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Zhan Q, He Q, Tiedje KE, Day KP, Pascual M. Hyper-diverse antigenic variation and resilience to transmission-reducing intervention in falciparum malaria. medRxiv 2024:2024.02.01.24301818. [PMID: 38370729 PMCID: PMC10871444 DOI: 10.1101/2024.02.01.24301818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Intervention against falciparum malaria in high transmission regions remains challenging, with relaxation of control efforts typically followed by rapid resurgence. Resilience to intervention co-occurs with incomplete immunity, whereby children eventually become protected from severe disease but not infection and a large transmission reservoir results from high asymptomatic prevalence across all ages. Incomplete immunity relates to the vast antigenic variation of the parasite, with the major surface antigen of the blood stage of infection encoded by the multigene family known as var. Recent deep sampling of var sequences from individual isolates in northern Ghana showed that parasite population structure exhibited persistent features of high-transmission regions despite the considerable decrease in prevalence during transient intervention with indoor residual spraying (IRS). We ask whether despite such apparent limited impact, the transmission system had been brought close to a transition in both prevalence and resurgence ability. With a stochastic agent-based model, we investigate the existence of such a transition to pre-elimination with intervention intensity, and of molecular indicators informative of its approach. We show that resurgence ability decreases sharply and nonlinearly across a narrow region of intervention intensities in model simulations, and identify informative molecular indicators based on var gene sequences. Their application to the survey data indicates that the transmission system in northern Ghana was brought close to transition by IRS. These results suggest that sustaining and intensifying intervention would have pushed malaria dynamics to a slow-rebound regime with an increased probability of local parasite extinction.
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Affiliation(s)
- Qi Zhan
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago; Chicago, IL, 60637, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University; West Lafayette, IN, 47907, USA
| | - Kathryn E Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Karen P Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Mercedes Pascual
- Department of Biology, New York University; New York, NY, 10012, USA
- Department of Environmental Studies, New York University; New York, NY, 10012, USA
- Santa Fe Institute; Santa Fe, NM, 87501, USA
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Korsah MA, Johnston ST, Tiedje KE, Day KP, Flegg JA, Walker CR. Mathematical assessment of the role of intervention programs for malaria control. medRxiv 2023:2023.12.18.23300185. [PMID: 38196597 PMCID: PMC10775318 DOI: 10.1101/2023.12.18.23300185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Malaria remains a global health problem despite the many attempts to control and eradicate it. There is an urgent need to understand the current transmission dynamics of malaria and to determine the interventions necessary to control malaria. In this paper, we seek to develop a fit-for-purpose mathematical model to assess the interventions needed to control malaria in an endemic setting. To achieve this, we formulate a malaria transmission model to analyse the spread of malaria in the presence of interventions. A sensitivity analysis of the model is performed to determine the relative impact of the model parameters on disease transmission. We explore how existing variations in the recruitment and management of intervention strategies affect malaria transmission. Results obtained from the study imply that the discontinuation of existing interventions has a significant effect on malaria prevalence. Thus, the maintenance of interventions is imperative for malaria elimination and eradication. In a scenario study aimed at assessing the impact of long-lasting insecticidal nets (LLINs), indoor residual spraying (IRS), and localized individual measures, our findings indicate that increased LLINs utilization and extended IRS coverage (with longer-lasting insecticides) cause a more pronounced reduction in symptomatic malaria prevalence compared to a reduced LLINs utilization and shorter IRS coverage. Additionally, our study demonstrates the impact of localized preventive measures in mitigating the spread of malaria when compared to the absence of interventions.
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Affiliation(s)
- Maame Akua Korsah
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Stuart T Johnston
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Kathryn E Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Karen P Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Jennifer A Flegg
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
| | - Camelia R Walker
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
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Tan MH, Tiedje KE, Feng Q, Zhan Q, Pascual M, Shim H, Chan YB, Day KP. A paradoxical population structure of var DBLα types in Africa. bioRxiv 2023:2023.11.05.565723. [PMID: 37986738 PMCID: PMC10659346 DOI: 10.1101/2023.11.05.565723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
The var multigene family encodes the P. falciparum erythrocyte membrane protein 1 (PfEMP1), which is important in host-parasite interaction as a virulence factor and major surface antigen of the blood stages of the parasite, responsible for maintaining chronic infection. Whilst important in the biology of P. falciparum, these genes (50 to 60 genes per parasite genome) are routinely excluded from whole genome analyses due to their hyper-diversity, achieved primarily through recombination. The PfEMP1 head structure almost always consists of a DBLα-CIDR tandem. Categorised into different groups (upsA, upsB, upsC), different head structures have been associated with different ligand-binding affinities and disease severities. We study how conserved individual DBLα types are at the country, regional, and local scales in Sub-Saharan Africa. Using publicly-available sequence datasets and a novel ups classification algorithm, cUps, we performed an in silico exploration of DBLα conservation through time and space in Africa. In all three ups groups, the population structure of DBLα types in Africa consists of variants occurring at rare, low, moderate, and high frequencies. Non-rare variants were found to be temporally stable in a local area in endemic Ghana. When inspected across different geographical scales, we report different levels of conservation; while some DBLα types were consistently found in high frequencies in multiple African countries, others were conserved only locally, signifying local preservation of specific types. Underlying this population pattern is the composition of DBLα types within each isolate DBLα repertoire, revealed to also consist of a mix of types found at rare, low, moderate, and high frequencies in the population. We further discuss the adaptive forces and balancing selection, including host genetic factors, potentially shaping the evolution and diversity of DBLα types in Africa.
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Affiliation(s)
- Mun Hua Tan
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Kathryn E Tiedje
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
| | - Qian Feng
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Qi Zhan
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago; Chicago, Illinois, USA
| | - Heejung Shim
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Yao-Ban Chan
- School of Mathematics and Statistics / Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Karen P Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, AU
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Tiedje KE, Zhan Q, Ruybal-Pésantez S, Tonkin-Hill G, He Q, Tan MH, Argyropoulos DC, Deed SL, Ghansah A, Bangre O, Oduro AR, Koram KA, Pascual M, Day KP. Measuring changes in Plasmodium falciparum census population size in response to sequential malaria control interventions. medRxiv 2023:2023.05.18.23290210. [PMID: 37292908 PMCID: PMC10246142 DOI: 10.1101/2023.05.18.23290210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we introduce a new endpoint "census population size" to evaluate the epidemiology and control of Plasmodium falciparum infections, where the parasite, rather than the infected human host, is the unit of measurement. To calculate census population size, we rely on a definition of parasite variation known as multiplicity of infection (M O I v a r ), based on the hyper-diversity of the v a r multigene family. We present a Bayesian approach to estimate M O I v a r from sequencing and counting the number of unique DBLα tags (or DBLα types) of v a r genes, and derive from it census population size by summation of M O I v a r in the human population. We track changes in this parasite population size and structure through sequential malaria interventions by indoor residual spraying (IRS) and seasonal malaria chemoprevention (SMC) from 2012 to 2017 in an area of high-seasonal malaria transmission in northern Ghana. Following IRS, which reduced transmission intensity by > 90% and decreased parasite prevalence by ~40-50%, significant reductions in v a r diversity, M O I v a r , and population size were observed in ~2,000 humans across all ages. These changes, consistent with the loss of diverse parasite genomes, were short lived and 32-months after IRS was discontinued and SMC was introduced, v a r diversity and population size rebounded in all age groups except for the younger children (1-5 years) targeted by SMC. Despite major perturbations from IRS and SMC interventions, the parasite population remained very large and retained the v a r population genetic characteristics of a high-transmission system (high v a r diversity; low v a r repertoire similarity) demonstrating the resilience of P. falciparum to short-term interventions in high-burden countries of sub-Saharan Africa.
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Affiliation(s)
- Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Qi Zhan
- Committee on Genetics, Genomics and Systems Biology, The University of Chicago; Chicago, Illinois, USA
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
| | - Shazia Ruybal-Pésantez
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Gerry Tonkin-Hill
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute; Melbourne, Australia
| | - Qixin He
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
| | - Samantha L. Deed
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana; Legon, Ghana
| | - Oscar Bangre
- Navrongo Health Research Centre, Ghana Health Service; Navrongo, Ghana
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service; Navrongo, Ghana
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana; Legon, Ghana
| | - Mercedes Pascual
- Department of Ecology and Evolution, The University of Chicago; Chicago, Illinois, USA
- Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne; Melbourne, Australia
- School of BioSciences, Bio21 Institute, The University of Melbourne; Melbourne, Australia
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Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
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Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
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Ghansah A, Tiedje KE, Argyropoulos DC, Onwona CO, Deed SL, Labbé F, Oduro AR, Koram KA, Pascual M, Day KP. Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission. Front Parasitol 2023; 2:1067966. [PMID: 38031549 PMCID: PMC10686283 DOI: 10.3389/fpara.2023.1067966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
A major motivation for developing molecular methods for malaria surveillance is to measure the impact of control interventions on the population genetics of Plasmodium falciparum as a potential marker of progress towards elimination. Here we assess three established methods (i) single nucleotide polymorphism (SNP) barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in 82.3% (median 3; range 1-18) and 57.8% (median 2; range 1-12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose ~200 low-complexity infections biased to single and double clone infections for analysis. Each genotyping method presented a different pattern of change in diversity and population structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (i.e., SNPs < microsatellites < var). Varcoding and microsatellite genotyping showed the overall failure of the IRS intervention to significantly change the population structure from pre-IRS characteristics (i.e., many diverse genomes of low genetic similarity). The 24-SNP barcode provided limited information for analysis, largely due to the biallelic nature of SNPs leading to a high proportion of double-allele calls and a view of more isolate relatedness compared to microsatellites and varcoding. Relative performance, suitability, and cost-effectiveness of the methods relevant to sample size and local malaria elimination in high-transmission endemic areas are discussed.
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Affiliation(s)
- Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Dionne C. Argyropoulos
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Christiana O. Onwona
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Samantha L. Deed
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Frédéric Labbé
- Department Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mercedes Pascual
- Department Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Santa Fe Institute, Santa Fe, NM, United States
| | - Karen P. Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
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Ruybal-Pesántez S, Sáenz FE, Deed SL, Johnson EK, Larremore DB, Vera-Arias CA, Tiedje KE, Day KP. Molecular epidemiology of continued Plasmodium falciparum disease transmission after an outbreak in Ecuador. Front Trop Dis 2023. [DOI: 10.3389/fitd.2023.1085862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023] Open
Abstract
To better understand the factors underlying the continued incidence of clinical episodes of falciparum malaria in E-2025 countries targeting elimination, we characterized the molecular epidemiology of Plasmodium falciparum disease transmission after a clonal outbreak in Ecuador. Here we study disease transmission by documenting the diversity and population structure of the major variant surface antigen of the blood stages of P. falciparum encoded by the var multigene family. We used a high-resolution genotyping method, “varcoding”, involving targeted amplicon sequencing to fingerprint the DBLα encoding region of var genes to describe both antigenic var diversity and var repertoire similarity or relatedness in parasite isolates from clinical cases. We identified nine genetic varcodes in 58 P. falciparum isolates causing clinical disease in 2013-2015. Network analyses revealed that four of the varcodes were highly related to the outbreak varcode, with identification of possible diversification of the outbreak parasites by recombination as seen in three of those varcodes. The majority of clinical cases in Ecuador were associated with parasites with highly related or recombinant varcodes to the outbreak clone and due to local transmission rather than recent importation of parasites from other endemic countries. Sharing of types in Ecuadorian varcodes to those sampled in South American varcodes reflects historical parasite importation of some varcodes, especially from Colombia and Peru. Our findings highlight the translational application of varcoding for outbreak surveillance in epidemic/unstable malaria transmission, such as in E-2025 countries, and point to the need for surveillance of local reservoirs of infection in Ecuador to achieve the malaria elimination goal by 2025.
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Labbé F, He Q, Zhan Q, Tiedje KE, Argyropoulos DC, Tan MH, Ghansah A, Day KP, Pascual M. Neutral vs. non-neutral genetic footprints of Plasmodium falciparum multiclonal infections. PLoS Comput Biol 2023; 19:e1010816. [PMID: 36595546 PMCID: PMC9838855 DOI: 10.1371/journal.pcbi.1010816] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 01/13/2023] [Accepted: 12/14/2022] [Indexed: 01/04/2023] Open
Abstract
At a time when effective tools for monitoring malaria control and eradication efforts are crucial, the increasing availability of molecular data motivates their application to epidemiology. The multiplicity of infection (MOI), defined as the number of genetically distinct parasite strains co-infecting a host, is one key epidemiological parameter for evaluating malaria interventions. Estimating MOI remains a challenge for high-transmission settings where individuals typically carry multiple co-occurring infections. Several quantitative approaches have been developed to estimate MOI, including two cost-effective ones relying on molecular data: i) THE REAL McCOIL method is based on putatively neutral single nucleotide polymorphism loci, and ii) the varcoding method is a fingerprinting approach that relies on the diversity and limited repertoire overlap of the var multigene family encoding the major Plasmodium falciparum blood-stage antigen PfEMP1 and is therefore under selection. In this study, we assess the robustness of the MOI estimates generated with these two approaches by simulating P. falciparum malaria dynamics under three transmission conditions using an extension of a previously developed stochastic agent-based model. We demonstrate that these approaches are complementary and best considered across distinct transmission intensities. While varcoding can underestimate MOI, it allows robust estimation, especially under high transmission where repertoire overlap is extremely limited from frequency-dependent selection. In contrast, THE REAL McCOIL often considerably overestimates MOI, but still provides reasonable estimates for low and moderate transmission. Regardless of transmission intensity, results for THE REAL McCOIL indicate that an inaccurate tail at high MOI values is generated, and that at high transmission, an apparently reasonable estimated MOI distribution can arise from some degree of compensation between overestimation and underestimation. As many countries pursue malaria elimination targets, defining the most suitable approach to estimate MOI based on sample size and local transmission intensity is highly recommended for monitoring the impact of intervention programs.
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Affiliation(s)
- Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indianapolis, United States of America
| | - Qi Zhan
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Dionne C. Argyropoulos
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Mun Hua Tan
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Science, University of Ghana, Legon, Ghana
| | - Karen P. Day
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, The University of Chicago, Chicago, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
- * E-mail:
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Ruybal-Pesántez S, Tiedje KE, Pilosof S, Tonkin-Hill G, He Q, Rask TS, Amenga-Etego L, Oduro AR, Koram KA, Pascual M, Day KP. Age-specific patterns of DBLα var diversity can explain why residents of high malaria transmission areas remain susceptible to Plasmodium falciparum blood stage infection throughout life. Int J Parasitol 2022; 52:721-731. [PMID: 35093396 PMCID: PMC9339046 DOI: 10.1016/j.ijpara.2021.12.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 12/26/2022]
Abstract
Immunity to Plasmodium falciparum is non-sterilising, thus individuals residing in malaria-endemic areas are at risk of infection throughout their lifetime. Here we seek to find a genomic epidemiological explanation for why residents of all ages harbour blood stage infections despite lifelong exposure to P. falciparum in areas of high transmission. We do this by exploring, for the first known time, the age-specific patterns of diversity of variant antigen encoding (var) genes in the reservoir of infection. Microscopic and submicroscopic P. falciparum infections were analysed at the end of the wet and dry seasons in 2012-2013 for a cohort of 1541 residents aged from 1 to 91 years in an area characterised by high seasonal malaria transmission in Ghana. By sequencing the near ubiquitous Duffy-binding-like alpha domain (DBLα) that encodes immunogenic domains, we defined var gene diversity in an estimated 1096 genomes detected in sequential wet and dry season sampling of this cohort. Unprecedented var (DBLα) diversity was observed in all ages with 42,399 unique var types detected. There was a high degree of maintenance of types between seasons (>40% seen more than once), with many of the same types, especially upsA, appearing multiple times in isolates from different individuals. Children and adolescents were found to be significant reservoirs of var DBLα diversity compared with adults. Var repertoires within individuals were highly variable, with children having more related var repertoires compared to adolescents and adults. Individuals of all ages harboured multiple genomes with var repertoires unrelated to those infecting other hosts. High turnover of parasites with diverse isolate var repertoires was also observed in all ages. These age-specific patterns are best explained by variant-specific immune selection. The observed level of var diversity for the population was then used to simulate the development of variant-specific immunity to the diverse var types under conservative assumptions. Simulations showed that the extent of observed var diversity with limited repertoire relatedness was sufficient to explain why adolescents and adults in this community remain susceptible to blood stage infection, even with multiple genomes.
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Affiliation(s)
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute, The University of Melbourne, Australia,Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Australia
| | - Shai Pilosof
- Department of Ecology and Evolution, University of Chicago, USA,Department of Life Sciences, Ben-Gurion University, Be’er-Sheva, Israel
| | - Gerry Tonkin-Hill
- School of BioSciences, Bio21 Institute, The University of Melbourne, Australia,Bioinformatics Division, Walter and Eliza Hall Institute of Medial Research, Australia
| | - Qixin He
- Department of Ecology and Evolution, University of Chicago, USA
| | - Thomas S. Rask
- School of BioSciences, Bio21 Institute, The University of Melbourne, Australia
| | - Lucas Amenga-Etego
- West African Centre for Cell Biology and Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Ghana,Navrongo Health Research Centre, Ghana Health Service, Ghana
| | | | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana
| | | | - Karen P. Day
- School of BioSciences, Bio21 Institute, The University of Melbourne, Australia,Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Australia,Corresponding author. (K.P. Day)
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He Q, Pilosof S, Tiedje KE, Day KP, Pascual M. Corrigendum: Frequency-dependent competition between strains imparts persistence to perturbations in a model of Plasmodium falciparum malaria transmission. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.971161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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11
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Tiedje KE, Oduro AR, Bangre O, Amenga-Etego L, Dadzie SK, Appawu MA, Frempong K, Asoala V, Ruybal-Pésantez S, Narh CA, Deed SL, Argyropoulos DC, Ghansah A, Agyei SA, Segbaya S, Desewu K, Williams I, Simpson JA, Malm K, Pascual M, Koram KA, Day KP. Indoor residual spraying with a non-pyrethroid insecticide reduces the reservoir of Plasmodium falciparum in a high-transmission area in northern Ghana. PLOS Glob Public Health 2022; 2:e0000285. [PMID: 35600674 PMCID: PMC9121889 DOI: 10.1371/journal.pgph.0000285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
High-malaria burden countries in sub-Saharan Africa are shifting from malaria control towards elimination. Hence, there is need to gain a contemporary understanding of how indoor residual spraying (IRS) with non-pyrethroid insecticides when combined with long-lasting insecticidal nets (LLINs) impregnated with pyrethroid insecticides, contribute to the efforts of National Malaria Control Programmes to interrupt transmission and reduce the reservoir of Plasmodium falciparum infections across all ages. Using an interrupted time-series study design, four age-stratified malariometric surveys, each of ~2,000 participants, were undertaken pre- and post-IRS in Bongo District, Ghana. Following the application of three-rounds of IRS, P. falciparum transmission intensity declined, as measured by a >90% reduction in the monthly entomological inoculation rate. This decline was accompanied by reductions in parasitological parameters, with participants of all ages being significantly less likely to harbor P. falciparum infections at the end of the wet season post-IRS (aOR = 0.22 [95% CI: 0.19-0.26], p-value < 0.001). In addition, multiplicity of infection (MOI var ) was measured using a parasite fingerprinting tool, designed to capture within-host genome diversity. At the end of the wet season post-IRS, the prevalence of multi-genome infections declined from 75.6% to 54.1%. This study demonstrates that in areas characterized by high seasonal malaria transmission, IRS in combination with LLINs can significantly reduce the reservoir of P. falciparum infection. Nonetheless despite this success, 41.6% of the population, especially older children and adolescents, still harboured multi-genome infections. Given the persistence of this diverse reservoir across all ages, these data highlight the importance of sustaining vector control in combination with targeted chemotherapy to move high-transmission settings towards pre-elimination. This study also points to the benefits of molecular surveillance to ensure that incremental achievements are not lost and that the goals advocated for in the WHO's High Burden to High Impact strategy are realized.
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Affiliation(s)
- Kathryn E. Tiedje
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Oscar Bangre
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Lucas Amenga-Etego
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Samuel K. Dadzie
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Maxwell A. Appawu
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kwadwo Frempong
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Victor Asoala
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Shazia Ruybal-Pésantez
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Charles A. Narh
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Samantha L. Deed
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Dionne C. Argyropoulos
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Anita Ghansah
- Parasitology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Samuel A. Agyei
- AngloGold Ashanti (Ghana) Malaria Control Programme, Obuasi, Ghana
| | | | - Kwame Desewu
- AngloGold Ashanti (Ghana) Malaria Control Programme, Obuasi, Ghana
| | | | - Julie A. Simpson
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Australia
| | - Keziah Malm
- Ghana National Malaria Control Programme, Public Health Division, Ghana Health Service, Accra, Ghana
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States of America
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karen P. Day
- School of BioSciences, The University of Melbourne, at the Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
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12
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Feng Q, Tiedje KE, Ruybal-Pesántez S, Tonkin-Hill G, Duffy MF, Day KP, Shim H, Chan YB. An accurate method for identifying recent recombinants from unaligned sequences. Bioinformatics 2022; 38:1823-1829. [PMID: 35025988 PMCID: PMC8963311 DOI: 10.1093/bioinformatics/btac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/18/2021] [Indexed: 11/12/2022] Open
Abstract
Abstract
Motivation
Recombination is a fundamental process in molecular evolution, and the identification of recombinant sequences is thus of major interest. However, current methods for detecting recombinants are primarily designed for aligned sequences. Thus they struggle with analyses of highly diverse genes, such as the var genes of the malaria parasite Plasmodium falciparum, which are known to diversify primarily through recombination.
Results
We introduce an algorithm to detect recent recombinant sequences from a dataset without a full multiple alignment. Our algorithm can handle thousands of gene-length sequences without the need for a reference panel. We demonstrate the accuracy of our algorithm through extensive numerical simulations; in particular, it maintains its effectiveness in the presence of insertions and deletions. We apply our algorithm to a dataset of 17,335 DBLα types in var genes from Ghana, observing that sequences belonging to the same ups group or domain subclass recombine amongst themselves more frequently, and that non-recombinant DBLα types are more conserved than recombinant ones.
Availability
Source code is freely available at https://github.com/qianfeng2/detREC_program.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Qian Feng
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Kathryn E Tiedje
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3000, Australia
| | - Shazia Ruybal-Pesántez
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, 3010, Australia
- Burnet Institute, Melbourne, VIC, 3004, Australia
| | - Gerry Tonkin-Hill
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, 3052, Australia
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, CB10 1SA, United Kingdom
| | - Michael F Duffy
- Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, 3004, Australia
| | - Karen P Day
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3010, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity and Bio21 Molecular Science and Biotechnology Institute, Melbourne, VIC, 3000, Australia
| | - Heejung Shim
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Yao-Ban Chan
- Melbourne Integrative Genomics/School of Mathematics and Statistics, The University of Melbourne, Melbourne, VIC, 3010, Australia
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Argyropoulos DC, Ruybal‐Pesántez S, Deed SL, Oduro AR, Dadzie SK, Appawu MA, Asoala V, Pascual M, Koram KA, Day KP, Tiedje KE. The impact of indoor residual spraying on Plasmodium falciparum microsatellite variation in an area of high seasonal malaria transmission in Ghana, West Africa. Mol Ecol 2021; 30:3974-3992. [PMID: 34143538 PMCID: PMC8456823 DOI: 10.1111/mec.16029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 05/26/2021] [Accepted: 06/01/2021] [Indexed: 01/16/2023]
Abstract
Here, we report the first population genetic study to examine the impact of indoor residual spraying (IRS) on Plasmodium falciparum in humans. This study was conducted in an area of high seasonal malaria transmission in Bongo District, Ghana. IRS was implemented during the dry season (November-May) in three consecutive years between 2013 and 2015 to reduce transmission and attempt to bottleneck the parasite population in humans towards lower diversity with greater linkage disequilibrium. The study was done against a background of widespread use of long-lasting insecticidal nets, typical for contemporary malaria control in West Africa. Microsatellite genotyping with 10 loci was used to construct 392 P. falciparum multilocus infection haplotypes collected from two age-stratified cross-sectional surveys at the end of the wet seasons pre- and post-IRS. Three-rounds of IRS, under operational conditions, led to a >90% reduction in transmission intensity and a 35.7% reduction in the P. falciparum prevalence (p < .001). Despite these declines, population genetic analysis of the infection haplotypes revealed no dramatic changes with only a slight, but significant increase in genetic diversity (He : pre-IRS = 0.79 vs. post-IRS = 0.81, p = .048). Reduced relatedness of the parasite population (p < .001) was observed post-IRS, probably due to decreased opportunities for outcrossing. Spatiotemporal genetic differentiation between the pre- and post-IRS surveys (D = 0.0329 [95% CI: 0.0209 - 0.0473], p = .034) was identified. These data provide a genetic explanation for the resilience of P. falciparum to short-term IRS programmes in high-transmission settings in sub-Saharan Africa.
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Affiliation(s)
- Dionne C. Argyropoulos
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Shazia Ruybal‐Pesántez
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical ResearchMelbourneVic.Australia
- Present address:
Department of Medical Biology and Bio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Present address:
Burnet InstituteMelbourneVic.Australia
| | - Samantha L. Deed
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Abraham R. Oduro
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Samuel K. Dadzie
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Maxwell A. Appawu
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Victor Asoala
- Navrongo Health Research CentreGhana Health ServiceNavrongoGhana
| | - Mercedes Pascual
- Department of Ecology and EvolutionUniversity of ChicagoChicagoUSA
| | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical ResearchUniversity of GhanaLegonGhana
| | - Karen P. Day
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
| | - Kathryn E. Tiedje
- School of BioSciencesBio21 InstituteThe University of MelbourneMelbourneVic.Australia
- Department of Microbiology and ImmunologyBio21 Institute and Peter Doherty InstituteThe University of MelbourneMelbourneVic.Australia
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14
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He Q, Pilosof S, Tiedje KE, Day KP, Pascual M. Frequency-Dependent Competition Between Strains Imparts Persistence to Perturbations in a Model of Plasmodium falciparum Malaria Transmission. Front Ecol Evol 2021; 9. [PMID: 35433714 PMCID: PMC9012452 DOI: 10.3389/fevo.2021.633263] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In high-transmission endemic regions, local populations of Plasmodium falciparum exhibit vast diversity of the var genes encoding its major surface antigen, with each parasite comprising multiple copies from this diverse gene pool. This strategy to evade the immune system through large combinatorial antigenic diversity is common to other hyperdiverse pathogens. It underlies a series of fundamental epidemiological characteristics, including large reservoirs of transmission from high prevalence of asymptomatics and long-lasting infections. Previous theory has shown that negative frequency-dependent selection (NFDS) mediated by the acquisition of specific immunity by hosts structures the diversity of var gene repertoires, or strains, in a pattern of limiting similarity that is both non-random and non-neutral. A combination of stochastic agent-based models and network analyses has enabled the development and testing of theory in these complex adaptive systems, where assembly of local parasite diversity occurs under frequency-dependent selection and large pools of variation. We show here the application of these approaches to theory comparing the response of the malaria transmission system to intervention when strain diversity is assembled under (competition-based) selection vs. a form of neutrality, where immunity depends only on the number but not the genetic identity of previous infections. The transmission system is considerably more persistent under NFDS, exhibiting a lower extinction probability despite comparable prevalence during intervention. We explain this pattern on the basis of the structure of strain diversity, in particular the more pronounced fraction of highly dissimilar parasites. For simulations that survive intervention, prevalence under specific immunity is lower than under neutrality, because the recovery of diversity is considerably slower than that of prevalence and decreased var gene diversity reduces parasite transmission. A Principal Component Analysis of network features describing parasite similarity reveals that despite lower overall diversity, NFDS is quickly restored after intervention constraining strain structure and maintaining patterns of limiting similarity important to parasite persistence. Given the described enhanced persistence under perturbation, intervention efforts will likely require longer times than the usual practice to eliminate P. falciparum populations. We discuss implications of our findings and potential analogies for ecological communities with non-neutral assembly processes involving frequency-dependence.
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Affiliation(s)
- Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States
| | - Shai Pilosof
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, United States
- Santa Fe Institute, Santa Fe, NM, United States
- Correspondence: Mercedes Pascual,
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15
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Tonkin-Hill G, Ruybal-Pesántez S, Tiedje KE, Rougeron V, Duffy MF, Zakeri S, Pumpaibool T, Harnyuttanakorn P, Branch OH, Ruiz-Mesía L, Rask TS, Prugnolle F, Papenfuss AT, Chan YB, Day KP. Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents. PLoS Genet 2021; 17:e1009269. [PMID: 33630855 PMCID: PMC7906310 DOI: 10.1371/journal.pgen.1009269] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 11/10/2020] [Indexed: 11/18/2022] Open
Abstract
Malaria remains a major public health problem in many countries. Unlike influenza and HIV, where diversity in immunodominant surface antigens is understood geographically to inform disease surveillance, relatively little is known about the global population structure of PfEMP1, the major variant surface antigen of the malaria parasite Plasmodium falciparum. The complexity of the var multigene family that encodes PfEMP1 and that diversifies by recombination, has so far precluded its use in malaria surveillance. Recent studies have demonstrated that cost-effective deep sequencing of the region of var genes encoding the PfEMP1 DBLα domain and subsequent classification of within host sequences at 96% identity to define unique DBLα types, can reveal structure and strain dynamics within countries. However, to date there has not been a comprehensive comparison of these DBLα types between countries. By leveraging a bioinformatic approach (jumping hidden Markov model) designed specifically for the analysis of recombination within var genes and applying it to a dataset of DBLα types from 10 countries, we are able to describe population structure of DBLα types at the global scale. The sensitivity of the approach allows for the comparison of the global dataset to ape samples of Plasmodium Laverania species. Our analyses show that the evolution of the parasite population emerging out of Africa underlies current patterns of DBLα type diversity. Most importantly, we can distinguish geographic population structure within Africa between Gabon and Ghana in West Africa and Uganda in East Africa. Our evolutionary findings have translational implications in the context of globalization. Firstly, DBLα type diversity can provide a simple diagnostic framework for geographic surveillance of the rapidly evolving transmission dynamics of P. falciparum. It can also inform efforts to understand the presence or absence of global, regional and local population immunity to major surface antigen variants. Additionally, we identify a number of highly conserved DBLα types that are present globally that may be of biological significance and warrant further characterization.
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Affiliation(s)
- Gerry Tonkin-Hill
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, Australia
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Shazia Ruybal-Pesántez
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Virginie Rougeron
- Laboratoire MIVEGEC, Université de Montpellier-CNRS-IRD, Montpellier, France
| | - Michael F. Duffy
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
| | - Sedigheh Zakeri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Tepanata Pumpaibool
- Biomedical Science, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
| | - Pongchai Harnyuttanakorn
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - OraLee H. Branch
- Concordia University, Portland, Oregon, United States of America
- Universidad Nacional de la Amazonía Peruana, Iquitos, Perú
| | | | - Thomas S. Rask
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Franck Prugnolle
- Laboratoire MIVEGEC, Université de Montpellier-CNRS-IRD, Montpellier, France
| | - Anthony T. Papenfuss
- Bioinformatics Division, Walter and Eliza Hall Institute, Melbourne, Australia
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
- Peter MacCallum Cancer Centre, Victorian Comprehensive Cancer Centre, Melbourne, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - Yao-ban Chan
- School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia
- Melbourne Integrative Genomics, The University of Melbourne, Melbourne, Australia
| | - Karen P. Day
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, Australia
- * E-mail:
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Narh CA, Ghansah A, Duffy MF, Ruybal-Pesántez S, Onwona CO, Oduro AR, Koram KA, Day KP, Tiedje KE. Evolution of Antimalarial Drug Resistance Markers in the Reservoir of Plasmodium falciparum Infections in the Upper East Region of Ghana. J Infect Dis 2020; 222:1692-1701. [PMID: 32459360 PMCID: PMC7982568 DOI: 10.1093/infdis/jiaa286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 05/22/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The majority of Plasmodium falciparum infections, constituting the reservoir in all ages, are asymptomatic in high-transmission settings in Africa. The role of this reservoir in the evolution and spread of drug resistance was explored. METHODS Population genetic analyses of the key drug resistance-mediating polymorphisms were analyzed in a cross-sectional survey of asymptomatic P. falciparum infections across all ages in Bongo District, Ghana. RESULTS Seven years after the policy change to artemisinin-based combination therapies in 2005, the pfcrt K76 and pfmdr1 N86 wild-type alleles have nearly reached fixation and have expanded via soft selective sweeps on multiple genetic backgrounds. By constructing the pfcrt-pfmdr1-pfdhfr-pfdhps multilocus haplotypes, we found that the alleles at these loci were in linkage equilibrium and that multidrug-resistant parasites have not expanded in this reservoir. For pfk13, 32 nonsynonymous mutations were identified; however, none were associated with artemisinin-based combination therapy resistance. CONCLUSIONS The prevalence and selection of alleles/haplotypes by antimalarials were similar to that observed among clinical cases in Ghana, indicating that they do not represent 2 subpopulations with respect to these markers. Thus, the P. falciparum reservoir in all ages can contribute to the maintenance and spread of antimalarial resistance.
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Affiliation(s)
- Charles A Narh
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Michael F Duffy
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute and Peter Doherty Institute, Melbourne, Australia
| | - Shazia Ruybal-Pesántez
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
| | - Christiana O Onwona
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Abraham R Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Kwadwo A Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karen P Day
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute and Peter Doherty Institute, Melbourne, Australia
| | - Kathryn E Tiedje
- School of BioSciences, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute, Melbourne, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Molecular Science and Biotechnology Institute and Peter Doherty Institute, Melbourne, Australia
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17
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Pilosof S, He Q, Tiedje KE, Ruybal-Pesántez S, Day KP, Pascual M. Competition for hosts modulates vast antigenic diversity to generate persistent strain structure in Plasmodium falciparum. PLoS Biol 2019; 17:e3000336. [PMID: 31233490 PMCID: PMC6611651 DOI: 10.1371/journal.pbio.3000336] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 07/05/2019] [Accepted: 06/05/2019] [Indexed: 01/14/2023] Open
Abstract
In their competition for hosts, parasites with antigens that are novel to the host immune system will be at a competitive advantage. The resulting frequency-dependent selection can structure parasite populations into strains of limited genetic overlap. For the causative agent of malaria, Plasmodium falciparum, the high recombination rates and associated vast diversity of its highly antigenic and multicopy var genes preclude such clear clustering in endemic regions. This undermines the definition of strains as specific, temporally persisting gene variant combinations. We use temporal multilayer networks to analyze the genetic similarity of parasites in both simulated data and in an extensively and longitudinally sampled population in Ghana. When viewed over time, populations are structured into modules (i.e., groups) of parasite genomes whose var gene combinations are more similar within than between the modules and whose persistence is much longer than that of the individual genomes that compose them. Comparison to neutral models that retain parasite population dynamics but lack competition reveals that the selection imposed by host immunity promotes the persistence of these modules. The modular structure is, in turn, associated with a slower acquisition of immunity by individual hosts. Modules thus represent dynamically generated niches in host immune space, which can be interpreted as strains. Negative frequency-dependent selection therefore shapes the organization of the var diversity into parasite genomes, leaving a persistence signature over ecological time scales. Multilayer networks extend the scope of phylodynamics analyses by allowing quantification of temporal genetic structure in organisms that generate variation via recombination or other non-bifurcating processes. A strain structure similar to the one described here should apply to other pathogens with large antigenic spaces that evolve via recombination. For malaria, the temporal modular structure should enable the formulation of tractable epidemiological models that account for parasite antigenic diversity and its influence on intervention outcomes. A combination of computational modeling and empirical data reveals persistent strain structure despite vast antigenic diversity in the human malaria parasite Plasmodium falciparum, with potential consequences for the acquisition of immunity.
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Affiliation(s)
- Shai Pilosof
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
| | - Qixin He
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | | | - Karen P. Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
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18
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Rorick MM, Artzy-Randrup Y, Ruybal-Pesántez S, Tiedje KE, Rask TS, Oduro A, Ghansah A, Koram K, Day KP, Pascual M. Signatures of competition and strain structure within the major blood-stage antigen of Plasmodium falciparum in a local community in Ghana. Ecol Evol 2018; 8:3574-3588. [PMID: 29686839 PMCID: PMC5901166 DOI: 10.1002/ece3.3803] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 10/31/2017] [Accepted: 12/06/2017] [Indexed: 11/12/2022] Open
Abstract
The concept of niche partitioning has received considerable theoretical attention at the interface of ecology and evolution of infectious diseases. Strain theory postulates that pathogen populations can be structured into distinct nonoverlapping strains by frequency-dependent selection in response to intraspecific competition for host immune space. The malaria parasite Plasmodium falciparum presents an opportunity to investigate this phenomenon in nature, under conditions of high recombination rate and extensive antigenic diversity. The parasite's major blood-stage antigen, Pf EMP1, is encoded by the hyperdiverse var genes. With a dataset that includes thousands of var DBLα sequence types sampled from asymptomatic cases within an area of high endemicity in Ghana, we address how var diversity is distributed within isolates and compare this to the distribution of microsatellite allelic diversity within isolates to test whether antigenic and neutral regions of the genome are structured differently. With respect to var DBLα sequence types, we find that on average isolates exhibit significantly lower overlap than expected randomly, but that there also exists frequent pairs of isolates that are highly related. Furthermore, the linkage network of var DBLα sequence types reveals a pattern of nonrandom modularity unique to these antigenic genes, and we find that modules of highly linked DBLα types are not explainable by neutral forces related to var recombination constraints, microsatellite diversity, sampling location, host age, or multiplicity of infection. These findings of reduced overlap and modularity among the var antigenic genes are consistent with a role for immune selection as proposed by strain theory. Identifying the evolutionary and ecological dynamics that are responsible for the nonrandom structure in P. falciparum antigenic diversity is important for designing effective intervention in endemic areas.
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Affiliation(s)
- Mary M Rorick
- Department of Ecology and Evolution University of Chicago Chicago IL USA.,Department of Biology University of Utah Salt Lake City UT USA
| | - Yael Artzy-Randrup
- Theoretical Ecology Group Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Shazia Ruybal-Pesántez
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Kathryn E Tiedje
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Thomas S Rask
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research University of Ghana Legon Ghana
| | - Kwadwo Koram
- Noguchi Memorial Institute for Medical Research University of Ghana Legon Ghana
| | - Karen P Day
- School of Biosciences Bio21 Institute The University of Melbourne Melbourne Vic. Australia.,Department of Microbiology New York University New York NY USA
| | - Mercedes Pascual
- Department of Ecology and Evolution University of Chicago Chicago IL USA.,The Santa Fe Institute Santa Fe NM USA
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19
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Rougeron V, Tiedje KE, Chen DS, Rask TS, Gamboa D, Maestre A, Musset L, Legrand E, Noya O, Yalcindag E, Renaud F, Prugnolle F, Day KP. Evolutionary structure of Plasmodium falciparum major variant surface antigen genes in South America: Implications for epidemic transmission and surveillance. Ecol Evol 2017; 7:9376-9390. [PMID: 29187975 PMCID: PMC5696401 DOI: 10.1002/ece3.3425] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 07/07/2017] [Accepted: 08/19/2017] [Indexed: 11/11/2022] Open
Abstract
Strong founder effects resulting from human migration out of Africa have led to geographic variation in single nucleotide polymorphisms (SNPs) and microsatellites (MS) of the malaria parasite, Plasmodium falciparum. This is particularly striking in South America where two major founder populations of P. falciparum have been identified that are presumed to have arisen from the transatlantic slave trade. Given the importance of the major variant surface antigen of the blood stages of P. falciparum as both a virulence factor and target of immunity, we decided to investigate the population genetics of the genes encoding “Plasmodium falciparum Erythrocyte Membrane Protein 1” (PfEMP1) among several countries in South America, in order to evaluate the transmission patterns of malaria in this continent. Deep sequencing of the DBLα domain of var genes from 128 P. falciparum isolates from five locations in South America was completed using a 454 high throughput sequencing protocol. Striking geographic variation in var DBLα sequences, similar to that seen for SNPs and MS markers, was observed. Colombia and French Guiana had distinct var DBLα sequences, whereas Peru and Venezuela showed an admixture. The importance of such geographic variation to herd immunity and malaria vaccination is discussed.
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Affiliation(s)
- Virginie Rougeron
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Kathryn E Tiedje
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Donald S Chen
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA
| | - Thomas S Rask
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt and Departamento de Ciencias Celulares y Moleculares Facultad de Ciencias y Filosofia Universidad Peruana Cayetano Heredia Lima Peru
| | - Amanda Maestre
- Grupo Salud y Comunidad Facultad de Medicina Universidad de Antioquía Medellín Colombia
| | - Lise Musset
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana
| | - Eric Legrand
- Parasitology UnitInstitut Pasteur de Guyane Cayenne Cedex French Guiana.,Unit of Genetics and Genomics on Insect Vectors Institut Pasteur Paris France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria Instituto de Altos Estudios en Salud "Dr. Arnoldo Gabaldón" Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical Universidad Central de Venezuela Caracas Venezuela
| | - Erhan Yalcindag
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - François Renaud
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Franck Prugnolle
- MIVEGEC (Laboratoire Maladies Infectieuses et Vecteurs, Ecologie, Génétique, Evolution et Contrôle), UMR CNRS 5290/IRD 224 Université Montpellier 1 Université Montpellier 2 Montpellier France
| | - Karen P Day
- Department of Microbiology Division of Parasitology New York University School of Medicine New York NY USA.,School of BioSciences Bio21 Institute/University of Melbourne Parkville Vic. Australia
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20
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Ruybal-Pesántez S, Tiedje KE, Rorick MM, Amenga-Etego L, Ghansah A, R. Oduro A, Koram KA, Day KP. Lack of Geospatial Population Structure Yet Significant Linkage Disequilibrium in the Reservoir of Plasmodium falciparum in Bongo District, Ghana. Am J Trop Med Hyg 2017; 97:1180-1189. [PMID: 28722587 PMCID: PMC5637601 DOI: 10.4269/ajtmh.17-0119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/22/2017] [Indexed: 11/07/2022] Open
Abstract
Malaria control in West Africa is impeded by the large reservoir of chronic asymptomatic Plasmodium falciparum infections in the human population. This study aimed to assess the extent of diversity in the P. falciparum reservoir in Bongo District (BD), Ghana, at the end of the dry season, the lowest point in malaria transmission over the course of the year. Analysis of the variation in 12 microsatellite loci was completed for 200 P. falciparum isolates collected from a cross-sectional survey of residents of all ages from two catchment areas in BD. Analysis of the multilocus haplotypes showed high levels of genetic diversity (He = 0.74), no population differentiation yet significant linkage disequilibrium (LD) (ISA = 0.0127, P = 0.006) in BD. Multilocus LD was significant between and within catchment areas even though every haplotype in the population was unique and the majority of individuals (84.0%) harbored multiple-clone infections. The linkage structure among multilocus haplotypes was not associated with sampling location. These data provide the first study with deep sampling of the P. falciparum reservoir in an area of seasonal malaria transmission in West Africa. The co-occurrence of high multiplicity of infection (multiple-clone infections) with significant multilocus LD is surprising given the likelihood of high recombination rates in BD. The results suggest that the linkage structure among multilocus haplotypes has not been shaped by geographic separation of parasite populations. Furthermore, the observed LD levels provide a baseline population genetic metric with putatively neutral markers to evaluate the effects of seasonality and malaria control efforts in BD.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- School of BioSciences, Bio21 Institute/The University of Melbourne, Melbourne, Australia
- Department of Microbiology, New York University, New York, New York
| | - Kathryn E. Tiedje
- School of BioSciences, Bio21 Institute/The University of Melbourne, Melbourne, Australia
- Department of Microbiology, New York University, New York, New York
| | - Mary M. Rorick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
- Howard Hughes Medical Institute, Ann Arbor, Michigan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
| | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Kwadwo A. Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karen P. Day
- School of BioSciences, Bio21 Institute/The University of Melbourne, Melbourne, Australia
- Department of Microbiology, New York University, New York, New York
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21
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Ruybal-Pesántez S, Tiedje KE, Tonkin-Hill G, Rask TS, Kamya MR, Greenhouse B, Dorsey G, Duffy MF, Day KP. Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda. Sci Rep 2017; 7:11810. [PMID: 28924231 PMCID: PMC5603532 DOI: 10.1038/s41598-017-11814-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 08/30/2017] [Indexed: 12/18/2022] Open
Abstract
Plasmodium falciparum causes a spectrum of malarial disease from asymptomatic to uncomplicated through to severe. Investigations of parasite virulence have associated the expression of distinct variants of the major surface antigen of the blood stages known as Pf EMP1 encoded by up to 60 var genes per genome. Looking at the population genomics of var genes in cases of uncomplicated malaria, we set out to determine if there was any evidence of a selective sweep of specific var genes or clonal epidemic structure related to the incidence of uncomplicated disease in children. By sequencing the conserved DBLα domain of var genes from six sentinel sites in Uganda we found that the parasites causing uncomplicated P. falciparum disease in children were highly diverse and that every child had a unique var DBLα repertoire. Despite extensive var DBLα diversity and minimal overlap between repertoires, specific DBLα types and groups were conserved at the population level across Uganda. This pattern was the same regardless of the geographic distance or malaria transmission intensity. These data lead us to propose that any parasite can cause uncomplicated malarial disease and that these diverse parasite repertoires are composed of both upsA and non-upsA var gene groups.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Kathryn E Tiedje
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | | | - Thomas S Rask
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia.,Department of Microbiology, New York University, New York, USA
| | - Moses R Kamya
- School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, USA
| | - Grant Dorsey
- Department of Medicine, University of California, San Francisco, USA
| | - Michael F Duffy
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | - Karen P Day
- School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia. .,Department of Microbiology, New York University, New York, USA.
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22
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Tiedje KE, Oduro AR, Agongo G, Anyorigiya T, Azongo D, Awine T, Ghansah A, Pascual M, Koram KA, Day KP. Seasonal Variation in the Epidemiology of Asymptomatic Plasmodium falciparum Infections across Two Catchment Areas in Bongo District, Ghana. Am J Trop Med Hyg 2017; 97:199-212. [PMID: 28719306 DOI: 10.4269/ajtmh.16-0959] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Understanding the epidemiology of asymptomatic Plasmodium falciparum infections is critical for countries to move toward malaria elimination. Using different methods for parasite detection, we evaluated how seasonality, spatial location, and other factors affect the age-specific epidemiology of asymptomatic malaria in Bongo District, Ghana. Asymptomatic prevalence by microscopy decreased significantly from 42.5% at the end of the wet to 27.5% at the end of the dry season (P < 0.001). Using the 18S rRNA polymerase chain reactions (PCRs), all microscopy-negative samples were screened and prevalence of submicroscopic infections also decreased significantly from the wet (55.4%) to the dry (20.7%) season (P < 0.001). Combining detection methods, 74.4% and 42.5% of the population in the wet and dry seasons, respectively, had evidence of a P. falciparum infection. Interestingly in those > 20 years of age, we found evidence of infection in 64.3% of the population in the wet and 27.0% in the dry season. Using both microscopy and PCR, the asymptomatic P. falciparum reservoir peaks at the end of the wet season and infections in all age groups constitute the reservoir of malaria infection. At the end of the wet season, spatial heterogeneity in the prevalence and density of P. falciparum infections was observed between the two catchment areas surveyed in Bongo District. These results indicate that if elimination is to succeed, interventions will need to target not just P. falciparum infections in children but also in adults, and be implemented toward the end of the dry season in this area of West Africa.
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Affiliation(s)
- Kathryn E Tiedje
- Department of Microbiology, New York University, New York, New York.,School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
| | | | | | | | | | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mercedes Pascual
- Santa Fe Institute, Sante Fe, New Mexico.,Department of Ecology and Evolution, University of Chicago, Chicago, Illinois
| | - Kwadwo A Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Karen P Day
- Department of Microbiology, New York University, New York, New York.,School of BioSciences, Bio21 Institute/University of Melbourne, Melbourne, Australia
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23
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Day KP, Artzy-Randrup Y, Tiedje KE, Rougeron V, Chen DS, Rask TS, Rorick MM, Migot-Nabias F, Deloron P, Luty AJF, Pascual M. Evidence of strain structure in Plasmodium falciparum var gene repertoires in children from Gabon, West Africa. Proc Natl Acad Sci U S A 2017; 114:E4103-E4111. [PMID: 28461509 PMCID: PMC5441825 DOI: 10.1073/pnas.1613018114] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Existing theory on competition for hosts between pathogen strains has proposed that immune selection can lead to the maintenance of strain structure consisting of discrete, weakly overlapping antigenic repertoires. This prediction of strain theory has conceptual overlap with fundamental ideas in ecology on niche partitioning and limiting similarity between coexisting species in an ecosystem, which oppose the hypothesis of neutral coexistence. For Plasmodium falciparum, strain theory has been specifically proposed in relation to the major surface antigen of the blood stage, known as PfEMP1 and encoded by the multicopy multigene family known as the var genes. Deep sampling of the DBLα domain of var genes in the local population of Bakoumba, West Africa, was completed to define whether patterns of repertoire overlap support a role of immune selection under the opposing force of high outcrossing, a characteristic of areas of intense malaria transmission. Using a 454 high-throughput sequencing protocol, we report extremely high diversity of the DBLα domain and a large parasite population with DBLα repertoires structured into nonrandom patterns of overlap. Such population structure, significant for the high diversity of var genes that compose it at a local level, supports the existence of "strains" characterized by distinct var gene repertoires. Nonneutral, frequency-dependent competition would be at play and could underlie these patterns. With a computational experiment that simulates an intervention similar to mass drug administration, we argue that the observed repertoire structure matters for the antigenic var diversity of the parasite population remaining after intervention.
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Affiliation(s)
- Karen P Day
- School of Biosciences, The University of Melbourne, Parkville, VIC 3052, Australia;
- Department of Microbiology, New York University, New York, NY 10016
| | - Yael Artzy-Randrup
- Theoretical Ecology Group, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1090 GE Amsterdam, The Netherlands
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kathryn E Tiedje
- School of Biosciences, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Microbiology, New York University, New York, NY 10016
| | - Virginie Rougeron
- Department of Microbiology, New York University, New York, NY 10016
- Laboratoire Maladies Infectieuses et Vecteurs: Ecologie, Génétique, Evolution et Contrôle, UMR 224-5290 CNRS, Institut de Recherche pour le Développement-Université de Montpellier, Centre Institut de Recherche pour le Développement de Montpellier, 34394 Montpellier, France
| | - Donald S Chen
- Department of Microbiology, New York University, New York, NY 10016
- Department of Medicine, New York Medical College, Valhalla, NY 10595
| | - Thomas S Rask
- School of Biosciences, The University of Melbourne, Parkville, VIC 3052, Australia
- Department of Microbiology, New York University, New York, NY 10016
| | - Mary M Rorick
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
| | - Florence Migot-Nabias
- Institut de Recherche pour le Développement, UMR 216 Mère et Enfant Face aux Infections Tropicales, 75006 Paris, France
- Communautés d'Universités et Établissements, Sorbonne Paris Cité, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France
| | - Philippe Deloron
- Institut de Recherche pour le Développement, UMR 216 Mère et Enfant Face aux Infections Tropicales, 75006 Paris, France
- Communautés d'Universités et Établissements, Sorbonne Paris Cité, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France
| | - Adrian J F Luty
- Institut de Recherche pour le Développement, UMR 216 Mère et Enfant Face aux Infections Tropicales, 75006 Paris, France
- Communautés d'Universités et Établissements, Sorbonne Paris Cité, Université Paris Descartes, Faculté des Sciences Pharmaceutiques et Biologiques, 75006 Paris, France
| | - Mercedes Pascual
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637
- Santa Fe Institute, Santa Fe, NM 87501
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24
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Rougeron V, Woods CM, Tiedje KE, Bodeau-Livinec F, Migot-Nabias F, Deloron P, Luty AJF, Fowkes FJI, Day KP. Epistatic Interactions between apolipoprotein E and hemoglobin S Genes in regulation of malaria parasitemia. PLoS One 2013; 8:e76924. [PMID: 24116184 PMCID: PMC3792892 DOI: 10.1371/journal.pone.0076924] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 09/04/2013] [Indexed: 11/18/2022] Open
Abstract
Apolipoprotein E is a monomeric protein secreted by the liver and responsible for the transport of plasma cholesterol and triglycerides. The APOE gene encodes 3 isoforms Ɛ4, Ɛ3 and Ɛ2 with APOE Ɛ4 associated with higher plasma cholesterol levels and increased pathogenesis in several infectious diseases (HIV, HSV). Given that cholesterol is an important nutrient for malaria parasites, we examined whether APOE Ɛ4 was a risk factor for Plasmodium infection, in terms of prevalence or parasite density. A cross sectional survey was performed in 508 children aged 1 to 12 years in Gabon during the wet season. Children were screened for Plasmodium spp. infection, APOE and hemoglobin S (HbS) polymorphisms. Median parasite densities were significantly higher in APOE Ɛ4 children for Plasmodium spp. densities compared to non-APOE Ɛ4 children. When stratified for HbS polymorphisms, median Plasmodium spp. densities were significantly higher in HbAA children if they had an APOE Ɛ4 allele compared to those without an APOE Ɛ4 allele. When considering non-APOE Ɛ4 children, there was no quantitative reduction of Plasmodium spp. parasite densities for HbAS compared to HbAA phenotypes. No influence of APOE Ɛ4 on successful Plasmodium liver cell invasion was detected by multiplicity of infection. These results show that the APOE Ɛ4 allele is associated with higher median malaria parasite densities in children likely due to the importance of cholesterol availability to parasite growth and replication. Results suggest an epistatic interaction between APOE and HbS genes such that sickle cell trait only had an effect on parasite density in APOE Ɛ4 children. This suggests a linked pathway of regulation of parasite density involving expression of these genes. These findings have significance for understanding host determinants of regulation of malaria parasite density, the design of clinical trials as well as studies of co-infection with Plasmodium and other pathogens.
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Affiliation(s)
- Virginie Rougeron
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Caira M. Woods
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Kathryn E. Tiedje
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
| | - Florence Bodeau-Livinec
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- UMR216, Institut de Recherche pour le Développement, Paris, France
| | | | - Philippe Deloron
- UMR216, Institut de Recherche pour le Développement, Paris, France
- PRES, Paris Sorbonne Cité, Université Paris Descartes, Paris, France
| | | | - Freya J. I. Fowkes
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- Centre for Population Health, Macfarlane Burnet Institute of Medical Research and Public Health, Melbourne, Victoria, Australia
| | - Karen P. Day
- Department of Microbiology, Division of Medical Parasitology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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25
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de Sousa A, Tiedje KE, Recht J, Bjelic I, Hamer DH. Community case management of childhood illnesses: policy and implementation in Countdown to 2015 countries. Bull World Health Organ 2011; 90:183-90. [PMID: 22461713 DOI: 10.2471/blt.11.093989] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/16/2011] [Accepted: 11/07/2011] [Indexed: 11/27/2022] Open
Abstract
OBJECTIVE To explore the policies for, and implementation of, the community case management (CCM) of childhood illnesses in the 68 countries that were prioritized by the "Countdown to 2015" initiative in 2008. METHODS In 2009-2010, community approaches concerning CCM policy and implementation, the roles of community health workers (CHWs) and the availability of medicines for the treatment of malaria, diarrhoea, pneumonia and neonatal infections were investigated by sending questionnaires to implementers and policy-makers and through telephone discussions with appropriate researchers and experts. FINDINGS Of the 59 countries that responded, 81%, 75%, 54% and 14% had a policy for the CCM of diarrhoea, malaria, pneumonia and neonatal infections, respectively. Only three (6%) of the 53 malaria-endemic countries providing responses had policies for all four of these conditions, although 17 (32%) had CCM policies for malaria, diarrhoea and pneumonia. Some CCM of childhood illnesses was being implemented--more commonly for diarrhoea and malaria than for pneumonia or neonatal infections--in 88% of the countries providing responses. According to the responses received, CHWs administered the recommended treatments for diarrhoea, malaria or pneumonia in 34% (17/50), 100% (41/41) and 100% (34/34) of the countries implementing CCM of these conditions, respectively. Common programme concerns were drug supplies, quality of care and CHW incentives, training and supervision. CONCLUSION Despite progress, further efforts are needed towards policy reform and the expansion of CCM programmes. Ensuring the availability of recommended medicines and operational research, to assure quality, remain priorities.
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