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Ali Albsheer MM, Hubbard A, Dieng CC, Gebremeskel EI, Ahmed S, Rougeron V, Ibrahim ME, Lo E, Abdel Hamid MM. Extensive genetic diversity in Plasmodium vivax from Sudan and its genetic relationships with other geographical isolates. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105643. [PMID: 39053565 DOI: 10.1016/j.meegid.2024.105643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/03/2024] [Accepted: 07/13/2024] [Indexed: 07/27/2024]
Abstract
Plasmodium vivax, traditionally overlooked has experienced a notable increase in cases in East Africa. This study investigated the geographical origin and genetic diversity of P. vivax in Sudan using 14 microsatellite markers. A total of 113 clinical P. vivax samples were collected from two different ecogeographical zones, New Halfa and Khartoum, in Sudan. Additionally, 841 geographical samples from the database were incorporated for a global genetic analysis to discern genetic relationships among P. vivax isolates on regional and worldwide scales. On the regional scale, our findings revealed 91 unique and 8 shared haplotypes among the Sudan samples, showcasing a remarkable genetic diversity compared to other geographical isolates and supporting the hypothesis that P. vivax originated from Africa. On a global scale, distinct genetic clustering of P. vivax isolates from Africa, South America, and Asia (including Papua New Guinea and Solomon Island) was observed, with limited admixture among the three clusters. Principal component analysis emphasized the substantial contribution of African isolates to the observed global genetic variation. The Sudanese populations displayed extensive genetic diversity, marked by significant multi-locus linkage disequilibrium, suggesting an ancestral source of P. vivax variation globally and frequent recombination among the isolates. Notably, the East African P. vivax exhibited similarity with some Asian isolates, indicating potential recent introductions. Overall, our results underscore the effectiveness of utilizing microsatellite markers for implementing robust control measures, given their ability to capture extensive genetic diversity and linkage disequilibrium patterns.
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Affiliation(s)
- Musab M Ali Albsheer
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan; Faculty of Medical Laboratory Sciences, Sinnar University, Sudan
| | - Alfred Hubbard
- Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC 28223, USA
| | - Cheikh Cambel Dieng
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA 19129, USA
| | | | - Safaa Ahmed
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, 34394 Montpellier, France
| | - Muntaser E Ibrahim
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan
| | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA 19129, USA.
| | - Muzamil M Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.
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2
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal. Malar J 2024; 23:68. [PMID: 38443939 PMCID: PMC10916253 DOI: 10.1186/s12936-024-04897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Medoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Fatou Ba
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jessica Ribado
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua Suresh
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Albert Lee
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Katherine E Battle
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin A Bever
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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Holzschuh A, Ewnetu Y, Carlier L, Lerch A, Gerlovina I, Baker SC, Yewhalaw D, Haileselassie W, Berhane N, Lemma W, Koepfli C. Plasmodium falciparum transmission in the highlands of Ethiopia is driven by closely related and clonal parasites. Mol Ecol 2024; 33:e17292. [PMID: 38339833 DOI: 10.1111/mec.17292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Malaria cases are frequently recorded in the Ethiopian highlands even at altitudes above 2000 m. The epidemiology of malaria in the Ethiopian highlands, and, in particular, the role of importation by human migration from the highly endemic lowlands is not well understood. We sequenced 187 Plasmodium falciparum samples from two sites in the Ethiopian highlands, Gondar (n = 159) and Ziway (n = 28), using a multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug resistance loci. Here, we characterize the parasite population structure and genetic relatedness. We identify moderate parasite diversity (mean HE : 0.54) and low infection complexity (74.9% monoclonal). A significant percentage of infections share microhaplotypes, even across transmission seasons and sites, indicating persistent local transmission. We identify multiple clusters of clonal or near-clonal infections, highlighting high genetic relatedness. Only 6.3% of individuals diagnosed with P. falciparum reported recent travel. Yet, in clonal or near-clonal clusters, infections of travellers were frequently observed first in time, suggesting that parasites may have been imported and then transmitted locally. 31.1% of infections are pfhrp2-deleted and 84.4% pfhrp3-deleted, and 28.7% have pfhrp2/3 double deletions. Parasites with pfhrp2/3 deletions and wild-type parasites are genetically distinct. Mutations associated with resistance to sulphadoxine-pyrimethamine or suggested to reduce sensitivity to lumefantrine are observed at near-fixation. In conclusion, genomic data corroborate local transmission and the importance of intensified control in the Ethiopian highlands.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yalemwork Ewnetu
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Lise Carlier
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
- Noul Inc., Seoul, Republic of Korea
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Inna Gerlovina
- Department of Medicine, Division of HIV, ID and Global Medicine, EPPIcenter Research Program, University of California, San Francisco, California, USA
| | - Sarah Cate Baker
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
| | - Delenasaw Yewhalaw
- Tropical and Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | | | - Nega Berhane
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Wossenseged Lemma
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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4
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Ruybal-Pesántez S, McCann K, Vibin J, Siegel S, Auburn S, Barry AE. Molecular markers for malaria genetic epidemiology: progress and pitfalls. Trends Parasitol 2024; 40:147-163. [PMID: 38129280 DOI: 10.1016/j.pt.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023]
Abstract
Over recent years, progress in molecular markers for genotyping malaria parasites has enabled informative studies of epidemiology and transmission dynamics. Results have highlighted the value of these tools for surveillance to support malaria control and elimination strategies. There are many different types and panels of markers available for malaria parasite genotyping, and for end users, the nuances of these markers with respect to 'use case', resolution, and accuracy, are not well defined. This review clarifies issues surrounding different molecular markers and their application to malaria control and elimination. We describe available marker panels, use cases, implications for different transmission settings, limitations, access, cost, and data accuracy. The information provided can be used as a guide for molecular epidemiology and surveillance of malaria.
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Affiliation(s)
- Shazia Ruybal-Pesántez
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK; Institute of Microbiology, Universidad San Francisco de Quito, Quito, Ecuador
| | - Kirsty McCann
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Jessy Vibin
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia
| | | | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Darwin, Northern Territory, Australia; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Alyssa E Barry
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia; Centre for Innovation in Infectious Disease and Immunology Research (CIIDIR), Institute for Mental and Physical Health and Clinical Translation (IMPACT) and School of Medicine, Deakin University, Geelong, Victoria, Australia.
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5
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Potter GE, Callier V, Shrestha B, Joshi S, Dwivedi A, Silva JC, Laurens MB, Follmann DA, Deye GA. Can incorporating genotyping data into efficacy estimators improve efficiency of early phase malaria vaccine trials? Malar J 2023; 22:383. [PMID: 38115002 PMCID: PMC10729369 DOI: 10.1186/s12936-023-04802-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/22/2023] [Indexed: 12/21/2023] Open
Abstract
BACKGROUND Early phase malaria vaccine field trials typically measure malaria infection by PCR or thick blood smear microscopy performed on serially sampled blood. Vaccine efficacy (VE) is the proportion reduction in an endpoint due to vaccination and is often calculated as VEHR = 1-hazard ratio or VERR = 1-risk ratio. Genotyping information can distinguish different clones and distinguish multiple infections over time, potentially increasing statistical power. This paper investigates two alternative VE endpoints incorporating genotyping information: VEmolFOI, the vaccine-induced proportion reduction in incidence of new clones acquired over time, and VEC, the vaccine-induced proportion reduction in mean number of infecting clones per exposure. METHODS Power of VEmolFOI and VEC was compared to that of VEHR and VERR by simulations and analytic derivations, and the four VE methods were applied to three data sets: a Phase 3 trial of RTS,S malaria vaccine in 6912 African infants, a Phase 2 trial of PfSPZ Vaccine in 80 Burkina Faso adults, and a trial comparing Plasmodium vivax incidence in 466 Papua New Guinean children after receiving chloroquine + artemether lumefantrine with or without primaquine (as these VE methods can also quantify effects of other prevention measures). By destroying hibernating liver-stage P. vivax, primaquine reduces subsequent reactivations after treatment completion. RESULTS In the trial of RTS,S vaccine, a significantly reduced number of clones at first infection was observed, but this was not the case in trials of PfSPZ Vaccine or primaquine, although the PfSPZ trial lacked power to show a reduction. Resampling smaller data sets from the large RTS,S trial to simulate phase 2 trials showed modest power gains from VEC compared to VEHR for data like those from RTS,S, but VEC is less powerful than VEHR for trials in which the number of clones at first infection is not reduced. VEmolFOI was most powerful in model-based simulations, but only the primaquine trial collected enough serial samples to precisely estimate VEmolFOI. The primaquine VEmolFOI estimate decreased after most control arm liver-stage infections reactivated (which mathematically resembles a waning vaccine), preventing VEmolFOI from improving power. CONCLUSIONS The power gain from the genotyping methods depends on the context. Because input parameters for early phase power calculations are often uncertain, these estimators are not recommended as primary endpoints for small trials unless supported by targeted data analysis. TRIAL REGISTRATIONS NCT00866619, NCT02663700, NCT02143934.
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Affiliation(s)
- Gail E Potter
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA.
| | - Viviane Callier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Biraj Shrestha
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sudhaunshu Joshi
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Ankit Dwivedi
- Institute for Genomic Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Joana C Silva
- Institute for Genomic Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Dean A Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
| | - Gregory A Deye
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, USA
- AstraZeneca PLC, Gaithersburg, MD, USA
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Reda AG, Huwe T, Koepfli C, Assefa A, Tessema SK, Messele A, Golassa L, Mamo H. Amplicon deep sequencing of five highly polymorphic markers of Plasmodium falciparum reveals high parasite genetic diversity and moderate population structure in Ethiopia. Malar J 2023; 22:376. [PMID: 38087335 PMCID: PMC10714478 DOI: 10.1186/s12936-023-04814-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Plasmodium falciparum genetic diversity can add information on transmission intensity and can be used to track control and elimination interventions. METHODS Dried blood spots (DBS) were collected from patients who were recruited for a P. falciparum malaria therapeutic efficacy trial in three malaria endemic sites in Ethiopia from October to December 2015, and November to December 2019. qPCR-confirmed infections were subject to amplicon sequencing of polymorphic markers ama1-D3, csp, cpp, cpmp, msp7. Genetic diversity, the proportion of multiclonal infections, multiplicity of infection, and population structure were analysed. RESULTS Among 198 samples selected for sequencing, data was obtained for 181 samples. Mean MOI was 1.38 (95% CI 1.24-1.53) and 17% (31/181) of infections were polyclonal. Mean He across all markers was 0.730. Population structure was moderate; populations from Metema and Metehara 2015 were very similar to each other, but distinct from Wondogent 2015 and Metehara 2019. CONCLUSION The high level of parasite genetic diversity and moderate population structure in this study suggests frequent gene flow of parasites among sites. The results obtained can be used as a baseline for additional parasite genetic diversity and structure studies, aiding in the formulation of appropriate control strategies in Ethiopia.
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Affiliation(s)
- Abeba Gebretsadik Reda
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Tiffany Huwe
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA.
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Ashenafi Assefa
- Malaria and Neglected Tropical Diseases Research Team, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Alebachew Messele
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Hassen Mamo
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
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7
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal. RESEARCH SQUARE 2023:rs.3.rs-3516287. [PMID: 37961451 PMCID: PMC10635402 DOI: 10.21203/rs.3.rs-3516287/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Here, we examined parasites from 3,147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, we constructed a series of Poisson generalized linear mixed-effects models to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. We compared the model-predicted incidence with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (<10/1000/annual [‰]). When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence >10 ‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was <10 ‰, we found that many of the correlations between parasite genetics and incidence were reversed, which we hypothesize reflects the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
| | | | | | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic
| | | | - Fatou Ba
- Programme National de Lutte Contre le Paludisme
| | - Ibrahima Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jessica Ribado
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Joshua Suresh
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Albert Lee
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Joshua L Proctor
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Caitlin A Bever
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
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8
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Potter GE, Callier V, Shrestha B, Joshi S, Dwivedi A, Silva JC, Laurens MB, Follmann DA, Deye GA. Can incorporating genotyping data into efficacy estimators improve efficiency of early phase malaria vaccine trials? RESEARCH SQUARE 2023:rs.3.rs-3370731. [PMID: 37790581 PMCID: PMC10543529 DOI: 10.21203/rs.3.rs-3370731/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Background Early phase malaria vaccine field trials typically measure malaria infection by PCR or thick blood smear microscopy performed on serially sampled blood. Vaccine efficacy (VE) is the proportion reduction in an endpoint due to vaccination and is often calculated as V E H R = 1 - hazard ratio or V E R R = 1 - risk ratio. Genotyping information can distinguish different clones and distinguish multiple infections over time, potentially increasing statistical power. This paper investigates two alternative VE endpoints incorporating genotyping information: V E m o l F O I , the vaccine-induced proportion reduction in incidence of new clones acquired over time, and V E C , the vaccine-induced proportion reduction in mean number of infecting clones per exposure. Methods We used simulations and analytic derivations to compare power of these methods to V E H R and V E R R and applied them to three data sets: a Phase 3 trial of RTS,S malaria vaccine in 6912 African infants, a Phase 2 trial of PfSPZ Vaccine in 80 Burkina Faso adults, and a trial comparing Plasmodium vivax incidence in 466 Papua New Guinean children after receiving chloroquine + artemether lumefantrine with or without primaquine (as these VE methods can also quantify effects of other prevention measures). By destroying hibernating liver-stage P. vivax, primaquine reduces subsequent reactivations after treatment completion. Results The RTS,S vaccine significantly reduced the number of clones at first infection, but PfSPZ vaccine and primaquine did not. Resampling smaller data sets from the large RTS,S trial to simulate phase 2 trials showed modest power gains from V E C compared to V E H R for data like RTS,S, but V E C is less powerful than V E H R for vaccines which do not reduce the number of clones at first infection. V E m o l F O I was most powerful in model-based simulations, but only the primaquine trial collected enough serial samples to precisely estimate V E m o l F O I . The primaquine V E m o l F O I estimate decreased after most control arm liver-stage infections reactivated (which mathematically resembles a waning vaccine), preventing V E m o l F O I from improving power. Conclusions The power gain from the genotyping methods depends on the context. Because input parameters for early phase power calculations are often uncertain, we recommend against these estimators as primary endpoints for small trials unless supported by targeted data analysis. Trial registrations NCT00866619, NCT02663700, NCT02143934.
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Affiliation(s)
- Gail E Potter
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Viviane Callier
- Clinical Monitoring Research Program Directorate, Frederick National Laboratory for Cancer Research
| | | | | | - Ankit Dwivedi
- Institute for Genomic Sciences, University of Maryland School of Medicine
| | - Joana C Silva
- Institute for Genomic Sciences and Department of Microbiology & Immunology, University of Maryland School of Medicine
| | - Matthew B Laurens
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine
| | - Dean A Follmann
- Biostatistics Research Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health
| | - Gregory A Deye
- Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health
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9
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Andika B, Mobegi V, Gathii K, Nyataya J, Maina N, Awinda G, Mutai B, Waitumbi J. Plasmodium falciparum population structure inferred by msp1 amplicon sequencing of parasites collected from febrile patients in Kenya. Malar J 2023; 22:263. [PMID: 37689681 PMCID: PMC10492417 DOI: 10.1186/s12936-023-04700-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/01/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Multiplicity of infection (MOI) is an important measure of Plasmodium falciparum diversity, usually derived from the highly polymorphic genes, such as msp1, msp2 and glurp as well as microsatellites. Conventional methods of deriving MOI lack fine resolution needed to discriminate minor clones. This study used amplicon sequencing (AmpliSeq) of P. falciparum msp1 (Pfmsp1) to measure spatial and temporal genetic diversity of P. falciparum. METHODS 264 P. falciparum positive blood samples collected from areas of differing malaria endemicities between 2010 and 2019 were used. Pfmsp1 gene was amplified and amplicon libraries sequenced on Illumina MiSeq. Sequences were aligned against a reference sequence (NC_004330.2) and clustered to detect fragment length polymorphism and amino acid variations. RESULTS Children < 5 years had higher parasitaemia (median = 23.5 ± 5 SD, p = 0.03) than the > 5-14 (= 25.3 ± 5 SD), and those > 15 (= 25.1 ± 6 SD). Of the alleles detected, 553 (54.5%) were K1, 250 (24.7%) MAD20 and 211 (20.8%) RO33 that grouped into 19 K1 allelic families (108-270 bp), 14 MAD20 (108-216 bp) and one RO33 (153 bp). AmpliSeq revealed nucleotide polymorphisms in alleles that had similar sizes, thus increasing the K1 to 104, 58 for MAD20 and 14 for RO33. By AmpliSeq, the mean MOI was 4.8 (± 0.78, 95% CI) for the malaria endemic Lake Victoria region, 4.4 (± 1.03, 95% CI) for the epidemic prone Kisii Highland and 3.4 (± 0.62, 95% CI) for the seasonal malaria Semi-Arid region. MOI decreased with age: 4.5 (± 0.76, 95% CI) for children < 5 years, compared to 3.9 (± 0.70, 95% CI) for ages 5 to 14 and 2.7 (± 0.90, 95% CI) for those > 15. Females' MOI (4.2 ± 0.66, 95% CI) was not different from males 4.0 (± 0.61, 95% CI). In all regions, the number of alleles were high in the 2014-2015 period, more so in the Lake Victoria and the seasonal transmission arid regions. CONCLUSION These findings highlight the added advantages of AmpliSeq in haplotype discrimination and the associated improvement in unravelling complexity of P. falciparum population structure.
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Affiliation(s)
- Brian Andika
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Victor Mobegi
- Department of Biochemistry, University of Nairobi, Nairobi, Kenya
| | - Kimita Gathii
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Josphat Nyataya
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Naomi Maina
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - George Awinda
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - Beth Mutai
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya
| | - John Waitumbi
- Basic Science Laboratory, United States Army Medical Research Directorate, Kisumu, Kenya.
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10
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Holzschuh A, Lerch A, Gerlovina I, Fakih BS, Al-Mafazy AWH, Reaves EJ, Ali A, Abbas F, Ali MH, Ali MA, Hetzel MW, Yukich J, Koepfli C. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat Commun 2023; 14:3699. [PMID: 37349311 PMCID: PMC10287761 DOI: 10.1038/s41467-023-39417-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA
| | - Inna Gerlovina
- EPPIcenter Research Program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | | | - Erik J Reaves
- U.S. Centers for Disease Control and Prevention, President's Malaria Initiative, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Faiza Abbas
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
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11
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Alemayehu A. Biology and epidemiology of Plasmodium falciparum and Plasmodium vivax gametocyte carriage: Implication for malaria control and elimination. Parasite Epidemiol Control 2023; 21:e00295. [PMID: 36950502 PMCID: PMC10025134 DOI: 10.1016/j.parepi.2023.e00295] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 01/01/2023] [Accepted: 02/27/2023] [Indexed: 03/09/2023] Open
Abstract
Malaria is among the leading public health problems worldwide. Female anopheles mosquito orchestrates the transmission of malaria by taking gametocytes and introducing sporozoite while taking blood meals. Interrupting transmission is the major strategy for malaria elimination. The gametocyte stage is essential for the onward transmission of malaria. Thus, understanding its basic biology and epidemiology is key to malaria control and elimination. Therefore, the current review focuses on revealing the biology, prevalence, and determinants of gametocyte carriage as well as its implication on mitigation of malaria. It also illustrates the role of asymptomatic and sub-microscopic Plasmodium infections and G-6-PD deficiency in gametocyte carriage and hence malaria transmission. Gametocytogenesis is initiated at committed merozoites and gives rise to the development of gametocytes. The trigger for gametocytogenesis depends on the host, parasite, and intervention factors. Gametocytes pass through five developmental stages identifiable by molecular markers. A considerable number of malaria patients carry gametocytes at a sub-microscopic level, thereby serving as a potential infectious reservoir of transmission. Factors involving the human host, Plasmodium parasite, and intervention parameters play a critical role in gametocyte biology and prevalence. The contribution of asymptomatic and sub-microscopic infections to malaria transmission is unknown. The clear impact of G-6-PD deficiency on malaria control and elimination remains unclear. Lack of clarity on such issues might impede the success of interventions. Basic science and epidemiological studies should continue to overcome the challenges and cope with the ever-evolving parasite and guide interventions.
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Affiliation(s)
- Aklilu Alemayehu
- School of Medical Laboratory Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Arba Minch University, Arba Minch, Ethiopia
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12
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Kattenberg JH, Van Dijk NJ, Fernández-Miñope CA, Guetens P, Mutsaers M, Gamboa D, Rosanas-Urgell A. Molecular Surveillance of Malaria Using the PF AmpliSeq Custom Assay for Plasmodium falciparum Parasites from Dried Blood Spot DNA Isolates from Peru. Bio Protoc 2023; 13:e4621. [PMID: 36908639 PMCID: PMC9993081 DOI: 10.21769/bioprotoc.4621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/15/2022] [Accepted: 02/13/2023] [Indexed: 03/07/2023] Open
Abstract
Malaria molecular surveillance has great potential to support national malaria control programs (NMCPs), informing policy for its control and elimination. Here, we present a new three-day workflow for targeted resequencing of markers in 13 resistance-associated genes, histidine rich protein 2 and 3 (hrp2&3), a country (Peru)-specific 28 SNP-barcode for population genetic analysis, and apical membrane antigen 1 (ama1), using Illumina short-read sequencing technology. The assay applies a multiplex PCR approach to amplify all genomic regions of interest in a rapid and easily standardizable procedure and allows simultaneous amplification of a high number of targets at once, therefore having great potential for implementation into routine surveillance practice by NMCPs. The assay can be performed on routinely collected filter paper blood spots and can be easily adapted to different regions to investigate either regional trends or in-country epidemiological changes.
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Affiliation(s)
| | - Norbert J Van Dijk
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Carlos A Fernández-Miñope
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru.,Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Pieter Guetens
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Mathijs Mutsaers
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical "Alexander von Humboldt", Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Biomedical Sciences Department, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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13
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Neal A, Sassi J, Vardo-Zalik A. Drought correlates with reduced infection complexity and possibly prevalence in a decades-long study of the lizard malaria parasite Plasmodium mexicanum. PeerJ 2023; 11:e14908. [PMID: 36860770 PMCID: PMC9969858 DOI: 10.7717/peerj.14908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 01/25/2023] [Indexed: 03/03/2023] Open
Abstract
Microparasites often exist as a collection of genetic 'clones' within a single host (termed multi-clonal, or complex, infections). Malaria parasites are no exception, with complex infections playing key roles in parasite ecology. Even so, we know little about what factors govern the distribution and abundance of complex infections in natural settings. Utilizing a natural dataset that spans more than 20 years, we examined the effects of drought conditions on infection complexity and prevalence in the lizard malaria parasite Plasmodium mexicanum and its vertebrate host, the western fence lizard, Sceloporus occidentalis. We analyzed data for 14,011 lizards sampled from ten sites over 34 years with an average infection rate of 16.2%. Infection complexity was assessed for 546 infected lizards sampled during the most recent 20 years. Our data illustrate significant, negative effects of drought-like conditions on infection complexity, with infection complexity expected to increase by a factor of 2.27 from the lowest to highest rainfall years. The relationship between rainfall and parasite prevalence is somewhat more ambiguous; when prevalence is modeled over the full range in years, a 50% increase in prevalence is predicted between the lowest and highest rainfall years, but this trend is not apparent or is reversed when data are analyzed over a shorter timeframe. To our knowledge, this is the first reported evidence for drought affecting the abundance of multi-clonal infections in malaria parasites. It is not yet clear what mechanism might connect drought with infection complexity, but the correlation we observed suggests that additional research on how drought influences parasite features like infection complexity, transmission rates and within-host competition may be worthwhile.
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Affiliation(s)
- Allison Neal
- Norwich University, Northfield, VT, United States
| | - Joshua Sassi
- Norwich University, Northfield, VT, United States
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14
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Kattenberg JH, Fernandez-Miñope C, van Dijk NJ, Llacsahuanga Allcca L, Guetens P, Valdivia HO, Van geertruyden JP, Rovira-Vallbona E, Monsieurs P, Delgado-Ratto C, Gamboa D, Rosanas-Urgell A. Malaria Molecular Surveillance in the Peruvian Amazon with a Novel Highly Multiplexed Plasmodium falciparum AmpliSeq Assay. Microbiol Spectr 2023; 11:e0096022. [PMID: 36840586 PMCID: PMC10101074 DOI: 10.1128/spectrum.00960-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/02/2022] [Indexed: 02/24/2023] Open
Abstract
Molecular surveillance for malaria has great potential to support national malaria control programs (NMCPs). To bridge the gap between research and implementation, several applications (use cases) have been identified to align research, technology development, and public health efforts. For implementation at NMCPs, there is an urgent need for feasible and cost-effective tools. We designed a new highly multiplexed deep sequencing assay (Pf AmpliSeq), which is compatible with benchtop sequencers, that allows high-accuracy sequencing with higher coverage and lower cost than whole-genome sequencing (WGS), targeting genomic regions of interest. The novelty of the assay is its high number of targets multiplexed into one easy workflow, combining population genetic markers with 13 nearly full-length resistance genes, which is applicable for many different use cases. We provide the first proof of principle for hrp2 and hrp3 deletion detection using amplicon sequencing. Initial sequence data processing can be performed automatically, and subsequent variant analysis requires minimal bioinformatic skills using any tabulated data analysis program. The assay was validated using a retrospective sample collection (n = 254) from the Peruvian Amazon between 2003 and 2018. By combining phenotypic markers and a within-country 28-single-nucleotide-polymorphism (SNP) barcode, we were able to distinguish different lineages with multiple resistance haplotypes (in dhfr, dhps, crt and mdr1) and hrp2 and hrp3 deletions, which have been increasing in recent years. We found no evidence to suggest the emergence of artemisinin (ART) resistance in Peru. These findings indicate a parasite population that is under drug pressure but is susceptible to current antimalarials and demonstrate the added value of a highly multiplexed molecular tool to inform malaria strategies and surveillance systems. IMPORTANCE While the power of next-generation sequencing technologies to inform and guide malaria control programs has become broadly recognized, the integration of genomic data for operational incorporation into malaria surveillance remains a challenge in most countries where malaria is endemic. The main obstacles include limited infrastructure, limited access to high-throughput sequencing facilities, and the need for local capacity to run an in-country analysis of genomes at a large-enough scale to be informative for surveillance. In addition, there is a lack of standardized laboratory protocols and automated analysis pipelines to generate reproducible and timely results useful for relevant stakeholders. With our standardized laboratory and bioinformatic workflow, malaria genetic surveillance data can be readily generated by surveillance researchers and malaria control programs in countries of endemicity, increasing ownership and ensuring timely results for informed decision- and policy-making.
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Affiliation(s)
| | - Carlos Fernandez-Miñope
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Norbert J. van Dijk
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Lidia Llacsahuanga Allcca
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Pieter Guetens
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Hugo O. Valdivia
- Department of Parasitology, U.S. Naval Medical Research Unit No. 6 (NAMRU-6), Lima, Peru
| | | | - Eduard Rovira-Vallbona
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Pieter Monsieurs
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
| | - Christopher Delgado-Ratto
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Global Health Institute, University of Antwerp, Antwerp, Belgium
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Departamento de Ciencias Celulares y Moleculares, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Anna Rosanas-Urgell
- Institute of Tropical Medicine Antwerp, Biomedical Sciences Department, Antwerp, Belgium
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15
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Weiland AS. Recent Advances in Imported Malaria Pathogenesis, Diagnosis, and Management. CURRENT EMERGENCY AND HOSPITAL MEDICINE REPORTS 2023; 11:49-57. [PMID: 37213266 PMCID: PMC10091340 DOI: 10.1007/s40138-023-00264-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2023] [Indexed: 05/23/2023]
Abstract
Purpose of Review Malaria is an important human parasitic disease affecting the population of tropical, subtropical regions as well as travelers to these areas.The purpose of this article is to provide clinicians practicing in non-endemic areas with a comprehensive overview of the recent data on microbiologic and pathophysiologic features of five Plasmodium parasites, clinical presentation of uncomplicated and severe cases, modern diagnostic methods, and treatment of malaria. Recent Findings Employment of robust surveillance programs, rapid diagnostic tests, highly active artemisinin-based therapy, and the first malaria vaccine have led to decline in malaria incidence; however, emerging drug resistance, disruptions due to the COVID-19 pandemic, and other socio-economic factors have stalled the progress. Summary Clinicians practicing in non-endemic areas such as the United States should consider a diagnosis of malaria in returning travelers presenting with fever, utilize rapid diagnostic tests if available at their practice locations in addition to microscopy, and timely initiate guideline-directed management as delays in treatment can lead to poor clinical outcomes.
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Affiliation(s)
- Anastasia S. Weiland
- Department of Medicine, Case Western Reserve University/University Hospitals Cleveland Medical Center, Cleveland, OH USA
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16
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Wong W, Volkman S, Daniels R, Schaffner S, Sy M, Ndiaye YD, Badiane AS, Deme AB, Diallo MA, Gomis J, Sy N, Ndiaye D, Wirth DF, Hartl DL. R H: a genetic metric for measuring intrahost Plasmodium falciparum relatedness and distinguishing cotransmission from superinfection. PNAS NEXUS 2022; 1:pgac187. [PMID: 36246152 PMCID: PMC9552330 DOI: 10.1093/pnasnexus/pgac187] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 09/08/2022] [Indexed: 01/29/2023]
Abstract
Multiple-strain (polygenomic) infections are a ubiquitous feature of Plasmodium falciparum parasite population genetics. Under simple assumptions of superinfection, polygenomic infections are hypothesized to be the result of multiple infectious bites. As a result, polygenomic infections have been used as evidence of repeat exposure and used to derive genetic metrics associated with high transmission intensity. However, not all polygenomic infections are the result of multiple infectious bites. Some result from the transmission of multiple, genetically related strains during a single infectious bite (cotransmission). Superinfection and cotransmission represent two distinct transmission processes, and distinguishing between the two could improve inferences regarding parasite transmission intensity. Here, we describe a new metric, R H, that utilizes the correlation in allelic state (heterozygosity) within polygenomic infections to estimate the likelihood that the observed complexity resulted from either superinfection or cotransmission. R H is flexible and can be applied to any type of genetic data. As a proof of concept, we used R H to quantify polygenomic relatedness and estimate cotransmission and superinfection rates from a set of 1,758 malaria infections genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode. Contrary to expectation, we found that cotransmission was responsible for a significant fraction of 43% to 53% of the polygenomic infections collected in three distinct epidemiological regions in Senegal. The prediction that polygenomic infections frequently result from cotransmission stresses the need to incorporate estimates of relatedness within polygenomic infections to ensure the accuracy of genomic epidemiology surveillance data for informing public health activities.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
| | - Sarah Volkman
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA 02115, USA
| | - Rachel Daniels
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Stephen Schaffner
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Mouhamad Sy
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Yaye Die Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Aida S Badiane
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Mamadou Alpha Diallo
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Jules Gomis
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Ngayo Sy
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Aristide le Dantec Hospital, Cheikh Anta Diop University, Dakar 10200, Senegal
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, 665 Huntington Ave, Boston, MA 02115, USA
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA 02142, USA
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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17
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Huwe T, Kibria MG, Johora FT, Phru CS, Jahan N, Hossain MS, Khan WA, Price RN, Ley B, Alam MS, Koepfli C. Heterogeneity in prevalence of subclinical Plasmodium falciparum and Plasmodium vivax infections but no parasite genomic clustering in the Chittagong Hill Tracts, Bangladesh. Malar J 2022; 21:218. [PMID: 35836171 PMCID: PMC9281141 DOI: 10.1186/s12936-022-04236-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/22/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Malaria remains endemic in Bangladesh, with the majority of cases occurring in forested, mountainous region in the Chittagong Hill Tracts (CHT). This area is home to Bengali and diverse groups of indigenous people (Pahari) residing largely in mono-ethnic villages. METHODS 1002 individuals of the 9 most prominent Pahari and the Bengali population were randomly selected and screened by RDT and qPCR. Parasites were genotyped by msp2 and deep sequencing of 5 amplicons (ama1-D3, cpmp, cpp, csp, and msp7) for Plasmodium falciparum (n = 20), and by microsatellite (MS) typing of ten loci and amplicon sequencing of msp1 for Plasmodium vivax (n = 21). Population structure was analysed using STRUCTURE software. Identity-by-state (IBS) was calculated as a measure of parasite relatedness and used to generate relatedness networks. RESULTS The prevalence of P. falciparum and P. vivax infection was 0.7% by RDT (P. falciparum 6/1002; P. vivax 0/1002, mixed: 1/1002) and 4% by qPCR (P. falciparum 21/1002; P. vivax 16/1002, mixed: 5/1002). Infections were highly clustered, with 64% (27/42) of infections occurring in only two Pahari groups, the Khumi and Mro. Diversity was high; expected heterozygosity was 0.93 for P. falciparum and 0.81 for P. vivax. 85.7% (18/21) of P. vivax and 25% (5/20) of P. falciparum infections were polyclonal. No population structure was evident for either species, suggesting high transmission and gene flow among Pahari groups. CONCLUSIONS High subclinical infection prevalence and genetic diversity mirror ongoing transmission. Control activities should be specifically directed to Pahari groups at greatest risk.
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Affiliation(s)
- Tiffany Huwe
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Mohammad Golam Kibria
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Fatema Tuj Johora
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
- Georgia State University, Atlanta, GA, USA
| | - Ching Swe Phru
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Nusrat Jahan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Mohammad Sharif Hossain
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Wasif Ali Khan
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh
| | - Ric N Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Benedikt Ley
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia.
| | - Mohammad Shafiul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research Bangladesh (Icddr, B), Dhaka, Bangladesh.
| | - Cristian Koepfli
- Department of Biological Sciences and Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA.
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18
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Tenfold difference in DNA recovery rate: systematic comparison of whole blood vs. dried blood spot sample collection for malaria molecular surveillance. Malar J 2022; 21:88. [PMID: 35292038 PMCID: PMC8922754 DOI: 10.1186/s12936-022-04122-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/07/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Molecular and genomic surveillance is becoming increasingly used to track malaria control and elimination efforts. Blood samples can be collected as whole blood and stored at - 20 °C until DNA extraction, or as dried blood spots (DBS), circumventing the need for a cold chain. Despite the wide use of either method, systematic comparisons of how the method of blood sample preservation affects the limit of detection (LOD) of molecular diagnosis and the proportion of DNA recovered for downstream applications are lacking. METHODS Extractions based on spin columns, magnetic beads, Tween-Chelex, and direct PCR without prior extraction were compared for whole blood and dried blood spots (DBS) using dilution series of Plasmodium falciparum culture samples. Extracted DNA was quantified by qPCR and droplet digital PCR (ddPCR). RESULTS DNA recovery was 5- to 10-fold higher for whole blood compared to DBS, resulting in a 2- to 3-fold lower LOD for both extraction methods compared to DBS. For whole blood, a magnetic bead-based method resulted in a DNA recovery rate of 88-98% when extracting from whole blood compared to 17-33% for a spin-column based method. For extractions from DBS, the magnetic bead-based method resulted in 8-20% DNA recovery, while the spin-column based method resulted in only 2% DNA recovery. The Tween-Chelex method was superior to other methods with 15-21% DNA recovery, and even more sensitive than extractions from whole blood samples. The direct PCR method was found to have the lowest LOD overall for both, whole blood and DBS. CONCLUSIONS Pronounced differences in LOD and DNA yield need to be considered when comparing prevalence estimates based on molecular methods and when selecting sampling protocols for other molecular surveillance applications.
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19
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Sy M, Deme AB, Warren JL, Early A, Schaffner S, Daniels RF, Dieye B, Ndiaye IM, Diedhiou Y, Mbaye AM, Volkman SK, Hartl DL, Wirth DF, Ndiaye D, Bei AK. Plasmodium falciparum genomic surveillance reveals spatial and temporal trends, association of genetic and physical distance, and household clustering. Sci Rep 2022; 12:938. [PMID: 35042879 PMCID: PMC8766587 DOI: 10.1038/s41598-021-04572-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/24/2021] [Indexed: 11/15/2022] Open
Abstract
Molecular epidemiology using genomic data can help identify relationships between malaria parasite population structure, malaria transmission intensity, and ultimately help generate actionable data to assess the effectiveness of malaria control strategies. Genomic data, coupled with geographic information systems data, can further identify clusters or hotspots of malaria transmission, parasite genetic and spatial connectivity, and parasite movement by human or mosquito mobility over time and space. In this study, we performed longitudinal genomic surveillance in a cohort of 70 participants over four years from different neighborhoods and households in Thiès, Senegal—a region of exceptionally low malaria transmission (entomological inoculation rate less than 1). Genetic identity (identity by state, IBS) was established using a 24-single nucleotide polymorphism molecular barcode, identity by descent was calculated from whole genome sequence data, and a hierarchical Bayesian regression model was used to establish genetic and spatial relationships. Our results show clustering of genetically similar parasites within households and a decline in genetic similarity of parasites with increasing distance. One household showed extremely high diversity and warrants further investigation as to the source of these diverse genetic types. This study illustrates the utility of genomic data with traditional epidemiological approaches for surveillance and detection of trends and patterns in malaria transmission not only by neighborhood but also by household. This approach can be implemented regionally and countrywide to strengthen and support malaria control and elimination efforts.
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Affiliation(s)
- Mouhamad Sy
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Awa B Deme
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal.,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Angela Early
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stephen Schaffner
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rachel F Daniels
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Baba Dieye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Younous Diedhiou
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Amadou Moctar Mbaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,College of Natural, Behavioral and Health Sciences, Simmons University, Boston, MA, USA
| | - Daniel L Hartl
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal
| | - Amy K Bei
- Laboratory of Parasitology and Mycology, Cheikh Anta Diop University, Aristide le Dantec Hospital, Dakar, Senegal. .,Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA. .,Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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20
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Ayanful-Torgby R, Sarpong E, Abagna HB, Donu D, Obboh E, Mensah BA, Adjah J, Williamson KC, Amoah LE. Persistent Plasmodium falciparum infections enhance transmission-reducing immunity development. Sci Rep 2021; 11:21380. [PMID: 34725428 PMCID: PMC8560775 DOI: 10.1038/s41598-021-00973-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 10/21/2021] [Indexed: 11/09/2022] Open
Abstract
Subclinical infections that serve as reservoir populations to drive transmission remain a hurdle to malaria control. Data on infection dynamics in a geographical area is required to strategically design and implement malaria interventions. In a longitudinal cohort, we monitored Plasmodium falciparum infection prevalence and persistence, and anti-parasite immunity to gametocyte and asexual antigens for 10 weeks. Of the 100 participants, only 11 were never infected, whilst 16 had persistent infections detected by reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR), and one participant had microscopic parasites at all visits. Over 70% of the participants were infected three or more times, and submicroscopic gametocyte prevalence was high, ≥ 48% of the parasite carriers. Naturally induced responses against recombinant Pfs48/45.6C, Pfs230proC, and EBA175RIII-V antigens were not associated with either infection status or gametocyte carriage, but the antigen-specific IgG titers inversely correlated with parasite and gametocyte densities consistent with partial immunity. Longitudinal analysis of gametocyte diversity indicated at least four distinct clones circulated throughout the study period. The high prevalence of children infected with distinct gametocyte clones coupled with marked variation in infection status at the individual level suggests ongoing transmission and should be targeted in malaria control programs.
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Affiliation(s)
- Ruth Ayanful-Torgby
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
| | | | - Hamza B Abagna
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dickson Donu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Benedicta A Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Joshua Adjah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kim C Williamson
- Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Linda E Amoah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.
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21
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He X, Zhong D, Zou C, Pi L, Zhao L, Qin Y, Pan M, Wang S, Zeng W, Xiang Z, Chen X, Wu Y, Si Y, Cui L, Huang Y, Yan G, Yang Z. Unraveling the Complexity of Imported Malaria Infections by Amplicon Deep Sequencing. Front Cell Infect Microbiol 2021; 11:725859. [PMID: 34595134 PMCID: PMC8477663 DOI: 10.3389/fcimb.2021.725859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/16/2021] [Indexed: 11/22/2022] Open
Abstract
Imported malaria and recurrent infections are becoming an emerging issue in many malaria non-endemic countries. This study aimed to determine the molecular patterns of the imported malaria infections and recurrence. Blood samples were collected from patients with imported malaria infections during 2016-2018 in Guangxi Zhuang Autonomous Region, China. Next-generation amplicon deep-sequencing approaches were used to assess parasite genetic diversity, multiplexity of infection, relapse, recrudescence, and antimalarial drug resistance. A total of 44 imported malaria cases were examined during the study, of which 35 (79.5%) had recurrent malaria infections within 1 year. The majority (91.4%) had one recurrent malaria episode, whereas two patients had two recurrences and one patient had three recurrences. A total of 19 recurrence patterns (the species responsible for primary and successive clinical episodes) were found in patients returning from malaria epidemic countries. Four parasite species were detected with a higher than usual proportion (46.2%) of non-falciparum infections or mixed-species infections. An increasing trend of recurrence infections and reduced drug treatment efficacy were observed among the cases of imported malaria. The high recurrence rate and complex patterns of imported malaria from Africa to non-endemic countries have the potential to initiate local transmission, thereby undermining efforts to eliminate locally acquired malaria. Our findings highlight the power of amplicon deep-sequencing applications in molecular epidemiological studies of the imported malaria recurrences.
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Affiliation(s)
- Xi He
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, United States
| | - Chunyan Zou
- Department of Electrocardiogram, Guangxi Zhuang Autonomous Region People’s Hospital, Nanning, China
| | - Liang Pi
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Luyi Zhao
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yucheng Qin
- Department of Infectious Diseases, Shanglin County People’s Hospital, Shanglin, China
| | - Maohua Pan
- Department of Infectious Diseases, Shanglin County People’s Hospital, Shanglin, China
| | - Siqi Wang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Weiling Zeng
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Zheng Xiang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Xi Chen
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Yanrui Wu
- Department of Cell Biology & Genetics, Kunming Medical University, Kunming, China
| | - Yu Si
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
| | - Liwang Cui
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Yaming Huang
- Department of Protozoa, Guangxi Zhuang Autonomous Region Center for Disease Prevention and Control, Nanning, China
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, United States
| | - Zhaoqing Yang
- Department of Pathogen Biology and Immunology, Kunming Medical University, Kunming, China
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22
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Diagnosing the drug resistance signature in Plasmodium falciparum: a review from contemporary methods to novel approaches. J Parasit Dis 2021; 45:869-876. [PMID: 34475670 DOI: 10.1007/s12639-020-01333-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022] Open
Abstract
The genome sequence project of the human malaria parasite Plasmodium falciparum reveal variations in the parasite DNA sequence. Most of these variations are single nucleotide polymorphism (SNP). A high frequency of single nucleotide polymorphism (SNP) in the Plasmodium falciparum population is usually a benchmark for anti-malarial resistance which allows parasites to be elusive to the chemotherapeutic agents, vaccine and vector control strategies, resulting in the leading cause of morbidity and mortality globally. The high density of drug resistance signature markers such as pfcrt,pfmdr1, pfdhps, pfdhfr, pfkelch13, pfatpase6 and pfmrp1 in the genome opens up a scope for the study of the genetic basis of this elusive parasite. The precise and prompt diagnosis of resistance strains of parasite plays vital role in malaria elimination program.This review probably shed light on contemporary SNP diagnostic tools used in molecular surveillance of Plasmodium falciparum drug resistance in terms of mechanism, reaction modalities, and development with their virtues and shortcomings.
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23
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Lopez L, Koepfli C. Systematic review of Plasmodium falciparum and Plasmodium vivax polyclonal infections: Impact of prevalence, study population characteristics, and laboratory procedures. PLoS One 2021; 16:e0249382. [PMID: 34115783 PMCID: PMC8195386 DOI: 10.1371/journal.pone.0249382] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/17/2021] [Indexed: 12/27/2022] Open
Abstract
Multiple infections of genetically distinct clones of the same Plasmodium species are common in many malaria endemic settings. Mean multiplicity of infection (MOI) and the proportion of polyclonal infections are often reported as surrogate marker of transmission intensity, yet the relationship with traditional measures such as parasite prevalence is not well understood. We have searched Pubmed for articles on P. falciparum and P. vivax multiplicity, and compared the proportion of polyclonal infections and mean MOI to population prevalence. The impact of the genotyping method, number of genotyping markers, method for diagnosis (microscopy/RDT vs. PCR), presence of clinical symptoms, age, geographic region, and year of sample collection on multiplicity indices were assessed. For P. falciparum, 153 studies met inclusion criteria, yielding 275 individual data points and 33,526 genotyped individuals. The proportion of polyclonal infections ranged from 0-96%, and mean MOI from 1-6.1. For P. vivax, 54 studies met inclusion criteria, yielding 115 data points and 13,325 genotyped individuals. The proportion of polyclonal infections ranged from 0-100%, and mean MOI from 1-3.8. For both species, the proportion of polyclonal infections ranged from very low to close to 100% at low prevalence, while at high prevalence it was always high. Each percentage point increase in prevalence resulted in a 0.34% increase in the proportion of polyclonal P. falciparum infections (P<0.001), and a 0.78% increase in the proportion of polyclonal P. vivax infections (P<0.001). In multivariable analysis, higher prevalence, typing multiple markers, diagnosis of infections by PCR, and sampling in Africa were found to result in a higher proportion of P. falciparum polyclonal infections. For P. vivax, prevalence, year of study, typing multiple markers, and geographic region were significant predictors. In conclusion, polyclonal infections are frequently present in all settings, but the association between multiplicity and prevalence is weak.
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Affiliation(s)
- Luis Lopez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States of America
- Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN, United States of America
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24
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Kattenberg JH, Razook Z, Keo R, Koepfli C, Jennison C, Lautu-Gumal D, Fola AA, Ome-Kaius M, Barnadas C, Siba P, Felger I, Kazura J, Mueller I, Robinson LJ, Barry AE. Monitoring Plasmodium falciparum and Plasmodium vivax using microsatellite markers indicates limited changes in population structure after substantial transmission decline in Papua New Guinea. Mol Ecol 2020; 29:4525-4541. [PMID: 32985031 PMCID: PMC10008436 DOI: 10.1111/mec.15654] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/27/2020] [Indexed: 02/01/2023]
Abstract
Monitoring the genetic structure of pathogen populations may be an economical and sensitive approach to quantify the impact of control on transmission dynamics, highlighting the need for a better understanding of changes in population genetic parameters as transmission declines. Here we describe the first population genetic analysis of two major human malaria parasites, Plasmodium falciparum (Pf) and Plasmodium vivax (Pv), following nationwide distribution of long-lasting insecticide-treated nets (LLINs) in Papua New Guinea (PNG). Parasite isolates from pre- (2005-2006) and post-LLIN (2010-2014) were genotyped using microsatellite markers. Despite parasite prevalence declining substantially (East Sepik Province: Pf = 54.9%-8.5%, Pv = 35.7%-5.6%, Madang Province: Pf = 38.0%-9.0%, Pv: 31.8%-19.7%), genetically diverse and intermixing parasite populations remained. Pf diversity declined modestly post-LLIN relative to pre-LLIN (East Sepik: Rs = 7.1-6.4, HE = 0.77-0.71; Madang: Rs = 8.2-6.1, HE = 0.79-0.71). Unexpectedly, population structure present in pre-LLIN populations was lost post-LLIN, suggesting that more frequent human movement between provinces may have contributed to higher gene flow. Pv prevalence initially declined but increased again in one province, yet diversity remained high throughout the study period (East Sepik: Rs = 11.4-9.3, HE = 0.83-0.80; Madang: Rs = 12.2-14.5, HE = 0.85-0.88). Although genetic differentiation values increased between provinces over time, no significant population structure was observed at any time point. For both species, a decline in multiple infections and increasing clonal transmission and significant multilocus linkage disequilibrium post-LLIN were positive indicators of impact on the parasite population using microsatellite markers. These parameters may be useful adjuncts to traditional epidemiological tools in the early stages of transmission reduction.
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Affiliation(s)
- Johanna Helena Kattenberg
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea
| | - Zahra Razook
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Raksmei Keo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Cristian Koepfli
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Charlie Jennison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Abebe A Fola
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Ome-Kaius
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Céline Barnadas
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - James Kazura
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, OH, USA
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Leanne J Robinson
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Yagaum, Papua New Guinea.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia.,Disease Elimination, Burnet Institute, Melbourne, VIC, Australia
| | - Alyssa E Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
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25
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Ndiaye T, Sy M, Gaye A, Siddle KJ, Park DJ, Bei AK, Deme AB, Mbaye A, Dieye B, Ndiaye YD, Ndiaye IM, Diallo MA, Diongue K, Volkman SK, Badiane AS, Ndiaye D. Molecular epidemiology of Plasmodium falciparum by multiplexed amplicon deep sequencing in Senegal. Malar J 2020; 19:403. [PMID: 33172455 PMCID: PMC7654156 DOI: 10.1186/s12936-020-03471-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/30/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular epidemiology can provide important information regarding the genetic diversity and transmission of Plasmodium falciparum, which can assist in designing and monitoring elimination efforts. However, malaria molecular epidemiology including understanding the genetic diversity of the parasite and performing molecular surveillance of transmission has been poorly documented in Senegal. Next Generation Sequencing (NGS) offers a practical, fast and high-throughput approach to understand malaria population genetics. This study aims to unravel the population structure of P. falciparum and to estimate the allelic diversity, multiplicity of infection (MOI), and evolutionary patterns of the malaria parasite using the NGS platform. METHODS Multiplex amplicon deep sequencing of merozoite surface protein 1 (PfMSP1) and merozoite surface protein 2 (PfMSP2) in fifty-three P. falciparum isolates from two epidemiologically different areas in the South and North of Senegal, was carried out. RESULTS A total of 76 Pfmsp1 and 116 Pfmsp2 clones were identified and 135 different alleles were found, 56 and 79 belonged to the pfmsp1 and pfmsp2 genes, respectively. K1 and IC3D7 allelic families were most predominant in both sites. The local haplotype diversity (Hd) and nucleotide diversity (π) were higher in the South than in the North for both genes. For pfmsp1, a high positive Tajima's D (TD) value was observed in the South (D = 2.0453) while negative TD value was recorded in the North (D = - 1.46045) and F-Statistic (Fst) was 0.19505. For pfmsp2, non-directional selection was found with a highly positive TD test in both areas and Fst was 0.02111. The mean MOI for both genes was 3.07 and 1.76 for the South and the North, respectively, with a statistically significant difference between areas (p = 0.001). CONCLUSION This study revealed a high genetic diversity of pfmsp1 and pfmsp2 genes and low genetic differentiation in P. falciparum population in Senegal. The MOI means were significantly different between the Southern and Northern areas. Findings also showed that multiplexed amplicon deep sequencing is a useful technique to investigate genetic diversity and molecular epidemiology of P. falciparum infections.
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Affiliation(s)
- Tolla Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal.
| | - Mouhamad Sy
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Amy Gaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | | | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Amy K Bei
- Yale School of Public Health, 60 College Street, New Haven, CT, 06510, USA
| | - Awa B Deme
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Aminata Mbaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Baba Dieye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Yaye Die Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Ibrahima Mbaye Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Mamadou Alpha Diallo
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Khadim Diongue
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
| | - Aida Sadikh Badiane
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
| | - Daouda Ndiaye
- Laboratoire de Parasitologie-Mycologie, Université Cheikh Anta Diop de Dakar (UCAD), Hôpital Aristide Le Dantec, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard University, Cambridge, MA, USA
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26
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Briggs J, Teyssier N, Nankabirwa JI, Rek J, Jagannathan P, Arinaitwe E, Bousema T, Drakeley C, Murray M, Crawford E, Hathaway N, Staedke SG, Smith D, Rosenthal PJ, Kamya M, Dorsey G, Rodriguez-Barraquer I, Greenhouse B. Sex-based differences in clearance of chronic Plasmodium falciparum infection. eLife 2020; 9:59872. [PMID: 33107430 PMCID: PMC7591246 DOI: 10.7554/elife.59872] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Multiple studies have reported a male bias in incidence and/or prevalence of malaria infection in males compared to females. To test the hypothesis that sex-based differences in host-parasite interactions affect the epidemiology of malaria, we intensively followed Plasmodium falciparum infections in a cohort in a malaria endemic area of eastern Uganda and estimated both force of infection (FOI) and rate of clearance using amplicon deep-sequencing. We found no evidence of differences in behavioral risk factors, incidence of malaria, or FOI by sex. In contrast, females cleared asymptomatic infections at a faster rate than males (hazard ratio [HR]=1.82, 95% CI 1.20 to 2.75 by clone and HR = 2.07, 95% CI 1.24 to 3.47 by infection event) in multivariate models adjusted for age, timing of infection onset, and parasite density. These findings implicate biological sex-based differences as an important factor in the host response to this globally important pathogen.
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Affiliation(s)
- Jessica Briggs
- Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Noam Teyssier
- Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Joaniter I Nankabirwa
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - John Rek
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | | | - Emmanuel Arinaitwe
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands.,Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Margaret Murray
- Department of Medicine, Stanford University, Palo Alto, United States
| | | | - Nicholas Hathaway
- Department of Medicine, University of Massachusetts, Amherst, United States
| | - Sarah G Staedke
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - David Smith
- Institute for Health Metrics & Evaluation, University of Washington, Seattle, United States
| | - Phillip J Rosenthal
- Department of Medicine, University of California San Francisco, San Francisco, United States
| | - Moses Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda.,Department of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Grant Dorsey
- Department of Medicine, University of California San Francisco, San Francisco, United States
| | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, United States
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27
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Gruenberg M, Hofmann NE, Nate E, Karl S, Robinson LJ, Lanke K, Smith TA, Bousema T, Felger I. qRT-PCR versus IFA-based Quantification of Male and Female Gametocytes in Low-Density Plasmodium falciparum Infections and Their Relevance for Transmission. J Infect Dis 2020; 221:598-607. [PMID: 31437280 PMCID: PMC7325619 DOI: 10.1093/infdis/jiz420] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 08/14/2019] [Indexed: 11/22/2022] Open
Abstract
Background Accurate quantification of female and male gametocytes and sex ratios in asymptomatic low-density malaria infections are important for assessing their transmission potential. Gametocytes often escape detection even by molecular methods, therefore ultralow gametocyte densities were quantified in large blood volumes. Methods Female and male gametocytes were quantified in 161 PCR-positive Plasmodium falciparum infections from a cross-sectional survey in Papua New Guinea. Ten-fold concentrated RNA from 800 µL blood was analyzed using female-specific pfs25 and male-specific pfmget or mssp qRT-PCR. Gametocyte sex ratios from qRT-PCR were compared with those from immunofluorescence assays (IFA). Results Gametocytes were identified in 58% (93/161) P. falciparum-positive individuals. Mean gametocyte densities were frequently below 1 female and 1 male gametocyte/µL by qRT-PCR. The mean proportion of males was 0.39 (95% confidence interval, 0.33–0.44) by pfs25/pfmget qRT-PCR; this correlated well with IFA results (Pearsons r2 = 0.91; P < .001). A Poisson model fitted to our data predicted 16% P. falciparum-positive individuals that are likely to transmit, assuming at least 1 female and 1 male gametocyte per 2.5 µL mosquito bloodmeal. Conclusions Based on model estimates of female and male gametocytes per 2.5 µL blood, P. falciparum-positive individuals detected exclusively by ultrasensitive diagnostics are negligible for human-to-mosquito transmission. Estimating the transmission potential of ultralow-density malaria infections informs interventions. Almost all infections with ≥1 female and male gametocyte per 2.5 µL mosquito bloodmeal, and thus with highest likelihood of contributing to human-to-mosquito transmission, were detectable by standard molecular diagnostics.
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Affiliation(s)
- Maria Gruenberg
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Natalie E Hofmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Elma Nate
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Stephan Karl
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Leanne J Robinson
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Kjerstin Lanke
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Thomas A Smith
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Teun Bousema
- Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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28
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Hemming-Schroeder E, Zhong D, Kibret S, Chie A, Lee MC, Zhou G, Atieli H, Githeko A, Kazura JW, Yan G. Microgeographic Epidemiology of Malaria Parasites in an Irrigated Area of Western Kenya by Deep Amplicon Sequencing. J Infect Dis 2020; 223:1456-1465. [PMID: 32803223 DOI: 10.1093/infdis/jiaa520] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 08/11/2020] [Indexed: 11/14/2022] Open
Abstract
To improve food security, investments in irrigated agriculture are anticipated to increase throughout Africa. However, the extent to which environmental changes from water resource development will impact malaria epidemiology remains unclear. This study was designed to compare the sensitivity of molecular markers used in deep amplicon sequencing for evaluating malaria transmission intensities and to assess malaria transmission intensity at various proximities to an irrigation scheme. Compared to ama1, csp, and msp1 amplicons, cpmp required the smallest sample size to detect differences in infection complexity between transmission risk zones. Transmission intensity was highest within 5 km of the irrigation scheme by polymerase chain reaction positivity rate, infection complexity, and linkage disequilibrium. The irrigated area provided a source of parasite infections for the surrounding 2- to 10-km area. This study highlights the suitability of the cpmp amplicon as a measure for transmission intensities and the impact of irrigation on microgeographic epidemiology of malaria parasites.
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Affiliation(s)
- Elizabeth Hemming-Schroeder
- Program in Public Health, University of California, Irvine, Irvine, California, USA.,Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Daibin Zhong
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Solomon Kibret
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Amanda Chie
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Ming-Chieh Lee
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Guofa Zhou
- Program in Public Health, University of California, Irvine, Irvine, California, USA
| | - Harrysone Atieli
- School of Public Health and Community Development, Maseno University, Kisumu, Kenya
| | - Andrew Githeko
- Center for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - James W Kazura
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, Irvine, California, USA
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29
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Koehler AV, Jabbar A, Hall RS, Gasser RB. A Targeted "Next-Generation" Sequencing-Informatic Approach to Define Genetic Diversity in Theileria orientalis Populations within Individual Cattle: Proof-of-Principle. Pathogens 2020; 9:pathogens9060448. [PMID: 32517045 PMCID: PMC7350381 DOI: 10.3390/pathogens9060448] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/25/2020] [Accepted: 06/03/2020] [Indexed: 12/13/2022] Open
Abstract
Oriental theileriosis is an economically important tickborne disease of bovines, caused by some members of the Theileria orientalis complex. Currently, 11 distinct operational taxonomic units (OTUs), or genotypes, are recognized based on their major piroplasm surface protein (MPSP) gene sequences. Two of these genotypes (i.e., chitose and ikeda) are recognized as pathogenic in cattle, causing significant disease in countries of the Asia-Pacific region. However, the true extent of genetic variation and associated virulence/pathogenicity within this complex is unknown. Here, we undertook a proof-of-principle study of a small panel of genomic DNAs (n = 13) from blood samples originating from individual cattle known to harbor T. orientalis, in order to assess the performance of a targeted “next-generation” sequencing-informatic approach to identify genotypes. Five genotypes (chitose, ikeda, buffeli, type 4, and type 5) were defined; multiple genotypes were found within individual samples, with dominant and minor sequence types representing most genotypes. This study indicates that this sequencing-informatic workflow could be useful to assess the nature and extent of genetic variation within and among populations of T. orientalis on a large scale, and to potentially employ panels of distinct gene markers for expanded molecular epidemiological investigations of socioeconomically important protistan pathogens more generally.
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30
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Roh ME, Tessema SK, Murphy M, Nhlabathi N, Mkhonta N, Vilakati S, Ntshalintshali N, Saini M, Maphalala G, Chen A, Wilheim J, Prach L, Gosling R, Kunene S, S Hsiang M, Greenhouse B. High Genetic Diversity of Plasmodium falciparum in the Low-Transmission Setting of the Kingdom of Eswatini. J Infect Dis 2020; 220:1346-1354. [PMID: 31190073 PMCID: PMC6743842 DOI: 10.1093/infdis/jiz305] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/12/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND To better understand transmission dynamics, we characterized Plasmodium falciparum genetic diversity in Eswatini, where transmission is low and sustained by importation. METHODS Twenty-six P. falciparum microsatellites were genotyped in 66% of confirmed cases (2014-2016; N = 582). Population and within-host diversity were used to characterize differences between imported and locally acquired infections. Logistic regression was used to assess the added value of diversity metrics to classify imported and local infections beyond epidemiology data alone. RESULTS Parasite population in Eswatini was highly diverse (expected heterozygosity [HE] = 0.75) and complex: 67% polyclonal infections, mean multiplicity of infection (MOI) 2.2, and mean within-host infection fixation index (FWS) 0.84. Imported cases had comparable diversity to local cases but exhibited higher MOI (2.4 vs 2.0; P = .004) and lower mean FWS (0.82 vs 0.85; P = .03). Addition of MOI and FWS to multivariate analyses did not increase discrimination between imported and local infections. CONCLUSIONS In contrast to the common perception that P. falciparum diversity declines with decreasing transmission intensity, Eswatini isolates exhibited high parasite diversity consistent with high rates of malaria importation and limited local transmission. Estimates of malaria transmission intensity from genetic data need to consider the effect of importation, especially as countries near elimination.
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Affiliation(s)
- Michelle E Roh
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | - Sofonias K Tessema
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Maxwell Murphy
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | | | | | | | | | - Manik Saini
- Clinton Health Access Initiative, Mbabane, Eswatini
| | | | - Anna Chen
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Jordan Wilheim
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco
| | - Lisa Prach
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco
| | - Roly Gosling
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Epidemiology and Biostatistics, University of California, San Francisco
| | | | - Michelle S Hsiang
- Malaria Elimination Initiative, Institute of Global Health Sciences, University of California, San Francisco.,Department of Pediatrics, University of California, San Francisco.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas
| | - Bryan Greenhouse
- Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California, San Francisco.,Chan Zuckerberg Biohub, San Francisco, California
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31
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Nsanzabana C. Strengthening Surveillance Systems for Malaria Elimination by Integrating Molecular and Genomic Data. Trop Med Infect Dis 2019; 4:E139. [PMID: 31816974 PMCID: PMC6958499 DOI: 10.3390/tropicalmed4040139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 12/20/2022] Open
Abstract
Unprecedented efforts in malaria control over the last 15 years have led to a substantial decrease in both morbidity and mortality in most endemic settings. However, these progresses have stalled over recent years, and resurgence may cause dramatic impact on both morbidity and mortality. Nevertheless, elimination efforts are currently going on with the objective of reducing malaria morbidity and mortality by 90% and malaria elimination in at least 35 countries by 2030. Strengthening surveillance systems is of paramount importance to reach those targets, and the integration of molecular and genomic techniques into routine surveillance could substantially improve the quality and robustness of data. Techniques such as polymerase chain reaction (PCR) and quantitative PCR (qPCR) are increasingly available in malaria endemic countries, whereas others such as sequencing are already available in a few laboratories. However, sequencing, especially next-generation sequencing (NGS), requires sophisticated infrastructure with adequate computing power and highly trained personnel for data analysis that require substantial investment. Different techniques will be required for different applications, and cost-effective planning must ensure the appropriate use of available resources. The development of national and sub-regional reference laboratories could help in minimizing the resources required in terms of equipment and trained staff. Concerted efforts from different stakeholders at national, sub-regional, and global level are needed to develop the required framework to establish and maintain these reference laboratories.
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Affiliation(s)
- Christian Nsanzabana
- Department of Medicine, Swiss Tropical and Public Health Institute, 4051 Basel, Switzerland; ; Tel.: +41-61-284-82-52
- University of Basel, P.O. Box, CH-4003 Basel, Switzerland
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32
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Cheaveau J, Mogollon DC, Mohon MAN, Golassa L, Yewhalaw D, Pillai DR. Asymptomatic malaria in the clinical and public health context. Expert Rev Anti Infect Ther 2019; 17:997-1010. [PMID: 31718324 DOI: 10.1080/14787210.2019.1693259] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Introduction: Historically, the global community has focused on the control of symptomatic malaria. However, interest in asymptomatic malaria has been growing, particularly in the context of malaria elimination.Areas covered: We undertook a comprehensive PubMed literature review on asymptomatic malaria as it relates to detection and elimination with emphasis between 2014 and 2019. Diagnostic tools with a low limit of detection (LOD) have allowed us to develop a more detailed understanding of asymptomatic malaria and its impact. These highly sensitive diagnostics have demonstrated that the prevalence of asymptomatic malaria is greater than previously thought. In addition, it is now possible to detect the malaria reservoir in the community, something that was previously not feasible. Asymptomatic malaria has previously not been treated, but research has begun to examine whether treating individuals with asymptomatic malaria may lead to health benefits. Finally, we have begun to understand the importance of asymptomatic malaria in ongoing transmission.Expert opinion: Therefore, with malaria elimination back on the agenda, asymptomatic malaria can no longer be ignored, especially in light of new ultra-sensitive diagnostic tools.
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Affiliation(s)
- James Cheaveau
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Daniel Castaneda Mogollon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Md Abu Naser Mohon
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, Jimma, Ethiopia
| | - Dylan R Pillai
- Department of Microbiology, Immunology, and Infectious Diseases, University of Calgary, Canada, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada.,Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
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33
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Amambua-Ngwa A, Jeffries D, Mwesigwa J, Seedy-Jawara A, Okebe J, Achan J, Drakeley C, Volkman S, D'Alessandro U. Long-distance transmission patterns modelled from SNP barcodes of Plasmodium falciparum infections in The Gambia. Sci Rep 2019; 9:13515. [PMID: 31534181 PMCID: PMC6751170 DOI: 10.1038/s41598-019-49991-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 08/12/2019] [Indexed: 02/04/2023] Open
Abstract
Malaria has declined significantly in The Gambia and determining transmission dynamics of Plasmodium falciparum can help targeting control interventions towards elimination. This can be inferred from genetic similarity between parasite isolates from different sites and timepoints. Here, we imposed a P. falciparum life cycle time on a genetic distance likelihood model to determine transmission paths from a 54 SNP barcode of 355 isolates. Samples were collected monthly during the 2013 malaria season from six pairs of villages spanning 300 km from western to eastern Gambia. There was spatial and temporal hierarchy in pairwise genetic relatedness, with the most similar barcodes from isolates within the same households and village. Constrained by travel data, the model detected 60 directional transmission events, with 27% paths linking persons from different regions. We identified 13 infected individuals (4.2% of those genotyped) responsible for 2 to 8 subsequent infections within their communities. These super-infectors were mostly from high transmission villages. When considering paths between isolates from the most distant regions (west vs east) and travel history, there were 3 transmission paths from eastern to western Gambia, all at the peak (October) of the malaria transmission season. No paths with known travel originated from the extreme west to east. Although more than half of all paths were within-village, parasite flow from east to west may contribute to maintain transmission in western Gambia, where malaria transmission is already low. Therefore, interrupting malaria transmission in western Gambia would require targeting eastern Gambia, where malaria prevalence is substantially higher, with intensified malaria interventions.
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Affiliation(s)
- Alfred Amambua-Ngwa
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.
| | - David Jeffries
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Julia Mwesigwa
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Aminata Seedy-Jawara
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Joseph Okebe
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Jane Achan
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia
| | - Chris Drakeley
- London School of Hygiene and tropical Medicine, London, UK
| | - Sarah Volkman
- Harvard School of Public Health, Boston, Massachusetts, USA
| | - Umberto D'Alessandro
- Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine, Banjul, The Gambia.,London School of Hygiene and tropical Medicine, London, UK
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34
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Tessema SK, Raman J, Duffy CW, Ishengoma DS, Amambua-Ngwa A, Greenhouse B. Applying next-generation sequencing to track falciparum malaria in sub-Saharan Africa. Malar J 2019; 18:268. [PMID: 31477139 PMCID: PMC6720407 DOI: 10.1186/s12936-019-2880-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Accepted: 07/11/2019] [Indexed: 01/13/2023] Open
Abstract
Next-generation sequencing (NGS) technologies are increasingly being used to address a diverse range of biological and epidemiological questions. The current understanding of malaria transmission dynamics and parasite movement mainly relies on the analyses of epidemiologic data, e.g. case counts and self-reported travel history data. However, travel history data are often not routinely collected or are incomplete, lacking the necessary level of accuracy. Although genetic data from routinely collected field samples provides an unprecedented opportunity to track the spread of malaria parasites, it remains an underutilized resource for surveillance due to lack of local awareness and capacity, limited access to sensitive laboratory methods and associated computational tools and difficulty in interpreting genetic epidemiology data. In this review, the potential roles of NGS in better understanding of transmission patterns, accurately tracking parasite movement and addressing the emerging challenges of imported malaria in low transmission settings of sub-Saharan Africa are discussed. Furthermore, this review highlights the insights gained from malaria genomic research and challenges associated with integrating malaria genomics into existing surveillance tools to inform control and elimination strategies.
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Affiliation(s)
- Sofonias K Tessema
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.
| | - Jaishree Raman
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Disease, Sandringham, Gauteng, South Africa
| | - Craig W Duffy
- Department of Infection Biology, University of Liverpool, Liverpool, UK
| | - Deus S Ishengoma
- National Institute for Medical Research, Tanga Research Centre, Tanga, Tanzania
| | | | - Bryan Greenhouse
- EPPIcenter Program, Division of HIV, Infectious Diseases, and Global Medicine, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
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35
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Saravu K, Tellapragada C, Kulavalli S, Xavier W, Umakanth S, Brahmarouphu G, Srinivas NK, Channabasavaiah JP, Bava A, Saadi AV, Guddattu V, Satyamoorthy K, Bhat K. A pilot randomized controlled trial to compare the effectiveness of two 14-day primaquine regimens for the radical cure of vivax malaria in South India. Malar J 2018; 17:321. [PMID: 30176897 PMCID: PMC6122616 DOI: 10.1186/s12936-018-2472-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 08/30/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Radical cure of Plasmodium vivax malaria requires treatment with a blood schizonticide and a hypnozoitocide (primaquine) to eradicate the dormant liver stages. There has been uncertainty about the operational effectiveness and optimum dosing of the currently recommended 14-day primaquine (PQ) course. METHODS A two centre, randomized, open-label, two arm study was conducted in South India. Patients were randomized to receive either high dose (0.5 mg base/kg body weight) or conventional dose (0.25 mg/kg) PQ for 14 days. Plasma concentrations of PQ and carboxyprimaquine (CPQ) on the 7th day of treatment were measured by reverse phase high performance liquid chromatography. Study subjects were followed up for 6 months. Recurrent infections were genotyped using capillary fragment length polymorphism of two PCR-amplified microsatellite markers (MS07 and MS 10). RESULTS Fifty patients were enrolled. Baseline characteristics and laboratory features did not differ significantly between the groups. Mean age of the study population was 42 ± 16.0 years. Recurrences 80-105 days later occurred in 4 (8%) patients, two in each the groups. All recurrences had the same microsatellite genotype as that causing the index infection suggesting all were relapses. One relapse was associated with low CPQ concentrations suggesting poor adherence. CONCLUSIONS This small pilot trial supports the effectiveness of the currently recommended lower dose (0.25 mg/kg/day) 14 day PQ regimen for the radical cure of vivax malaria in South India. Trial registration Clinical Trials Registry-India, CTRI/2017/03/007999. Registered 3 March 2017, http://ctri.nic.in/Clinicaltrials/regtrial.php?modid=1&compid=19&EncHid=82755.86366 .
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Affiliation(s)
- Kavitha Saravu
- Department of Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, Karnataka, 576104, India. .,Manipal McGill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India.
| | - Chaitanya Tellapragada
- Department of Virus Research, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Shrivathsa Kulavalli
- Manipal McGill Centre for Infectious Diseases, Prasanna School of Public Health, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Wilbin Xavier
- Department of Medicine, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Shashikiran Umakanth
- Department of Medicine, Dr. TMA Pai Hospital, Udupi, Melaka Manipal Medical College, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Gouthami Brahmarouphu
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Navyasree Kola Srinivas
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Jagadish Puralae Channabasavaiah
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Anzil Bava
- Department of Cell & Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Abdul Vahab Saadi
- Department of Cell & Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Vasudev Guddattu
- Department of Statistics, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Kapaettu Satyamoorthy
- Department of Cell & Molecular Biology, School of Life Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
| | - Krishnamurthy Bhat
- Department of Pharmaceutical Quality Assurance, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Madhava Nagar, Manipal, Karnataka, 576104, India
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Zhong D, Lo E, Wang X, Yewhalaw D, Zhou G, Atieli HE, Githeko A, Hemming-Schroeder E, Lee MC, Afrane Y, Yan G. Multiplicity and molecular epidemiology of Plasmodium vivax and Plasmodium falciparum infections in East Africa. Malar J 2018; 17:185. [PMID: 29720181 PMCID: PMC5932820 DOI: 10.1186/s12936-018-2337-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 04/26/2018] [Indexed: 11/18/2022] Open
Abstract
Background Parasite genetic diversity and multiplicity of infection (MOI) affect clinical outcomes, response to drug treatment and naturally-acquired or vaccine-induced immunity. Traditional methods often underestimate the frequency and diversity of multiclonal infections due to technical sensitivity and specificity. Next-generation sequencing techniques provide a novel opportunity to study complexity of parasite populations and molecular epidemiology. Methods Symptomatic and asymptomatic Plasmodium vivax samples were collected from health centres/hospitals and schools, respectively, from 2011 to 2015 in Ethiopia. Similarly, both symptomatic and asymptomatic Plasmodium falciparum samples were collected, respectively, from hospitals and schools in 2005 and 2015 in Kenya. Finger-pricked blood samples were collected and dried on filter paper. Long amplicon (> 400 bp) deep sequencing of merozoite surface protein 1 (msp1) gene was conducted to determine multiplicity and molecular epidemiology of P. vivax and P. falciparum infections. The results were compared with those based on short amplicon (117 bp) deep sequencing. Results A total of 139 P. vivax and 222 P. falciparum samples were pyro-sequenced for pvmsp1 and pfmsp1, yielding a total of 21 P. vivax and 99 P. falciparum predominant haplotypes. The average MOI for P. vivax and P. falciparum were 2.16 and 2.68, respectively, which were significantly higher than that of microsatellite markers and short amplicon (117 bp) deep sequencing. Multiclonal infections were detected in 62.2% of the samples for P. vivax and 74.8% of the samples for P. falciparum. Four out of the five subjects with recurrent P. vivax malaria were found to be a relapse 44–65 days after clearance of parasites. No difference was observed in MOI among P. vivax patients of different symptoms, ages and genders. Similar patterns were also observed in P. falciparum except for one study site in Kenyan lowland areas with significantly higher MOI. Conclusions The study used a novel method to evaluate Plasmodium MOI and molecular epidemiological patterns by long amplicon ultra-deep sequencing. The complexity of infections were similar among age groups, symptoms, genders, transmission settings (spatial heterogeneity), as well as over years (pre- vs. post-scale-up interventions). This study demonstrated that long amplicon deep sequencing is a useful tool to investigate multiplicity and molecular epidemiology of Plasmodium parasite infections. Electronic supplementary material The online version of this article (10.1186/s12936-018-2337-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daibin Zhong
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA.
| | - Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Xiaoming Wang
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences, Faculty of Health Sciences, Jimma University, Jimma, Ethiopia.,Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
| | - Guofa Zhou
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Harrysone E Atieli
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Andrew Githeko
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | | | - Ming-Chieh Lee
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA
| | - Yaw Afrane
- Department of Medical Microbiology, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Guiyun Yan
- Program in Public Health, University of California at Irvine, Irvine, CA, 92617, USA.
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Plasmodium vivax and Plasmodium falciparum infection dynamics: re-infections, recrudescences and relapses. Malar J 2018; 17:170. [PMID: 29665803 PMCID: PMC5905131 DOI: 10.1186/s12936-018-2318-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/09/2018] [Indexed: 12/12/2022] Open
Abstract
Background In malaria endemic populations, complex patterns of Plasmodium vivax and Plasmodium falciparum blood-stage infection dynamics may be observed. Genotyping samples from longitudinal cohort studies for merozoite surface protein (msp) variants increases the information available in the data, allowing multiple infecting parasite clones in a single individual to be identified. msp genotyped samples from two longitudinal cohorts in Papua New Guinea (PNG) and Thailand were analysed using a statistical model where the times of acquisition and clearance of each clone in every individual were estimated using a process of data augmentation. Results For the populations analysed, the duration of blood-stage P. falciparum infection was estimated as 36 (95% Credible Interval (CrI): 29, 44) days in PNG, and 135 (95% CrI 94, 191) days in Thailand. Experiments on simulated data indicated that it was not possible to accurately estimate the duration of blood-stage P. vivax infections due to the lack of identifiability between a single blood-stage infection and multiple, sequential blood-stage infections caused by relapses. Despite this limitation, the method and data point towards short duration of blood-stage P. vivax infection with a lower bound of 24 days in PNG, and 29 days in Thailand. On an individual level, P. vivax recurrences cannot be definitively classified into re-infections, recrudescences or relapses, but a probabilistic relapse phenotype can be assigned to each P. vivax sample, allowing investigation of the association between epidemiological covariates and the incidence of relapses. Conclusion The statistical model developed here provides a useful new tool for in-depth analysis of malaria data from longitudinal cohort studies, and future application to data sets with multi-locus genotyping will allow more detailed investigation of infection dynamics. Electronic supplementary material The online version of this article (10.1186/s12936-018-2318-1) contains supplementary material, which is available to authorized users.
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Abstract
A curious aspect of the evolution of the hypnozoite theory of malarial relapse is its transmogrification from theory into 'fact', this being of historical, linguistic, scientific and sociological interest. As far as it goes, the hypnozoite explanation for relapse is almost certainly correct. I contend, however, that many of the genotypically homologous, non-reinfection, relapse-like Plasmodium vivax recurrences that researchers ascribe to hypnozoite activation are probably hypnozoite-independent. Indeed, some malariologists are starting to recognize that homologous P. vivax recurrences have most likely been overattributed to activation of hypnozoites. Hitherto identified, non-hypnozoite, possible plasmodial sources of recurrence that must be considered, besides circulating erythrocytic stages, include parasites in splenic dendritic cells, other cells in the spleen (in addition to infected erythrocytes there), bone marrow (importantly) and the skin. I argue that we need to take into account the possibility of a dual or multiple extra-vascular origin of P. vivax non-reinfection recurrences, not arbitrarily discount it. The existence of a P. vivax reservoir(s) is a topical subject and one of practical importance for malaria eradication. Pertinent drug-associated matters are also discussed, as is the dormancy-related significance of clues provided by blood-stage-induced malarial infection.
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