appears to now be well established in multiple areas in Eastern Africa. Intensive control in these regions to prevent spread and monitoring for partner drug resistance emergence in affected areas will be critical for preventing further reversal of malaria control efforts in the region and support progress to the elimination targets by 2023.