Dalmat, R., Naughton, B., Kwan-Gett, T. S., Slyker, J. & Stuckey, E. M. Use cases for genetic epidemiology in malaria elimination. Malar. J. 18, 163 (2019).
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).
Feleke, S. M. et al. Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia. Nat. Microbiol. 6, 1289–1299 (2021).
Ndwiga, L. et al. A review of the frequencies of Plasmodium falciparum Kelch 13 Artemisinin resistance mutations in Africa. Int. J. Parasitol. Drugs Drug Resist. 16, 155–161 (2021).
Rosenthal, P. J. et al. Cooperation in countering Artemisinin resistance in Africa: learning from COVID-19. Am. J. Trop. Med. Hyg. 106, 1568–1570 (2022).
Neafsey Daniel, E. et al. Genetic diversity and protective efficacy of the RTS,S/AS01 malaria vaccine. N Engl. J. Med. 373, 2025–2037 (2015).
Wesolowski, A. et al. Mapping malaria by combining parasite genomic and epidemiologic data. BMC Med. 16, 190 (2018).
Tessema, S. et al. Using parasite genetic and human mobility data to infer local and cross-border malaria connectivity in Southern Africa. eLife 8, e43510 (2019).
Tessema, S. K. et al. Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa. Malar. J. 18, 268 (2019).
Watson, O. J. et al. Evaluating the performance of malaria genetics for inferring changes in transmission intensity using transmission modeling. Mol. Biol. Evol. 38, 274–289 (2021).
Daniels, R. F. et al. Genetic evidence for imported malaria and local transmission in Richard toll, Senegal. Malar. J. 19, 276 (2020).
Mensah, B. A., Akyea-Bobi, N. E. & Ghansah, A. Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub–Saharan Africa. Front. Epidemiol. 2, 939291 (2022).
Schaffner, S. F. et al. Malaria surveillance reveals parasite relatedness, signatures of selection, and correlates of transmission across Senegal. Nat. Commun. 14, 7268 (2023).
Fola, A. A. et al. Temporal and Spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar. J. 22, 208 (2023).
Yeka, A. et al. Comparative efficacy of Artemether-Lumefantrine and Dihydroartemisinin-Piperaquine for the treatment of uncomplicated malaria in Ugandan children. J. Infect. Dis. 219, 1112–1120 (2019).
Snounou, G. & Beck, H. P. The use of PCR genotyping in the assessment of recrudescence or reinfection after antimalarial drug treatment. Parasitol. Today. 14, 462–467 (1998).
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).
Schnoz, A. et al. Genotyping methods to distinguish Plasmodium falciparum recrudescence from new infection for the assessment of antimalarial drug efficacy: an observational, single-centre, comparison study. Lancet Microbe 5, 100914 (2024).
Lover, A. A., Baird, J. K., Gosling, R. & Price, R. N. Malaria elimination: time to target all species. Am. J. Trop. Med. Hyg. 99, 17–23 (2018).
Mwesigwa, A. et al. Plasmodium falciparum genetic diversity and multiplicity of infection based on msp-1, msp-2, glurp and microsatellite genetic markers in sub-Saharan Africa: a systematic review and meta-analysis. Malar. J. 23, 97 (2024).
Briggs, J. et al. Within-household clustering of genetically related Plasmodium falciparum infections in a moderate transmission area of Uganda. Malar. J. 20, 68 (2021).
Brokhattingen, N. et al. Genomic malaria surveillance of antenatal care users detects reduced transmission following elimination interventions in Mozambique. Nat. Commun. 15, 2402 (2024).
Viriyakosol, S. et al. Genotyping of Plasmodium falciparum isolates by the polymerase chain reaction and potential uses in epidemiological studies. Bull. World Health Organ. 73, 85–95 (1995).
Anderson, T. J. C., Su, X. Z., Bockarie, M., Lagog, M. & Day, K. P. Twelve microsatellite markers for characterization of Plasmodium falciparum from finger-prick blood samples. Parasitology 119, 113–125 (1999).
Anderson, T. J. C. et al. Microsatellite markers reveal a spectrum of population structures in the malaria parasite Plasmodium falciparum. Mol. Biol. Evol. 17, 1467–1482 (2000).
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).
Kattenberg, J. H. et al. Molecular surveillance of malaria using the PF ampliseq custom assay for Plasmodium falciparum parasites from dried blood spot DNA isolates from Peru. Bio-Protoc 13, e4621 (2023).
Taylor, A. R., Jacob, P. E., Neafsey, D. E. & Buckee, C. O. Estimating Relatedness between Malar. Parasites Genet. 212, 1337–1351 (2019).
Tessema, S. K. et al. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J. Infect. Dis. 225, 1227–1237 (2022).
LaVerriere, E. et al. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: A malaria case study. Mol. Ecol. Resour. 22, 2285–2303 (2022).
de Cesare, M. et al. Flexible and cost-effective genomic surveillance of P. falciparum malaria with targeted nanopore sequencing. Nat. Commun. 15, 1413 (2024).
Holzschuh, A. et al. Using a mobile nanopore sequencing lab for end-to-end genomic surveillance of Plasmodium falciparum: A feasibility study. PLOS Glob Public. Health. 4, e0002743 (2024).
Girgis, S. T. et al. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana. Nat. Microbiol. 8, 2365–2377 (2023).
Melnikov, A. et al. Hybrid selection for sequencing pathogen genomes from clinical samples. Genome Biol. 12, R73 (2011).
Villena, F. E., Lizewski, S. E., Joya, C. A. & Valdivia, H. O. Population genomics and evidence of clonal replacement of Plasmodium falciparum in the Peruvian Amazon. Sci. Rep. 11, 21212 (2021).
Mathieu, L. C. et al. Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro Artemisinin resistance. eLife 9, e51015 (2020).
Cerqueira, G. C. et al. Longitudinal genomic surveillance of Plasmodium falciparum malaria parasites reveals complex genomic architecture of emerging Artemisinin resistance. Genome Biol. 18, 78 (2017).
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).
Pelleau, S. et al. Adaptive evolution of malaria parasites in French Guiana: reversal of chloroquine resistance by acquisition of a mutation in Pfcrt. Proc. Natl. Acad. Sci. 112, 11672–11677 (2015).
Dara, A. et al. New var reconstruction algorithm exposes high var sequence diversity in a single geographic location in Mali. Genome Med. 9, 30 (2017).
Tvedte, E. S. et al. Evaluation of a high-throughput, cost-effective illumina library Preparation kit. Sci. Rep. 11, 15925 (2021).
Ahouidi, A. & Ali, M. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open. Res. 6, 42 (2021).
Hathaway, N. A suite of computational tools to interrogate sequence data with local haplotype analysis within complex Plasmodium infections and other microbial mixtures. (2018). https://doi.org/10.13028/M2039K
Hathaway, N. J. et al. Interchromosomal segmental duplication drives translocation and loss of P. falciparum histidine-rich protein 3. eLife 13, (2024).
MalariaGEN et al. Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples. Wellcome Open. Res. 8, 22 (2023).
Gerlovina, I., Gerlovin, B., Rodríguez-Barraquer, I. & Greenhouse, B. Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections. Genetics 222, iyac126 (2022).
Murphy, M. & Greenhouse, B. MOIRE: a software package for the Estimation of allele frequencies and effective multiplicity of infection from polyallelic data. Bioinformatics 40, btae619 (2024).
Esayas, E. et al. Impact of nighttime human behavior on exposure to malaria vectors and effectiveness of using long-lasting insecticidal Nets in the Ethiopian lowlands and highlands. Parasit. Vectors. 17, 520 (2024).
Asua, V. et al. Plasmodium Species Infecting Children Presenting with Malaria in Uganda. (2017). https://doi.org/10.4269/ajtmh.17-0345
Rek, J. et al. Asymptomatic School-Aged children are important drivers of malaria transmission in a high endemicity setting in Uganda. J. Infect. Dis. 226, 708–713 (2022).
Andolina, C. et al. Sources of persistent malaria transmission in a setting with effective malaria control in Eastern Uganda: a longitudinal, observational cohort study. Lancet Infect. Dis. 21, 1568–1578 (2021).
Teyssier, N. B. et al. Optimization of whole-genome sequencing of Plasmodium falciparum from low-density dried blood spot samples. Malar. J. 20, 116 (2021).
Hugo, L. E. et al. Rapid low-resource detection of Plasmodium falciparum in infected Anopheles mosquitoes. Front. Trop. Dis. 5, 1287025 (2024).
Hofmann, N. et al. Ultra-Sensitive detection of plasmodium falciparum by amplification of Multi-Copy subtelomeric targets. PLOS Med. 12, e1001788 (2015).
Mayor, A. et al. Sub-microscopic infections and long-term recrudescence of Plasmodium falciparum in Mozambican pregnant women. Malar. J. 8, 9 (2009).
Molla, E. et al. Seasonal dynamics of symptomatic and asymptomatic Plasmodium falciparum and Plasmodium Vivax infections in coendemic Low-Transmission settings, South Ethiopia. (2024). https://doi.org/10.4269/ajtmh.24-0021
Paragon Genomics Product Documents. Paragon Genomics https://www.paragongenomics.com/customer-support/product_documents/
Di Tommaso, P. et al. Nextflow enables reproducible computational workflows. Nat. Biotechnol. 35, 316–319 (2017).
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10–12 (2011).
Callahan, B. J. et al. DADA2: High-resolution sample inference from illumina amplicon data. Nat. Methods. 13, 581–583 (2016).
Gupta, H. et al. Drug-Resistant polymorphisms and copy numbers in Plasmodium falciparum. Mozambique 2015 Emerg. Infect. Dis. 24, 40–48 (2018).
Grignard, L. et al. A novel multiplex qPCR assay for detection of Plasmodium falciparum with histidine-rich protein 2 and 3 (pfhrp2 and pfhrp3) deletions in polyclonal infections. EBioMedicine 55, 102757 (2020).
da Silva, C. et al. Targeted and whole-genome sequencing reveal a north-south divide in P. falciparum drug resistance markers and genetic structure in Mozambique. Commun. Biol. 6, 1–11 (2023).
Emiru, T. et al. Evidence for a role of Anopheles stephensi in the spread of drug- and diagnosis-resistant malaria in Africa. Nat. Med. 29, 3203–3211 (2023).
Daniels, R. F. et al. Modeling malaria genomics reveals transmission decline and rebound in Senegal. Proc. Natl. Acad. Sci. 112, 7067–7072 (2015).
Chang, H. H. et al. Mapping imported malaria in Bangladesh using parasite genetic and human mobility data. eLife 8, e43481 (2019).
Holzschuh, A. et al. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat. Commun. 14, 3699 (2023).
Hathaway, N. J., Parobek, C. M., Juliano, J. J. & Bailey, J. A. SeekDeep: single-base resolution de Novo clustering for amplicon deep sequencing. Nucleic Acids Res. 46, e21 (2018).
Lerch, A. et al. Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections. BMC Genom. 18, 864 (2017).
Schaffner, S. F., Taylor, A. R., Wong, W., Wirth, D. F. & Neafsey, D. E. HmmIBD: software to infer pairwise identity by descent between haploid genotypes. Malar. J. 17, 196 (2018).
Henden, L., Lee, S., Mueller, I., Barry, A. & Bahlo, M. Identity-by-descent analyses for measuring population dynamics and selection in recombining pathogens. PLOS Genet. 14, e1007279 (2018).
Chang, H. H. et al. THE REAL McCOIL: A method for the concurrent Estimation of the complexity of infection and SNP allele frequency for malaria parasites. PLOS Comput. Biol. 13, e1005348 (2017).
Collins, K. A., Snaith, R., Cottingham, M. G., Gilbert, S. C. & Hill, A. V. S. Enhancing protective immunity to malaria with a highly Immunogenic virus-like particle vaccine. Sci. Rep. 7, 46621 (2017).
Laurens, M. B. & RTS S/AS01 vaccine (Mosquirix™): an overview. Hum. Vaccines Immunother. 16, 480–489 (2020).
World Health Organization. Malaria vaccine: WHO position paper – May 2024. Wkly. Epidemiol. Rec. 19, 225–248 (2024).
Lagerborg, K. A. et al. Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows. Nat. Microbiol. 7, 108–119 (2022).
CleanPlex amplicon sequencing for targeted DNA and & Seq, R. N. A. Paragon Genomics https://www.paragongenomics.com/targeted-sequencing/amplicon-sequencing/cleanplex-ngs-amplicon-sequencing/
Resources | EPPIcenter. https://eppicenter.ucsf.edu/resources
Report on antimalarial. Drug efficacy, resistance and response: 10 years of surveillance (2010–2019). (2020) https://www.who.int/publications/i/item/9789240012813
Miotto, O. et al. Genetic architecture of artemisinin-resistant Plasmodium falciparum. Nat. Genet. 47, 226–234 (2015).