Julian Rayner

Professor Julian Rayner

Director, Wellcome Connecting Science
Programme and Strategy

Wellcome Connecting Science is led by its Director, Professor Julian Rayner. Julian combines his passion for malaria research with his conviction that dialogue, learning and public engagement are a fundamental and essential part of the research process. He provides strategic leadership to Connecting Science, ensuring our mission stays relevant and delivers the change we want to see. Julian also holds a Professorship in the University of Cambridge, and is the Director of the Cambridge Institute for Medical Research.

He is a member of Honorary Faculty at the Wellcome Sanger Institute and a member of the Sanger Institute Senior Leadership Team; an Elected Member of EMBO; and a Fellow of the Academy of Medical Sciences.

My publications

  • All
  • Selected
  • 2023
  • 2022

A systematic analysis of the human immune response to Plasmodium vivax.

Bach FA; Muñoz Sandoval D; Mazurczyk M; Themistocleous Y; Rawlinson TA; Harding AC; Kemp A; Silk SE; Barrett JR; Edwards NJ; Ivens A; Rayner JC; Minassian AM; Napolitani G; Draper SJ; Spence PJ

The Journal of clinical investigation 2023;133;20

BACKGROUNDThe biology of Plasmodium vivax is markedly different from that of P. falciparum; how this shapes the immune response to infection remains unclear. To address this shortfall, we inoculated human volunteers with a clonal field isolate of P. vivax and tracked their response through infection and convalescence.METHODSParticipants were injected intravenously with blood-stage parasites and infection dynamics were tracked in real time by quantitative PCR. Whole blood samples were used for high dimensional protein analysis, RNA sequencing, and cytometry by time of flight, and temporal changes in the host response to P. vivax were quantified by linear regression. Comparative analyses with P. falciparum were then undertaken using analogous data sets derived from prior controlled human malaria infection studies.RESULTSP. vivax rapidly induced a type I inflammatory response that coincided with hallmark features of clinical malaria. This acute-phase response shared remarkable overlap with that induced by P. falciparum but was significantly elevated (at RNA and protein levels), leading to an increased incidence of pyrexia. In contrast, T cell activation and terminal differentiation were significantly increased in volunteers infected with P. falciparum. Heterogeneous CD4+ T cells were found to dominate this adaptive response and phenotypic analysis revealed unexpected features normally associated with cytotoxicity and autoinflammatory disease.CONCLUSIONP. vivax triggers increased systemic interferon signaling (cf P. falciparum), which likely explains its reduced pyrogenic threshold. In contrast, P. falciparum drives T cell activation far in excess of P. vivax, which may partially explain why falciparum malaria more frequently causes severe disease.TRIAL NCT03797989.FUNDINGThe European Union's Horizon 2020 Research and Innovation programme, the Wellcome Trust, and the Royal Society.

Characterization of a novel Plasmodium falciparum merozoite surface antigen and potential vaccine target.

Niaré K; Chege T; Rosenkranz M; Mwai K; Saßmannshausen Z; Odera D; Nyamako L; Tuju J; Alfred T; Waitumbi JN; Ogutu B; Sirima SB; Awandare G; Kouriba B; Rayner JC; Osier FHA

Frontiers in immunology 2023;14;1156806

Detailed analyses of genetic diversity, antigenic variability, protein localization and immunological responses are vital for the prioritization of novel malaria vaccine candidates. Comprehensive approaches to determine the most appropriate antigen variants needed to provide broad protection are challenging and consequently rarely undertaken.

Chemogenomic Profiling of a Plasmodium falciparum Transposon Mutant Library Reveals Shared Effects of Dihydroartemisinin and Bortezomib on Lipid Metabolism and Exported Proteins.

Pires CV; Oberstaller J; Wang C; Casandra D; Zhang M; Chawla J; Adapa SR; Otto TD; Ferdig MT; Rayner JC; Jiang RHY; Adams JH

Microbiology spectrum 2023;11;3;e0501422

The antimalarial activity of the frontline drug artemisinin involves generation of reactive oxygen species (ROS) leading to oxidative damage of parasite proteins. To achieve homeostasis and maintain protein quality control in the overwhelmed parasite, the ubiquitin-proteasome system kicks in. Even though molecular markers for artemisinin resistance like pfkelch13 have been identified, the intricate network of mechanisms driving resistance remains to be elucidated. Here, we report a forward genetic screening strategy that enables a broader identification of genetic factors responsible for altering sensitivity to dihydroartemisinin (DHA) and a proteasome inhibitor, bortezomib (BTZ). Using a library of isogenic piggyBac mutants in P. falciparum, we defined phenotype-genotype associations influencing drug responses and highlighted shared mechanisms between the two processes, which mainly included proteasome-mediated degradation and the lipid metabolism genes. Additional transcriptomic analysis of a DHA/BTZ-sensitive piggyBac mutant showed it is possible to find differences between the two response mechanisms on the specific components for regulation of the exportome. Our results provide further insight into the molecular mechanisms of antimalarial drug resistance. IMPORTANCE Malaria control is seriously threatened by the emergence and spread of Plasmodium falciparum resistance to the leading antimalarial, artemisinin. The potent killing activity of artemisinin results from oxidative damage unleashed by free heme activation released by hemoglobin digestion. Although the ubiquitin-proteasome system is considered critical for parasite survival of this toxicity, the diverse genetic changes linked to artemisinin resistance are complex and, so far, have not included the ubiquitin-proteasome system. In this study, we use a systematic forward genetic approach by screening a library of P. falciparum random piggyBac mutants to decipher the genetic factors driving malaria parasite responses to the oxidative stress caused by antimalarial drugs. This study compares phenotype-genotype associations influencing dihydroartemisinin responses with the proteasome inhibitor bortezomib to delineate the role of ubiquitin-proteasome system. Our study highlights shared and unique pathways from the complex array of molecular processes critical for P. falciparum survival resulting from the oxidative damage of artemisinin.

Development of an Affordable ELISA Targeting the SARS-CoV-2 Nucleocapsid and Its Application to Samples from the Ongoing COVID-19 Epidemic in Ghana.

Tapela K; Opurum PC; Nuokpem FY; Tetteh B; Siaw GK; Humbert MV; Tawiah-Eshun S; Barakisu AI; Asiedu K; Arhin SK; Manu AA; Appiedu-Addo SNA; Obbeng L; Quansah D; Languon S; Anyigba C; Dosoo D; Edu NKO; Oduro-Mensah D; Ampofo W; Tagoe E; Quaye O; Donkor IO; Akorli J; Aniweh Y; Christodoulides M; Mutungi J; Bediako Y; Rayner JC; Awandare GA; McCormick CJ; Quashie PK

Molecular diagnosis & therapy 2023;27;5;583-592

The true nature of the population spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in populations is often not fully known as most cases, particularly in Africa, are asymptomatic. Finding the true magnitude of SARS-CoV-2 spread is crucial to provide actionable data about the epidemiological progress of the disease for researchers and policymakers. This study developed and optimized an antibody enzyme-linked immunosorbent assay (ELISA) using recombinant nucleocapsid antigen expressed in-house using a simple bacterial expression system.

Extracellular vesicles could be a putative posttranscriptional regulatory mechanism that shapes intracellular RNA levels in Plasmodium falciparum.

Kioko M; Pance A; Mwangi S; Goulding D; Kemp A; Rono M; Ochola-Oyier LI; Bull PC; Bejon P; Rayner JC; Abdi AI

Nature Communications 2023;14;1;6447

Plasmodium falciparum secretes extracellular vesicles (PfEVs) that contain parasite-derived RNA. However, the significance of the secreted RNA remains unexplored. Here, we compare secreted and intracellular RNA from asexual cultures of six P. falciparum lines. We find that secretion of RNA via extracellular vesicles is not only periodic throughout the asexual intraerythrocytic developmental cycle but is also highly conserved across P. falciparum isolates. We further demonstrate that the phases of RNA secreted via extracellular vesicles are discernibly shifted compared to those of the intracellular RNA within the secreting whole parasite. Finally, transcripts of genes with no known function during the asexual intraerythrocytic developmental cycle are enriched in PfEVs compared to the whole parasite. We conclude that the secretion of extracellular vesicles could be a putative posttranscriptional RNA regulation mechanism that is part of or synergise the classic RNA decay processes to maintain intracellular RNA levels in P. falciparum.

Lineage-informative microhaplotypes for spatio-temporal surveillance of Plasmodium vivax malaria parasites.

Siegel SV; Amato R; Trimarsanto H; Sutanto E; Kleinecke M; Murie K; Whitton G; Taylor AR; Watson JA; Imwong M; Assefa A; Rahim AG; Chau NH; Hien TT; Green JA; Koh G; White NJ; Day N; Kwiatkowski DP; Rayner JC; Price RN; Auburn S

medRxiv 2023

Challenges in understanding the origin of recurrent Plasmodium vivax infections constrains the surveillance of antimalarial efficacy and transmission of this neglected parasite. Recurrent infections within an individual may arise from activation of dormant liver stages (relapse), blood-stage treatment failure (recrudescence) or new inoculations (reinfection). Molecular inference of familial relatedness (identity-by-descent or IBD) based on whole genome sequence data, together with analysis of the intervals between parasitaemic episodes ("time-to-event" analysis), can help resolve the probable origin of recurrences. Whole genome sequencing of predominantly low-density P. vivax infections is challenging, so an accurate and scalable genotyping method to determine the origins of recurrent parasitaemia would be of significant benefit. We have developed a P. vivax genome-wide informatics pipeline to select specific microhaplotype panels that can capture IBD within small, amplifiable segments of the genome. Using a global set of 615 P. vivax genomes, we derived a panel of 100 microhaplotypes, each comprising 3-10 high frequency SNPs within <200 bp sequence windows. This panel exhibits high diversity in regions of the Asia-Pacific, Latin America and the horn of Africa (median HE = 0.70-0.81) and it captured 89% (273/307) of the polyclonal infections detected with genome-wide datasets. Using data simulations, we demonstrate lower error in estimating pairwise IBD using microhaplotypes, relative to traditional biallelic SNP barcodes. Our panel exhibited high accuracy in predicting the country of origin (median Matthew's correlation coefficient >0.9 in 90% countries tested) and it also captured local infection outbreak and bottlenecking events. The informatics pipeline is available open-source and yields microhaplotypes that can be readily transferred to high-throughput amplicon sequencing assays for surveillance in malaria-endemic regions.

Malaria: moving beyond the search for magic bullets.

Levashina E; Soldati-Favre D; Waters AP; Frischknecht F; Rayner JC

EMBO molecular medicine 2023;15;11;e18727

Round table discussion on challenges and opportunities in malaria research with Elena Levashina, Dominique Soldati-Favre, Andrew Waters, Friedrich Frischknecht, and Julian Rayner.

Pf7: an open dataset of Plasmodium falciparum genome variation in 20,000 worldwide samples.

; Abdel Hamid MM; Abdelraheem MH; Acheampong DO; Ahouidi A; Ali M; Almagro-Garcia J; Amambua-Ngwa A; Amaratunga C; Amenga-Etego L; Andagalu B; Anderson T; Andrianaranjaka V; Aniebo I; Aninagyei E; Ansah F; Ansah PO; Apinjoh T; Arnaldo P; Ashley E; Auburn S; Awandare GA; Ba H; Baraka V; Barry A; Bejon P; Bertin GI; Boni MF; Borrmann S; Bousema T; Bouyou-Akotet M; Branch O; Bull PC; Cheah H; Chindavongsa K; Chookajorn T; Chotivanich K; Claessens A; Conway DJ; Corredor V; Courtier E; Craig A; D'Alessandro U; Dama S; Day N; Denis B; Dhorda M; Diakite M; Djimde A; Dolecek C; Dondorp A; Doumbia S; Drakeley C; Drury E; Duffy P; Echeverry DF; Egwang TG; Enosse SMM; Erko B; Fairhurst RM; Faiz A; Fanello CA; Fleharty M; Forbes M; Fukuda M; Gamboa D; Ghansah A; Golassa L; Goncalves S; Harrison GLA; Healy SA; Hendry JA; Hernandez-Koutoucheva A; Hien TT; Hill CA; Hombhanje F; Hott A; Htut Y; Hussein M; Imwong M; Ishengoma D; Jackson SA; Jacob CG; Jeans J; Johnson KJ; Kamaliddin C; Kamau E; Keatley J; Kochakarn T; Konate DS; Konaté A; Kone A; Kwiatkowski DP; Kyaw MP; Kyle D; Lawniczak M; Lee SK; Lemnge M; Lim P; Lon C; Loua KM; Mandara CI; Marfurt J; Marsh K; Maude RJ; Mayxay M; Maïga-Ascofaré O; Miotto O; Mita T; Mobegi V; Mohamed AO; Mokuolu OA; Montgomery J; Morang'a CM; Mueller I; Murie K; Newton PN; Ngo Duc T; Nguyen T; Nguyen TN; Nguyen Thi Kim T; Nguyen Van H; Noedl H; Nosten F; Noviyanti R; Ntui VN; Nzila A; Ochola-Oyier LI; Ocholla H; Oduro A; Omedo I; Onyamboko MA; Ouedraogo JB; Oyebola K; Oyibo WA; Pearson R; Peshu N; Phyo AP; Plowe CV; Price RN; Pukrittayakamee S; Quang HH; Randrianarivelojosia M; Rayner JC; Ringwald P; Rosanas-Urgell A; Rovira-Vallbona E; Ruano-Rubio V; Ruiz L; Saunders D; Shayo A; Siba P; Simpson VJ; Sissoko MS; Smith C; Su XZ; Sutherland C; Takala-Harrison S; Talman A; Tavul L; Thanh NV; Thathy V; Thu AM; Toure M; Tshefu A; Verra F; Vinetz J; Wellems TE; Wendler J; White NJ; Whitton G; Yavo W; van der Pluijm RW

Wellcome open research 2023;8;22

We describe the MalariaGEN Pf7 data resource, the seventh release of Plasmodium falciparum genome variation data from the MalariaGEN network.  It comprises over 20,000 samples from 82 partner studies in 33 countries, including several malaria endemic regions that were previously underrepresented.  For the first time we include dried blood spot samples that were sequenced after selective whole genome amplification, necessitating new methods to genotype copy number variations.  We identify a large number of newly emerging crt mutations in parts of Southeast Asia, and show examples of heterogeneities in patterns of drug resistance within Africa and within the Indian subcontinent.  We describe the profile of variations in the C-terminal of the csp gene and relate this to the sequence used in the RTS,S and R21 malaria vaccines.  Pf7 provides high-quality data on genotype calls for 6 million SNPs and short indels, analysis of large deletions that cause failure of rapid diagnostic tests, and systematic characterisation of six major drug resistance loci, all of which can be freely downloaded from the MalariaGEN website.

Phenotypic Screens Identify Genetic Factors Associated with Gametocyte Development in the Human Malaria Parasite Plasmodium falciparum.

Chawla J; Goldowitz I; Oberstaller J; Zhang M; Pires CV; Navarro F; Sollelis L; Wang CCQ; Seyfang A; Dvorin J; Otto TD; Rayner JC; Marti M; Adams JH

Microbiology spectrum 2023;11;3;e0416422

Transmission of the deadly malaria parasite Plasmodium falciparum from humans to mosquitoes is achieved by specialized intraerythrocytic sexual forms called gametocytes. Though the crucial regulatory mechanisms leading to gametocyte commitment have recently come to light, networks of genes that control sexual development remain to be elucidated. Here, we report a pooled-mutant screen to identify genes associated with gametocyte development in P. falciparum. Our results categorized genes that modulate gametocyte progression as hypoproducers or hyperproducers of gametocytes, and the in-depth analysis of individual clones confirmed phenotypes in sexual commitment rates and putative functions in gametocyte development. We present a new set of genes that have not been implicated in gametocytogenesis before and demonstrate the potential of forward genetic screens in isolating genes impacting parasite sexual biology, an exciting step toward the discovery of new antimalarials for a globally significant pathogen. IMPORTANCE Blocking human-to-vector transmission is an essential step toward malaria elimination. Gametocytes are solely responsible for achieving this transmission and represent an opportunity for therapeutic intervention. While these falciform-shaped parasite stages were first discovered in the 1880s, our understanding of the genetic determinants responsible for their formation and molecular mechanisms that drive their development is limited. In this work, we developed a scalable screening methodology with piggyBac mutants to identify genes that influence the development of gametocytes in the most lethal human malaria parasite, P. falciparum. By doing so, we lay the foundation for large-scale functional genomic studies specifically designed to address remaining questions about sexual commitment, maturation, and mosquito infection in P. falciparum. Such functional genetic screens will serve to expedite the identification of essential pathways and processes for the development of novel transmission-blocking agents.

Protein KIC5 is a novel regulator of artemisinin stress response in the malaria parasite Plasmodium falciparum.

Simmons CF; Gibbons J; Zhang M; Oberstaller J; Pires CV; Casandra D; Wang C; Seyfang A; Otto TD; Rayner JC; Adams JH

Scientific reports 2023;13;1;399

Artemisinin combination therapies (ACTs) have led to a significant decrease in Plasmodium falciparum malaria mortality. This progress is now threatened by emerging artemisinin resistance (ART-R) linked originally in SE Asia to polymorphisms in the Kelch propeller protein (K13) and more recently to several other seemingly unrelated genetic mutations. To better understand the parasite response to ART, we are characterizing a P. falciparum mutant with altered sensitivity to ART that was created via piggyBac transposon mutagenesis. The transposon inserted near the putative transcription start site of a gene defined as a "Plasmodium-conserved gene of unknown function," now functionally linked to K13 as the Kelch13 Interacting Candidate 5 protein (KIC5). Phenotype analysis of the KIC5 mutant during intraerythrocytic asexual development identified transcriptional changes associated with DNA stress response and altered mitochondrial metabolism, linking dysregulation of the KIC5 gene to the parasite's ability to respond to ART exposure. Through characterization of the KIC5 transcriptome, we hypothesize that this gene may be essential under ART exposure to manage gene expression of the wild-type stress response at early ring stage, thereby providing a better understanding of the parasite's processes that can alter ART sensitivity.

Regulators of male and female sexual development are critical for the transmission of a malaria parasite.

Russell AJC; Sanderson T; Bushell E; Talman AM; Anar B; Girling G; Hunziker M; Kent RS; Martin JS; Metcalf T; Montandon R; Pandey V; Pardo M; Roberts AB; Sayers C; Schwach F; Choudhary JS; Rayner JC; Voet T; Modrzynska KK; Waters AP; Lawniczak MKN; Billker O

Cell host & microbe 2023;31;2;305-319.e10

Malaria transmission to mosquitoes requires a developmental switch in asexually dividing blood-stage parasites to sexual reproduction. In Plasmodium berghei, the transcription factor AP2-G is required and sufficient for this switch, but how a particular sex is determined in a haploid parasite remains unknown. Using a global screen of barcoded mutants, we here identify genes essential for the formation of either male or female sexual forms and validate their importance for transmission. High-resolution single-cell transcriptomics of ten mutant parasites portrays the developmental bifurcation and reveals a regulatory cascade of putative gene functions in the determination and subsequent differentiation of each sex. A male-determining gene with a LOTUS/OST-HTH domain as well as the protein interactors of a female-determining zinc-finger protein indicate that germ-granule-like ribonucleoprotein complexes complement transcriptional processes in the regulation of both male and female development of a malaria parasite.

The Dantu blood group prevents parasite growth in vivo: Evidence from a controlled human malaria infection study.

Kariuki SN; Macharia AW; Makale J; Nyamu W; Hoffman SL; Kapulu MC; Bejon P; Rayner JC; Williams TN;

eLife 2023;12

The long co-evolution of Homo sapiens and Plasmodium falciparum has resulted in the selection of numerous human genetic variants that confer an advantage against severe malaria and death. One such variant is the Dantu blood group antigen, which is associated with 74% protection against severe and complicated P. falciparum malaria infections in homozygous individuals, similar to that provided by the sickle haemoglobin allele (HbS). Recent in vitro studies suggest that Dantu exerts this protection by increasing the surface tension of red blood cells, thereby impeding the ability of P. falciparum merozoites to invade them and reducing parasite multiplication. However, no studies have yet explored this hypothesis in vivo.

The global transcriptome of Plasmodium falciparum mid-stage gametocytes (stages II-IV) appears largely conserved and gametocyte-specific gene expression patterns vary in clinical isolates.

Kengne-Ouafo JA; Bah SY; Kemp A; Stewart L; Amenga-Etego L; Deitsch KW; Rayner JC; Billker O; Binka FN; Sutherland CJ; Awandare GA; Urban BC; Dinko B

Microbiology spectrum 2023;11;5;e0382022

Our overall understanding of the developmental biology of malaria parasites has been greatly enhanced by recent advances in transcriptomic analysis. However, most of these investigations rely on laboratory strains (LS) that were adapted into in vitro culture many years ago, and the transcriptomes of clinical isolates (CI) circulating in human populations have not been assessed. In this study, RNA-seq was used to compare the global transcriptome of mid-stage gametocytes derived from three short-term cultured CI, with gametocytes derived from the NF54 reference laboratory strain. The core transcriptome appeared to be consistent between CI- and LS-derived gametocyte preparations, but some important differences were also observed. A majority of gametocyte-specific genes (43/53) appear to have relatively higher expression in CI-derived gametocytes than in LS-derived gametocytes, but a K-means clustering analysis showed that genes involved in flagellum- and microtubule-based processes (movement/motility) were more abundant in both groups, albeit with some differences between them. In addition, gametocytes from one CI described as CI group II gametocytes (CI:GGII) showed gene expression variation in the form of reduced gametocyte-specific gene expression compared to the other two CI-derived gametocytes (CI gametocyte group I, CI:GGI), although the mixed developmental stages used in our study is a potential confounder, only partially mitigated by the inclusion of multiple replicates for each CI. Overall, our study suggests that there may be subtle differences in the gene expression profiles of mid-stage gametocytes from CI relative to the NF54 reference strain of Plasmodium falciparum. Thus, it is necessary to deploy gametocyte-producing clinical parasite isolates to fully understand the diversity of gene expression strategies that may occur during the sequestered development of parasite sexual stages. IMPORTANCE Maturing gametocytes of Plasmodium falciparum are known to sequester away from peripheral circulation into the bone marrow until they are mature. Blocking gametocyte sequestration can prevent malaria transmission from humans to mosquitoes, but most studies aim to understand gametocyte development utilizing long-term adapted laboratory lines instead of clinical isolates. This is a particular issue for our understanding of the sexual stages, which are known to decrease rapidly during adaptation to long-term culture, meaning that many LS are unable to produce transmissible gametocytes. Using RNA-seq, we investigated the global transcriptome of mid-stage gametocytes derived from three clinical isolates and a reference strain (NF54). This identified important differences in gene expression profiles between immature gametocytes of CI and the NF54 reference strain of P. falciparum, suggesting increased investment in gametocytogenesis in clinical isolates. Our transcriptomic data highlight the use of clinical isolates in studying the morphological, cellular features and molecular biology of gametocytes.

The structure of a Plasmodium vivax Tryptophan Rich Antigen domain suggests a lipid binding function for a pan-Plasmodium multi-gene family.

Kundu P; Naskar D; McKie SJ; Dass S; Kanjee U; Introini V; Ferreira MU; Cicuta P; Duraisingh M; Deane JE; Rayner JC

Nature Communications 2023;14;1;5703

Tryptophan Rich Antigens (TRAgs) are encoded by a multi-gene family found in all Plasmodium species, but are significantly expanded in P. vivax and closely related parasites. We show that multiple P. vivax TRAgs are expressed on the merozoite surface and that one, PVP01_0000100 binds red blood cells with a strong preference for reticulocytes. Using X-ray crystallography, we solved the structure of the PVP01_0000100 C-terminal tryptophan rich domain, which defines the TRAg family, revealing a three-helical bundle that is conserved across Plasmodium and has structural homology with lipid-binding BAR domains involved in membrane remodelling. Biochemical assays confirm that the PVP01_0000100 C-terminal domain has lipid binding activity with preference for sulfatide, a glycosphingolipid present in the outer leaflet of plasma membranes. Deletion of the putative orthologue in P. knowlesi, PKNH_1300500, impacts invasion in reticulocytes, suggesting a role during this essential process. Together, this work defines an emerging molecular function for the Plasmodium TRAg family.

A molecular barcode and web-based data analysis tool to identify imported Plasmodium vivax malaria.

Trimarsanto H; Amato R; Pearson RD; Sutanto E; Noviyanti R; Trianty L; Marfurt J; Pava Z; Echeverry DF; Lopera-Mesa TM; Montenegro LM; Tobón-Castaño A; Grigg MJ; Barber B; William T; Anstey NM; Getachew S; Petros B; Aseffa A; Assefa A; Rahim AG; Chau NH; Hien TT; Alam MS; Khan WA; Ley B; Thriemer K; Wangchuck S; Hamedi Y; Adam I; Liu Y; Gao Q; Sriprawat K; Ferreira MU; Laman M; Barry A; Mueller I; Lacerda MVG; Llanos-Cuentas A; Krudsood S; Lon C; Mohammed R; Yilma D; Pereira DB; Espino FEJ; Chu CS; Vélez ID; Namaik-Larp C; Villegas MF; Green JA; Koh G; Rayner JC; Drury E; Gonçalves S; Simpson V; Miotto O; Miles A; White NJ; Nosten F; Kwiatkowski DP; Price RN; Auburn S

Communications biology 2022;5;1;1411

Traditionally, patient travel history has been used to distinguish imported from autochthonous malaria cases, but the dormant liver stages of Plasmodium vivax confound this approach. Molecular tools offer an alternative method to identify, and map imported cases. Using machine learning approaches incorporating hierarchical fixation index and decision tree analyses applied to 799 P. vivax genomes from 21 countries, we identified 33-SNP, 50-SNP and 55-SNP barcodes (GEO33, GEO50 and GEO55), with high capacity to predict the infection's country of origin. The Matthews correlation coefficient (MCC) for an existing, commonly applied 38-SNP barcode (BR38) exceeded 0.80 in 62% countries. The GEO panels outperformed BR38, with median MCCs > 0.80 in 90% countries at GEO33, and 95% at GEO50 and GEO55. An online, open-access, likelihood-based classifier framework was established to support data analysis (vivaxGEN-geo). The SNP selection and classifier methods can be readily amended for other use cases to support malaria control programs.