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Reda AG, Huwe T, Koepfli C, Assefa A, Tessema SK, Messele A, Golassa L, Mamo H. Amplicon deep sequencing of five highly polymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate population structure in Ethiopia. Malar J 2023; 22:376. [PMID: 38087335 PMCID: PMC10714478 DOI: 10.1186/s12936-023-04814-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Plasmodium falciparum genetic diversity can add information on transmission intensity and can be used to track control and elimination interventions. METHODS Dried blood spots (DBS) were collected from patients who were recruited for a P. falciparum malaria therapeutic efficacy trial in three malaria endemic sites in Ethiopia from October to December 2015, and November to December 2019. qPCR-confirmed infections were subject to amplicon sequencing of polymorphic markers ama1-D3, csp, cpp, cpmp, msp7. Genetic diversity, the proportion of multiclonal infections, multiplicity of infection, and population structure were analysed. RESULTS Among 198 samples selected for sequencing, data was obtained for 181 samples. Mean MOI was 1.38 (95% CI 1.24-1.53) and 17% (31/181) of infections were polyclonal. Mean He across all markers was 0.730. Population structure was moderate; populations from Metema and Metehara 2015 were very similar to each other, but distinct from Wondogent 2015 and Metehara 2019. CONCLUSION The high level of parasite genetic diversity and moderate population structure in this study suggests frequent gene flow of parasites among sites. The results obtained can be used as a baseline for additional parasite genetic diversity and structure studies, aiding in the formulation of appropriate control strategies in Ethiopia.
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Affiliation(s)
- Abeba Gebretsadik Reda
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Tiffany Huwe
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA.
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Ashenafi Assefa
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
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Rahmasari FV, Asih PBS, Dewayanti FK, Rotejanaprasert C, Charunwatthana P, Imwong M, Syafruddin D. Drug resistance of Plasmodium falciparum and Plasmodium vivax isolates in Indonesia. Malar J 2022; 21:354. [PMCID: PMC9703442 DOI: 10.1186/s12936-022-04385-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 11/14/2022] [Indexed: 11/29/2022] Open
Abstract
AbstractThis review article aims to investigate the genotypic profiles of Plasmodium falciparum and Plasmodium vivax isolates collected across a wide geographic region and their association with resistance to anti-malarial drugs used in Indonesia. A systematic review was conducted between 1991 and date. Search engines, such as PubMed, Science Direct, and Google Scholar, were used for articles published in English and Indonesian to search the literature. Of the 471 initially identified studies, 61 were selected for 4316 P. falciparum and 1950 P. vivax individual infections. The studies included 23 molecular studies and 38 therapeutic efficacy studies. K76T was the most common pfcrt mutation. K76N (2.1%) was associated with the haplotype CVMNN. By following dihydroartemisinin–piperaquine (DHA–PPQ) therapy, the mutant pfmdr1 alleles 86Y and 1034C were selected. Low prevalence of haplotype N86Y/Y184/D1246Ypfmdr1 reduces susceptibility to AS–AQ. SNP mutation pvmdr1 Y976F reached 96.1% in Papua and East Nusa Tenggara. Polymorphism analysis in the pfdhfr gene revealed 94/111 (84.7%) double mutants S108N/C59R or S108T/A16V in Central Java. The predominant pfdhfr haplotypes (based on alleles 16, 51, 59,108, 164) found in Indonesia were ANCNI, ANCSI, ANRNI, and ANRNL. Some isolates carried A437G (35.3%) or A437G/K540E SNPs (26.5%) in pfdhps. Two novel pfdhps mutant alleles, I588F/G and K540T, were associated with six pfdhps haplotypes. The highest prevalence of pvdhfr quadruple mutation (F57L/S58R/T61M/S117T) (61.8%) was detected in Papua. In pvdhps, the only polymorphism before and after 2008 was 383G mutation with 19% prevalence. There were no mutations in the pfk13 gene reported with validated and candidate or associated k13 mutation. An increased copy number of pfpm2, associated with piperaquine resistance, was found only in cases of reinfection. Meanwhile, mutation of pvk12 and pvpm4 I165V is unlikely associated with ART and PPQ drug resistance. DHA–PPQ is still effective in treating uncomplicated falciparum and vivax malaria. Serious consideration should be given to interrupt local malaria transmission and dynamic patterns of resistance to anti-malarial drugs to modify chemotherapeutic policy treatment strategies. The presence of several changes in pfk13 in the parasite population is of concern and highlights the importance of further evaluation of parasitic ART susceptibility in Indonesia.
Graphical Abstract
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Tsoungui Obama HCJ, Schneider KA. A maximum-likelihood method to estimate haplotype frequencies and prevalence alongside multiplicity of infection from SNP data. FRONTIERS IN EPIDEMIOLOGY 2022; 2:943625. [PMID: 38455338 PMCID: PMC10911023 DOI: 10.3389/fepid.2022.943625] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/26/2022] [Indexed: 03/09/2024]
Abstract
The introduction of genomic methods facilitated standardized molecular disease surveillance. For instance, SNP barcodes in Plasmodium vivax and Plasmodium falciparum malaria allows the characterization of haplotypes, their frequencies and prevalence to reveal temporal and spatial transmission patterns. A confounding factor is the presence of multiple genetically distinct pathogen variants within the same infection, known as multiplicity of infection (MOI). Disregarding ambiguous information, as usually done in ad-hoc approaches, leads to less confident and biased estimates. We introduce a statistical framework to obtain maximum-likelihood estimates (MLE) of haplotype frequencies and prevalence alongside MOI from malaria SNP data, i.e., multiple biallelic marker loci. The number of model parameters increases geometrically with the number of genetic markers considered and no closed-form solution exists for the MLE. Therefore, the MLE needs to be derived numerically. We use the Expectation-Maximization (EM) algorithm to derive the maximum-likelihood estimates, an efficient and easy-to-implement algorithm that yields a numerically stable solution. We also derive expressions for haplotype prevalence based on either all or just the unambiguous genetic information and compare both approaches. The latter corresponds to a biased ad-hoc estimate of prevalence. We assess the performance of our estimator by systematic numerical simulations assuming realistic sample sizes and various scenarios of transmission intensity. For reasonable sample sizes, and number of loci, the method has little bias. As an example, we apply the method to a dataset from Cameroon on sulfadoxine-pyrimethamine resistance in P. falciparum malaria. The method is not confined to malaria and can be applied to any infectious disease with similar transmission behavior. An easy-to-use implementation of the method as an R-script is provided.
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Transcending Dimensions in Apicomplexan Research: from Two-Dimensional to Three-Dimensional In Vitro Cultures. Microbiol Mol Biol Rev 2022; 86:e0002522. [PMID: 35412359 PMCID: PMC9199416 DOI: 10.1128/mmbr.00025-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Parasites belonging to the Apicomplexa phylum are among the most successful pathogens known in nature. They can infect a wide range of hosts, often remain undetected by the immune system, and cause acute and chronic illness. In this phylum, we can find parasites of human and veterinary health relevance, such as Toxoplasma, Plasmodium, Cryptosporidium, and Eimeria. There are still many unknowns about the biology of these pathogens due to the ethical and practical issues of performing research in their natural hosts. Animal models are often difficult or nonexistent, and as a result, there are apicomplexan life cycle stages that have not been studied. One recent alternative has been the use of three-dimensional (3D) systems such as organoids, 3D scaffolds with different matrices, microfluidic devices, organs-on-a-chip, and other tissue culture models. These 3D systems have facilitated and expanded the research of apicomplexans, allowing us to explore life stages that were previously out of reach and experimental procedures that were practically impossible to perform in animal models. Human- and animal-derived 3D systems can be obtained from different organs, allowing us to model host-pathogen interactions for diagnostic methods and vaccine development, drug testing, exploratory biology, and other applications. In this review, we summarize the most recent advances in the use of 3D systems applied to apicomplexans. We show the wide array of strategies that have been successfully used so far and apply them to explore other organisms that have been less studied.
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Juhairiyah J, Andiarsa D, Indriyati L, Ridha MR, Prasodjo RS, Dhewantara PW. Spatial analysis of malaria in Kotabaru, South Kalimantan, Indonesia: an evaluation to guide elimination strategies. Trans R Soc Trop Med Hyg 2021; 115:500-511. [PMID: 33169161 DOI: 10.1093/trstmh/traa125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/04/2020] [Accepted: 10/19/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Malaria remains a significant public health concern in Indonesia. Knowledge about spatial patterns of the residual malaria hotspots is critical to help design elimination strategies in Kotabaru district, South Kalimantan, Indonesia. METHODS Laboratory-confirmed malaria cases from 2012 to 2016 were analysed to examine the trend in malaria cases. Decomposition analysis was performed to assess seasonality. Annual spatial clustering of the incidence and hotspots were identified by Moran's I and the local indicator for spatial association, respectively. RESULTS The annual parasite incidence of malaria was significantly reduced by 87% from 2012 to 2016. Plasmodium vivax infections were significantly much more prevalent over time, followed by Plasmodium falciparum infections (p<0.001). The monthly seasonality of P. vivax and P. falciparum was distinct. High incidence was spatially clustered identified in the north, west and parts of south Kotabaru. Two persistent and four re-emerging high-risk clusters were identified during the period. Despite the significant reduction in the incidence of malaria, the residual high-risk villages remained clustered in the northern part of Kotabaru. CONCLUSIONS A spatially explicit decision support system is needed to support surveillance and control programs in the identified high-risk areas to succeed in the elimination goal of 2030.
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Affiliation(s)
- Juhairiyah Juhairiyah
- Tanah Bumbu Unit for Health Research and Development, National Institute of Health Research and Development, Jl. Loka Litbang, Komplek Perkantoran Pemerintah Daerah Kabupaten Tanah Bumbu, Tanah Bumbu, South Kalimantan 72171, Indonesia
| | - Dicky Andiarsa
- Tanah Bumbu Unit for Health Research and Development, National Institute of Health Research and Development, Jl. Loka Litbang, Komplek Perkantoran Pemerintah Daerah Kabupaten Tanah Bumbu, Tanah Bumbu, South Kalimantan 72171, Indonesia
| | - Liestiana Indriyati
- Tanah Bumbu Unit for Health Research and Development, National Institute of Health Research and Development, Jl. Loka Litbang, Komplek Perkantoran Pemerintah Daerah Kabupaten Tanah Bumbu, Tanah Bumbu, South Kalimantan 72171, Indonesia
| | - Muhammad Rasyid Ridha
- Tanah Bumbu Unit for Health Research and Development, National Institute of Health Research and Development, Jl. Loka Litbang, Komplek Perkantoran Pemerintah Daerah Kabupaten Tanah Bumbu, Tanah Bumbu, South Kalimantan 72171, Indonesia
| | - Rachmalina Soerachman Prasodjo
- Center for Public Health Research and Development, National Institute of Health Research and Development, Ministry of Health of Indonesia, Jl. Percetakan Negara No. 29, Jakarta 10560, Indonesia
| | - Pandji Wibawa Dhewantara
- Center for Public Health Research and Development, National Institute of Health Research and Development, Ministry of Health of Indonesia, Jl. Percetakan Negara No. 29, Jakarta 10560, Indonesia.,Pangandaran Unit for Health Research and Development, National Institute of Health Research and Development, Ministry of Health of Indonesia, Jl. Raya Pangandaran KM.3 Desa Babakan Kp Kamurang, Pangandaran 46396, West Java, Indonesia
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Systematic review of Plasmodium falciparum and Plasmodium vivax polyclonal infections: Impact of prevalence, study population characteristics, and laboratory procedures. PLoS One 2021; 16:e0249382. [PMID: 34115783 PMCID: PMC8195386 DOI: 10.1371/journal.pone.0249382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/17/2021] [Indexed: 12/27/2022] Open
Abstract
Multiple infections of genetically distinct clones of the same Plasmodium species are common in many malaria endemic settings. Mean multiplicity of infection (MOI) and the proportion of polyclonal infections are often reported as surrogate marker of transmission intensity, yet the relationship with traditional measures such as parasite prevalence is not well understood. We have searched Pubmed for articles on P. falciparum and P. vivax multiplicity, and compared the proportion of polyclonal infections and mean MOI to population prevalence. The impact of the genotyping method, number of genotyping markers, method for diagnosis (microscopy/RDT vs. PCR), presence of clinical symptoms, age, geographic region, and year of sample collection on multiplicity indices were assessed. For P. falciparum, 153 studies met inclusion criteria, yielding 275 individual data points and 33,526 genotyped individuals. The proportion of polyclonal infections ranged from 0–96%, and mean MOI from 1–6.1. For P. vivax, 54 studies met inclusion criteria, yielding 115 data points and 13,325 genotyped individuals. The proportion of polyclonal infections ranged from 0–100%, and mean MOI from 1–3.8. For both species, the proportion of polyclonal infections ranged from very low to close to 100% at low prevalence, while at high prevalence it was always high. Each percentage point increase in prevalence resulted in a 0.34% increase in the proportion of polyclonal P. falciparum infections (P<0.001), and a 0.78% increase in the proportion of polyclonal P. vivax infections (P<0.001). In multivariable analysis, higher prevalence, typing multiple markers, diagnosis of infections by PCR, and sampling in Africa were found to result in a higher proportion of P. falciparum polyclonal infections. For P. vivax, prevalence, year of study, typing multiple markers, and geographic region were significant predictors. In conclusion, polyclonal infections are frequently present in all settings, but the association between multiplicity and prevalence is weak.
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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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Miotto O, Sekihara M, Tachibana SI, Yamauchi M, Pearson RD, Amato R, Gonçalves S, Mehra S, Noviyanti R, Marfurt J, Auburn S, Price RN, Mueller I, Ikeda M, Mori T, Hirai M, Tavul L, Hetzel MW, Laman M, Barry AE, Ringwald P, Ohashi J, Hombhanje F, Kwiatkowski DP, Mita T. Emergence of artemisinin-resistant Plasmodium falciparum with kelch13 C580Y mutations on the island of New Guinea. PLoS Pathog 2020; 16:e1009133. [PMID: 33320907 PMCID: PMC7771869 DOI: 10.1371/journal.ppat.1009133] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 12/29/2020] [Accepted: 11/05/2020] [Indexed: 12/22/2022] Open
Abstract
The rapid and aggressive spread of artemisinin-resistant Plasmodium falciparum carrying the C580Y mutation in the kelch13 gene is a growing threat to malaria elimination in Southeast Asia, but there is no evidence of their spread to other regions. We conducted cross-sectional surveys in 2016 and 2017 at two clinics in Wewak, Papua New Guinea (PNG) where we identified three infections caused by C580Y mutants among 239 genotyped clinical samples. One of these mutants exhibited the highest survival rate (6.8%) among all parasites surveyed in ring-stage survival assays (RSA) for artemisinin. Analyses of kelch13 flanking regions, and comparisons of deep sequencing data from 389 clinical samples from PNG, Indonesian Papua and Western Cambodia, suggested an independent origin of the Wewak C580Y mutation, showing that the mutants possess several distinctive genetic features. Identity by descent (IBD) showed that multiple portions of the mutants' genomes share a common origin with parasites found in Indonesian Papua, comprising several mutations within genes previously associated with drug resistance, such as mdr1, ferredoxin, atg18 and pnp. These findings suggest that a P. falciparum lineage circulating on the island of New Guinea has gradually acquired a complex ensemble of variants, including kelch13 C580Y, which have affected the parasites' drug sensitivity. This worrying development reinforces the need for increased surveillance of the evolving parasite populations on the island, to contain the spread of resistance.
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Affiliation(s)
- Olivo Miotto
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, United Kingdom
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Makoto Sekihara
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Shin-Ichiro Tachibana
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Masato Yamauchi
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Richard D. Pearson
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | - Somya Mehra
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | | | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Sarah Auburn
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ivo Mueller
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Mie Ikeda
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Toshiyuki Mori
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Makoto Hirai
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
| | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel W. Hetzel
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Moses Laman
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Alyssa E. Barry
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
- University of Melbourne, Melbourne, Australia
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), Deakin University, Geelong, Australia
- Burnet Institute, Melbourne, Australia
| | | | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Madang, Papua New Guinea
| | - Dominic P. Kwiatkowski
- MRC Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University Faculty of Medicine, Tokyo, Japan
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