World Malaria Report 2022 (WHO, 2022).

Strategy to Respond to Antimalarial Drug Resistance in Africa (WHO, 2022).

van der Pluijm, R. W. et al. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study. Lancet Infect. Dis. 19, 952–961 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Dondorp, A. M. et al. Artemisinin resistance in Plasmodium falciparum malaria. N. Engl. J. Med. 361, 455–467 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Phyo A. P. et al. Emergence of artemisinin-resistant malaria on the western border of Thailand: a longitudinal study. Lancet https://doi.org/10.1016/S0140-6736(12)60484-X (2012).

Miotto, O. et al. Multiple populations of artemisinin-resistant Plasmodium falciparum in Cambodia. Nat. Genet. 45, 648–655 (2013).

Article  CAS  PubMed  Google Scholar 

Takala-Harrison, S. et al. Independent emergence of artemisinin resistance mutations among Plasmodium falciparum in Southeast Asia. J. Infect. Dis. 211, 670–679 (2015).

Article  CAS  PubMed  Google Scholar 

Miotto, O. et al. Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nat. Genet. 47, 226–234 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amato, R. et al. Origins of the current outbreak of multidrug-resistant malaria in southeast Asia: a retrospective genetic study. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(18)30068-9 (2018).

Hamilton, W. L. et al. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study. Lancet Infect. Dis. 19, 943–951 (2019).

Article  PubMed  PubMed Central  Google Scholar 

Jacob, C. G. et al. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination. Elife 10, e62997 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wasakul, V. et al. Malaria outbreak in Laos driven by a selective sweep for Plasmodium falciparum kelch13 R539T mutants: a genetic epidemiology analysis. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(22)00697-1 (2022).

Ariey, F. et al. A molecular marker of artemisinin-resistant Plasmodium falciparum malaria. Nature 505, 50–55 (2014).

Article  PubMed  Google Scholar 

Straimer, J. et al. K13-propeller mutations confer artemisinin resistance in Plasmodium falciparum clinical isolates. Science 347, 428–431 (2015).

Article  CAS  PubMed  Google Scholar 

Stokes, B. H. et al. Plasmodium falciparum k13 mutations in Africa and Asia impact artemisinin resistance and parasite fitness. Elife 10, e66277 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Uwimana, A. et al. Emergence and clonal expansion of in vitro artemisinin-resistant Plasmodium falciparum kelch13 R561H mutant parasites in Rwanda. Nat. Med. 26, 1602–1608 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Uwimana, A. et al. Association of Plasmodium falciparum kelch13 R561H genotypes with delayed parasite clearance in Rwanda: an open-label, single-arm, multicentre, therapeutic efficacy study. Lancet Infect. Dis. 21, 1120–1128 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Straimer, J., Gandhi, P., Renner, K. C. & Schmitt, E. K. High prevalence of Plasmodium falciparum K13 mutations in Rwanda is associated with slow parasite clearance after treatment with artemether-lumefantrine. J. Infect. Dis. 225, 1411–1414 (2022).

Article  CAS  PubMed  Google Scholar 

Balikagala, B. et al. Evidence of artemisinin-resistant malaria in Africa. N. Engl. J. Med. 385, 1163–1171 (2021).

Article  CAS  PubMed  Google Scholar 

Asua, V. et al. Changing prevalence of potential mediators of aminoquinoline, antifolate, and artemisinin resistance across Uganda. J. Infect. Dis. 223, 985–994 (2021).

Article  CAS  PubMed  Google Scholar 

Beshir, K. B. et al. Prevalence of Plasmodium falciparum haplotypes associated with resistance to sulfadoxine–pyrimethamine and amodiaquine before and after upscaling of seasonal malaria chemoprevention in seven African countries: a genomic surveillance study. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(22)00593-X (2022).

Amenga-Etego, L. N. et al. Temporal evolution of sulfadoxine-pyrimethamine resistance genotypes and genetic diversity in response to a decade of increased interventions against Plasmodium falciparum in northern Ghana. Malar J. https://doi.org/10.1186/s12936-021-03693-3 (2021).

Karema, C. et al. Molecular correlates of high-level antifolate resistance in Rwandan children with Plasmodium falciparum malaria. Antimicrob. Agents Chemother. 54, 477–483 (2010).

Article  CAS  PubMed  Google Scholar 

Maïga, O. et al. A shared Asian origin of the triple-mutant dhfr allele in Plasmodium falciparum from sites across Africa. J. Infect. Dis. 196, 165–172 (2007).

Article  PubMed  Google Scholar 

Naidoo, I. & Roper, C. Mapping ‘partially resistant’, ‘fully resistant’, and ‘super resistant’ malaria. Trends Parasitol. https://doi.org/10.1016/j.pt.2013.08.002 (2013).

Baba, E. et al. Effectiveness of seasonal malaria chemoprevention at scale in west and central Africa: an observational study. Lancet 396, 1829–1840 (2020).

Article  Google Scholar 

MalariaGEN et al. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples [version 1; peer review: 2 approved]. Wellcome Open Res. https://doi.org/10.12688/wellcomeopenres.16168.1 (2021).

Nwakanma, D. C. et al. Changes in malaria parasite drug resistance in an endemic population over a 25-year period with resulting genomic evidence of selection. J. Infect. Dis. 209, 1126–1135 (2014).

Article  CAS  PubMed  Google Scholar 

Wamea, K. et al. No evidence of Plasmodium falciparum k13 artemisinin resistance-conferring mutations over a 24-year analysis in coastal Kenya but a near complete reversion to chloroquine-sensitive parasites. Antimicrob. Agents Chemother. 63, e01067-19 (2019).

Google Scholar 

Omedo, I. et al. Spatio-temporal distribution of antimalarial drug resistant gene mutations in a Plasmodium falciparum parasite population from Kilifi, Kenya: a 25-year retrospective study. Wellcome Open Res. 7, 45 (2022).

Article  Google Scholar 

Verity, R. et al. The impact of antimalarial resistance on the genetic structure of Plasmodium falciparum in the DRC. Nat. Commun. https://doi.org/10.1038/s41467-020-15779-8 (2020).

Mobegi, V. A. et al. Population genetic structure of Plasmodium falciparum across a region of diverse endemicity in West Africa. Malar. J. 11, 223 (2012).

Article  PubMed  PubMed Central  Google Scholar 

Taylor, A. R. et al. Quantifying connectivity between local Plasmodium falciparum malaria parasite populations using identity by descent. PLoS Genet. 13, e1007065 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Parobek, C. M. et al. Partner-drug resistance and population substructuring of artemisinin-resistant Plasmodium falciparum in Cambodia. Genome Biol. Evol. 9, 1673–1686 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Amambua-Ngwa, A. et al. Major subpopulations of Plasmodium falciparum in sub-Saharan Africa. Science 365, 813–816 (2019).

Article  CAS  PubMed  Google Scholar 

Plowe, C. V., Alonso, P. & Hoffman, S. L. The potential role of vaccines in the elimination of falciparum malaria and the eventual eradication of malaria. J. Infect. Dis. 200, 1646–1649 (2009).

Article  PubMed  Google Scholar 

World Malaria Report 2021 (WHO, 2021).

Laurens, M. B. RTS,S/AS01 vaccine (MosquirixTM): an overview. Hum. Vaccin. Immunother. https://doi.org/10.1080/21645515.2019.1669415 (2019).

RTSS Clinical Trials Partnership. Efficacy and safety of RTS,S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial. Lancet https://doi.org/10.1016/S0140-6736(15)60721-8 (2015).

Datoo, M. S. et al. Efficacy of a low-dose candidate malaria vaccine, R21 in adjuvant Matrix-M, with seasonal administration to children in Burkina Faso: a randomised controlled trial. Lancet 397, 1809–1818 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Datoo, M. S. et al. Efficacy and immunogenicity of R21/Matrix-M vaccine against clinical malaria after 2 years’ follow-up in children in Burkina Faso: a phase 1/2b randomised controlled trial. Lancet Infect. Dis. 22, 1728–1736 (2022).

Article  CAS  PubMed  Google Scholar 

Gaudinski, M. R. et al. A monoclonal antibody for malaria prevention. N. Engl. J. Med. 385, 803–814 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wu, R. L. et al. Low-dose subcutaneous or intravenous monoclonal antibody to prevent malaria. N. Engl. J. Med. 387, 397–407 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kayentao, K. et al. Safety and efficacy of a monoclonal antibody against malaria in Mali. N. Engl. J. Med. 387, 1833–1842 (2022).

Accelerating Access to Genomics for Global Health: Promotion, Implementation, Collaboration, and Ethical, Legal, and Social Issues. A Report of the WHO Science Council (WHO, 2022).

Lyimo, B. M. et al. Potential opportunities and challenges of deploying next generation sequencing and CRISPR-Cas systems to support diagnostics and surveillance towards malaria control and elimination in Africa. Front. Cell. Infect. Microbiol. 12, 757844 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Inzaule, S. C., Tessema, S. K., Kebede, Y., Ogwell, Ouma A. E. & Nkengasong, J. N. Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Lancet Infect. Dis. https://doi.org/10.1016/S1473-3099(20)30939-7 (2021).

Meredith, L. W. et al. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect. Dis. 20, 1263–1271 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hamilton, W. L. et al. Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19. Lancet Infect. Dis. 21, 916–917 (2021).