1
|
Chen YA, Ng PY, Garcia D, Elliot A, Palmer B, Assunção Carvalho RMCD, Tseng LF, Lee CS, Tsai KH, Greenhouse B, Chang HH. Genetic surveillance reveals low, sustained malaria transmission with clonal replacement in Sao Tome and Principe. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.07.15.24309968. [PMID: 39072035 PMCID: PMC11275696 DOI: 10.1101/2024.07.15.24309968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Despite efforts to eliminate malaria in Sao Tome and Principe (STP), cases have recently increased. Understanding residual transmission structure is crucial for developing effective elimination strategies. This study collected surveillance data and generated amplicon sequencing data from 980 samples between 2010 and 2016 to examine the genetic structure of the parasite population. The mean multiplicity of infection (MOI) was 1.3, with 11% polyclonal infections, indicating low transmission intensity. Temporal trends of these genetic metrics did not align with incidence rates, suggesting that changes in genetic metrics may not straightforwardly reflect changes in transmission intensity, particularly in low transmission settings where genetic drift and importation have a substantial impact. While 88% of samples were genetically linked, continuous turnover in genetic clusters and changes in drug-resistance haplotypes were observed. Principal component analysis revealed some STP samples were genetically similar to those from Central and West Africa, indicating possible importation. These findings highlight the need to prioritize several interventions such as targeted interventions against transmission hotspots, reactive case detection, and strategies to reduce the introduction of new parasites into this island nation as it approaches elimination. This study also serves as a case study for implementing genetic surveillance in a low transmission setting.
Collapse
|
2
|
Badiane AS, Ngom B, Ndiaye T, Cunningham D, Campbell J, Gaye A, Sène A, Sy M, Ndiaye D, Nwakanma D, Langhorne J. Evidence of Plasmodium vivax circulation in western and eastern regions of Senegal: implications for malaria control. Malar J 2024; 23:149. [PMID: 38750583 PMCID: PMC11097470 DOI: 10.1186/s12936-024-04932-z] [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: 11/02/2023] [Accepted: 04/04/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Malaria elimination in Senegal requires accurate diagnosis of all Plasmodium species. Plasmodium falciparum is the most prevalent species in Senegal, although Plasmodium malariae, Plasmodium ovale, and recently Plasmodium vivax have also been reported. Nonetheless, most malaria control tools, such as Histidine Rich Protein 2 rapid diagnosis test (PfHRP2-RDT,) can only diagnose P. falciparum. Thus, PfHRP2-RDT misses non-falciparum species and P. falciparum infections that fall below the limit of detection. These limitations can be addressed using highly sensitive Next Generation Sequencing (NGS). This study assesses the burden of the four different Plasmodium species in western and eastern regions of Senegal using targeted PCR amplicon sequencing. METHODS Three thousand samples from symptomatic and asymptomatic individuals in 2021 from three sites in Senegal (Sessene, Diourbel region; Parcelles Assainies, Kaolack region; Gabou, Tambacounda region) were collected. All samples were tested using PfHRP2-RDT and photoinduced electron transfer polymerase chain reaction (PET-PCR), which detects all Plasmodium species. Targeted sequencing of the nuclear 18S rRNA and the mitochondrial cytochrome B genes was performed on PET-PCR positive samples. RESULTS Malaria prevalence by PfHRP2-RDT showed 9.4% (94/1000) and 0.2% (2/1000) in Diourbel (DBL) and Kaolack (KL), respectively. In Tambacounda (TAM) patients who had malaria symptoms and had a negative PfHRP2-RDT were enrolled. The PET-PCR had a positivity rate of 23.5% (295/1255) overall. The PET-PCR positivity rate was 37.6%, 12.3%, and 22.8% in Diourbel, Kaolack, and Tambacounda, respectively. Successful sequencing of 121/295 positive samples detected P. falciparum (93%), P. vivax (2.6%), P. malariae (4.4%), and P. ovale wallikeri (0.9%). Plasmodium vivax was co-identified with P. falciparum in thirteen samples. Sequencing also detected two PfHRP2-RDT-negative mono-infections of P. vivax in Tambacounda and Kaolack. CONCLUSION The findings demonstrate the circulation of P. vivax in western and eastern Senegal, highlighting the need for improved malaria control strategies and accurate diagnostic tools to better understand the prevalence of non-falciparum species countrywide.
Collapse
Affiliation(s)
- Aida S Badiane
- Laboratory of Parasitology and Mycology, Faculty of Medicine, Pharmacy and Odontology, Université Cheikh Anta Diop of Dakar, Darkar, Sénégal.
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal.
| | - Bassirou Ngom
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Tolla Ndiaye
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Deirdre Cunningham
- Malaria Immunology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - James Campbell
- Bioinformatics and Biostatistics Science Technology Platforms (STP), The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Amy Gaye
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Aita Sène
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Mouhamad Sy
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Daouda Ndiaye
- Laboratory of Parasitology and Mycology, Faculty of Medicine, Pharmacy and Odontology, Université Cheikh Anta Diop of Dakar, Darkar, Sénégal
- Centre International de Recherche et de Formation en Génomique Appliquée et de Surveillance Sanitaire (CIGASS), Dakar, Sénégal
| | - Davis Nwakanma
- Medical Research Council Unit The Gambia at London, School of Hygiene and Tropical Medicine, P.O Box 273, Banjul, The Gambia
| | - Jean Langhorne
- Malaria Immunology Laboratory, The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| |
Collapse
|
3
|
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and selection signals in Zambia. COMMUNICATIONS MEDICINE 2024; 4:67. [PMID: 38582941 PMCID: PMC10998850 DOI: 10.1038/s43856-024-00498-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 03/28/2024] [Indexed: 04/08/2024] Open
Abstract
BACKGROUND Genomic surveillance is crucial for monitoring malaria transmission and understanding parasite adaptation to interventions. Zambia lacks prior nationwide efforts in malaria genomic surveillance among African countries. METHODS We conducted genomic surveillance of Plasmodium falciparum parasites from the 2018 Malaria Indicator Survey in Zambia, a nationally representative household survey of children under five years of age. We whole-genome sequenced and analyzed 241 P. falciparum genomes from regions with varying levels of malaria transmission across Zambia and estimated genetic metrics that are informative about transmission intensity, genetic relatedness between parasites, and selection. RESULTS We provide genomic evidence of widespread within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in Zambia. Our analysis reveals country-level clustering of parasites from Zambia and neighboring regions, with distinct separation in West Africa. Within Zambia, identity by descent (IBD) relatedness analysis uncovers local spatial clustering and rare cases of long-distance sharing of closely related parasite pairs. Genomic regions with large shared IBD segments and strong positive selection signatures implicate genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Furthermore, differences in selection signatures, including drug resistance loci, are observed between eastern and western Zambian parasite populations, suggesting variable transmission intensity and ongoing drug pressure. CONCLUSIONS Our findings enhance our understanding of nationwide P. falciparum transmission in Zambia, establishing a baseline for analyzing parasite genetic metrics as they vary over time and space. These insights highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
Collapse
Affiliation(s)
- Abebe A Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Mulenga C Mwenda
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA.
| |
Collapse
|
4
|
Fola AA, He Q, Xie S, Thimmapuram J, Bhide KP, Dorman J, Ciubotariu II, Mwenda MC, Mambwe B, Mulube C, Hawela M, Norris DE, Moss WJ, Bridges DJ, Carpi G. Genomics reveals heterogeneous Plasmodium falciparum transmission and population differentiation in Zambia and bordering countries. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.09.24302570. [PMID: 38370674 PMCID: PMC10871455 DOI: 10.1101/2024.02.09.24302570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Genomic surveillance plays a critical role in monitoring malaria transmission and understanding how the parasite adapts in response to interventions. We conducted genomic surveillance of malaria by sequencing 241 Plasmodium falciparum genomes from regions with varying levels of malaria transmission across Zambia. We found genomic evidence of high levels of within-host polygenomic infections, regardless of epidemiological characteristics, underscoring the extensive and ongoing endemic malaria transmission in the country. We identified country-level clustering of parasites from Zambia and neighboring countries, and distinct clustering of parasites from West Africa. Within Zambia, our identity by descent (IBD) relatedness analysis uncovered spatial clustering of closely related parasite pairs at the local level and rare cases of long-distance sharing. Genomic regions with large shared IBD segments and strong positive selection signatures identified genes involved in sulfadoxine-pyrimethamine and artemisinin combination therapies drug resistance, but no signature related to chloroquine resistance. Together, our findings enhance our understanding of P. falciparum transmission nationwide in Zambia and highlight the urgency of strengthening malaria control programs and surveillance of antimalarial drug resistance.
Collapse
Affiliation(s)
- Abebe A. Fola
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, Purdue University, West Lafayette, IN, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | | | | | - Brenda Mambwe
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Moonga Hawela
- PATH-MACEPA, National Malaria Elimination Centre, Lusaka, Zambia
| | - Douglas E. Norris
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J. Moss
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
- The Johns Hopkins Malaria Research Institute, W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
- Purdue Institute for Inflammation, Immunology, & Infectious Disease, Purdue University, West Lafayette, IN, USA
| |
Collapse
|
5
|
Wotodjo AN, Oboh MA, Sokhna C, Diagne N, Diène-Sarr F, Trape JF, Doucouré S, Amambua-Ngwa A, D'Alessandro U. Plasmodium falciparum population structure and genetic diversity of cell traversal protein for ookinetes and sporozoites (CelTOS) during malaria resurgences in Dielmo, Senegal. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 116:105535. [PMID: 38030029 DOI: 10.1016/j.meegid.2023.105535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 11/20/2023] [Accepted: 11/25/2023] [Indexed: 12/01/2023]
Abstract
The ability to accurately measure the intensity of malaria transmission in areas with low transmission is extremely important to guide elimination efforts. Plasmodium falciparum Cell-traversal protein for ookinetes and sporozoites (PfCelTOS) is an important conserved sporozoite antigen reported as one of the promising malaria vaccine candidates, and could be used to estimate malaria transmission intensity. This study aimed at determining whether the diversity of PfCelTOS gene reflects the changes in malaria transmission that occurred between 2007 and 2014 in Dielmo, a Senegalese village, before and after the implementation of insecticide treated bed nets (ITNs). Of the 109 samples positive for PfCelTOS PCR, 96 (88%) were successfully sequenced and analysed for polymorphisms and population diversity. The number of segregating sites was higher during the pre-intervention period (13) and the malaria resurgences (11) than during the intervention period (5). Similarly, the number and diversity of haplotypes were higher during the pre-intervention period (16 and 0.914, respectively) and the malaria resurgences (6 and 0.821, respectively) than during the intervention period (4 and 0.758, respectively). Moreover, the average number of nucleotide differences was higher during the pre-intervention (3.792) and during malaria resurgences (3.467) than during the intervention period (2.189). The 3D7 KSSFNEP haplotype was only observed during the intervention period. Only two haplotypes were shared in both the pre-intervention and intervention periods while four haplotypes were shared between the pre-intervention and the malaria resurgences. The Fst values indicate moderate differentiation between pre-intervention and intervention periods (0.17433), and between intervention and malaria resurgences period (0.19198) as well as between pre-intervention and malaria resurgences periods (0.06607). PfCelTOS genetic diversity reflected changes of malaria transmission, with higher polymorphisms recorded before the large-scale implementation of ITNs and during the malaria resurgences. PfCelTOS is also a candidate vaccine; mapping its diversity across multiple endemic environments will facilitate the design and optimisation of a broad and efficacious vaccine.
Collapse
Affiliation(s)
- Amélé Nyedzie Wotodjo
- VITROME, UMR 257 IRD, Campus UCAD-IRD, Dakar, Senegal; Medical Research Council Unit, The Gambia, at the London School of Hygiene and Tropical Medicine, Fajara, Gambia.
| | - Mary Aigbiremo Oboh
- Medical Research Council Unit, The Gambia, at the London School of Hygiene and Tropical Medicine, Fajara, Gambia; Department of Biological Sciences, University of Medical Sciences, Ondo, Nigeria; Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, NY, United States of America
| | - Cheikh Sokhna
- VITROME, UMR 257 IRD, Campus UCAD-IRD, Dakar, Senegal
| | | | | | - Jean-François Trape
- UMR MIVEGEC, Laboratoire de Paludologie et Zoologie Médicale, IRD, Dakar, Senegal
| | | | - Alfred Amambua-Ngwa
- Medical Research Council Unit, The Gambia, at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| | - Umberto D'Alessandro
- Medical Research Council Unit, The Gambia, at the London School of Hygiene and Tropical Medicine, Fajara, Gambia
| |
Collapse
|
6
|
Mayor A, Ishengoma DS, Proctor JL, Verity R. Sampling for malaria molecular surveillance. Trends Parasitol 2023; 39:954-968. [PMID: 37730525 PMCID: PMC10580323 DOI: 10.1016/j.pt.2023.08.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/22/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023]
Abstract
Strategic use of Plasmodium falciparum genetic variation has great potential to inform public health actions for malaria control and elimination. Malaria molecular surveillance (MMS) begins with a strategy to identify and collect parasite samples, guided by public-health priorities. In this review we discuss sampling design practices for MMS and point out epidemiological, biological, and statistical factors that need to be considered. We present examples for different use cases, including detecting emergence and spread of rare variants, establishing transmission sources and inferring changes in malaria transmission intensity. This review will potentially guide the collection of samples and data, serve as a starting point for further methodological innovation, and enhance utilization of MMS to support malaria elimination.
Collapse
Affiliation(s)
- Alfredo Mayor
- ISGlobal, Hospital Clínic - Universitat de Barcelona, Barcelona, Spain; Centro de Investigação em Saúde de Manhiça (CISM), Maputo, Mozambique; Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique.
| | - Deus S Ishengoma
- National Institute for Medical Research (NIMR), Dar es Salaam, Tanzania; Faculty of Pharmaceutical Sciences, Monash University, Melbourne, VIC, Australia; Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling in Global Health, Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London, UK
| |
Collapse
|
7
|
Fola AA, Moser KA, Aydemir O, Hennelly C, Kobayashi T, Shields T, Hamapumbu H, Musonda M, Katowa B, Matoba J, Stevenson JC, Norris DE, Thuma PE, Wesolowski A, Moss WJ, Bailey JA, Juliano JJ. Temporal and spatial analysis of Plasmodium falciparum genomics reveals patterns of parasite connectivity in a low-transmission district in Southern Province, Zambia. Malar J 2023; 22:208. [PMID: 37420265 PMCID: PMC10327325 DOI: 10.1186/s12936-023-04637-9] [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: 04/20/2023] [Accepted: 06/30/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Understanding temporal and spatial dynamics of malaria transmission will help to inform effective interventions and strategies in regions approaching elimination. Parasite genomics are increasingly used to monitor epidemiologic trends, including assessing residual transmission across seasons and importation of malaria into these regions. METHODS In a low and seasonal transmission setting of southern Zambia, a total of 441 Plasmodium falciparum samples collected from 8 neighbouring health centres between 2012 and 2018 were genotyped using molecular inversion probes (MIPs n = 1793) targeting a total of 1832 neutral and geographically informative SNPs distributed across the parasite genome. After filtering for quality and missingness, 302 samples and 1410 SNPs were retained and used for downstream population genomic analyses. RESULTS The analyses revealed most (67%, n = 202) infections harboured one clone (monogenomic) with some variation at local level suggesting low, but heterogenous malaria transmission. Relatedness identity-by-descent (IBD) analysis revealed variable distribution of IBD segments across the genome and 6% of pairs were highly-related (IBD ≥ 0.25). Some of the highly-related parasite populations persisted across multiple seasons, suggesting that persistence of malaria in this low-transmission region is fueled by parasites "seeding" across the dry season. For recent years, clusters of clonal parasites were identified that were dissimilar to the general parasite population, suggesting parasite populations were increasingly fragmented at small spatial scales due to intensified control efforts. Clustering analysis using PCA and t-SNE showed a lack of substantial parasite population structure. CONCLUSION Leveraging both genomic and epidemiological data provided comprehensive picture of fluctuations in parasite populations in this pre-elimination setting of southern Zambia over 7 years.
Collapse
Affiliation(s)
- Abebe A. Fola
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Kara A. Moser
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Chris Hennelly
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - Tamaki Kobayashi
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Timothy Shields
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | | | - Ben Katowa
- Macha Research Trust, Choma District, Choma, Zambia
| | | | | | - Douglas E. Norris
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | | | - Amy Wesolowski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - William J. Moss
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
| | - Jonathan J. Juliano
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| | - the Southern, Central Africa International Center of Excellence for Malaria Research (ICEMR)
- Department of Pathology and Laboratory Medicine, Brown University, 55 Claverick Street, Providence, RI 02906 USA
- University of North Carolina Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Macha Research Trust, Choma District, Choma, Zambia
- Department of Molecular Microbiology and Immunology, The Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205 USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina Chapel Hill, Chapel Hill, NC 27599 USA
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
Argyropoulos DC, Tan MH, Adobor C, Mensah B, Labbé F, Tiedje KE, Koram KA, Ghansah A, Day KP. Performance of SNP barcodes to determine genetic diversity and population structure of Plasmodium falciparum in Africa. Front Genet 2023; 14:1071896. [PMID: 37323661 PMCID: PMC10267394 DOI: 10.3389/fgene.2023.1071896] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 05/17/2023] [Indexed: 06/17/2023] Open
Abstract
Panels of informative biallelic single nucleotide polymorphisms (SNPs) have been proposed to be an economical method to fast-track the population genetic analysis of Plasmodium falciparum in malaria-endemic areas. Whilst used successfully in low-transmission areas where infections are monoclonal and highly related, we present the first study to evaluate the performance of these 24- and 96-SNP molecular barcodes in African countries, characterised by moderate-to-high transmission, where multiclonal infections are prevalent. For SNP barcodes it is generally recommended that the SNPs chosen i) are biallelic, ii) have a minor allele frequency greater than 0.10, and iii) are independently segregating, to minimise bias in the analysis of genetic diversity and population structure. Further, to be standardised and used in many population genetic studies, these barcodes should maintain characteristics i) to iii) across various iv) geographies and v) time points. Using haplotypes generated from the MalariaGEN P. falciparum Community Project version six database, we investigated the ability of these two barcodes to fulfil these criteria in moderate-to-high transmission African populations in 25 sites across 10 countries. Predominantly clinical infections were analysed, with 52.3% found to be multiclonal, generating high proportions of mixed-allele calls (MACs) per isolate thereby impeding haplotype construction. Of the 24- and 96-SNPs, loci were removed if they were not biallelic and had low minor allele frequencies in all study populations, resulting in 20- and 75-SNP barcodes respectively for downstream population genetics analysis. Both SNP barcodes had low expected heterozygosity estimates in these African settings and consequently biased analyses of similarity. Both minor and major allele frequencies were temporally unstable. These SNP barcodes were also shown to identify weak genetic differentiation across large geographic distances based on Mantel Test and DAPC. These results demonstrate that these SNP barcodes are vulnerable to ascertainment bias and as such cannot be used as a standardised approach for malaria surveillance in moderate-to-high transmission areas in Africa, where the greatest genomic diversity of P. falciparum exists at local, regional and country levels.
Collapse
Affiliation(s)
- Dionne C. Argyropoulos
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Mun Hua Tan
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Courage Adobor
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Benedicta Mensah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Frédéric Labbé
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Karen P. Day
- Department of Microbiology and Immunology, Bio21 Institute and Peter Doherty Institute, The University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
10
|
Ghansah A, Tiedje KE, Argyropoulos DC, Onwona CO, Deed SL, Labbé F, Oduro AR, Koram KA, Pascual M, Day KP. Comparison of molecular surveillance methods to assess changes in the population genetics of Plasmodium falciparum in high transmission. FRONTIERS IN PARASITOLOGY 2023; 2:1067966. [PMID: 38031549 PMCID: PMC10686283 DOI: 10.3389/fpara.2023.1067966] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
A major motivation for developing molecular methods for malaria surveillance is to measure the impact of control interventions on the population genetics of Plasmodium falciparum as a potential marker of progress towards elimination. Here we assess three established methods (i) single nucleotide polymorphism (SNP) barcoding (panel of 24-biallelic loci), (ii) microsatellite genotyping (panel of 12-multiallelic loci), and (iii) varcoding (fingerprinting var gene diversity, akin to microhaplotyping) to identify changes in parasite population genetics in response to a short-term indoor residual spraying (IRS) intervention. Typical of high seasonal transmission in Africa, multiclonal infections were found in 82.3% (median 3; range 1-18) and 57.8% (median 2; range 1-12) of asymptomatic individuals pre- and post-IRS, respectively, in Bongo District, Ghana. Since directly phasing multilocus haplotypes for population genetic analysis is not possible for biallelic SNPs and microsatellites, we chose ~200 low-complexity infections biased to single and double clone infections for analysis. Each genotyping method presented a different pattern of change in diversity and population structure as a consequence of variability in usable data and the relative polymorphism of the molecular markers (i.e., SNPs < microsatellites < var). Varcoding and microsatellite genotyping showed the overall failure of the IRS intervention to significantly change the population structure from pre-IRS characteristics (i.e., many diverse genomes of low genetic similarity). The 24-SNP barcode provided limited information for analysis, largely due to the biallelic nature of SNPs leading to a high proportion of double-allele calls and a view of more isolate relatedness compared to microsatellites and varcoding. Relative performance, suitability, and cost-effectiveness of the methods relevant to sample size and local malaria elimination in high-transmission endemic areas are discussed.
Collapse
Affiliation(s)
- Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Kathryn E. Tiedje
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Dionne C. Argyropoulos
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Christiana O. Onwona
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Samantha L. Deed
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| | - Frédéric Labbé
- Department Ecology and Evolution, The University of Chicago, Chicago, IL, United States
| | - Abraham R. Oduro
- Navrongo Health Research Centre, Ghana Health Service, Navrongo, Ghana
| | - Kwadwo A. Koram
- Epidemiology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Mercedes Pascual
- Department Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Santa Fe Institute, Santa Fe, NM, United States
| | - Karen P. Day
- Department of Microbiology and Immunology, The University of Melbourne, Bio21 Institute and Peter Doherty Institute, Melbourne, VIC, Australia
| |
Collapse
|
11
|
Simpson SV, Nundu SS, Arima H, Kaneko O, Mita T, Culleton R, Yamamoto T. The diversity of Plasmodium falciparum isolates from asymptomatic and symptomatic school-age children in Kinshasa Province, Democratic Republic of Congo. Malar J 2023; 22:102. [PMID: 36941587 PMCID: PMC10025789 DOI: 10.1186/s12936-023-04528-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 03/10/2023] [Indexed: 03/22/2023] Open
Abstract
BACKGROUND Understanding Plasmodium falciparum population diversity and transmission dynamics provides information on the intensity of malaria transmission, which is needed for assessing malaria control interventions. This study aimed to determine P. falciparum allelic diversity and multiplicity of infection (MOI) among asymptomatic and symptomatic school-age children in Kinshasa Province, Democratic Republic of Congo (DRC). METHODS A total of 438 DNA samples (248 asymptomatic and 190 symptomatic) were characterized by nested PCR and genotyping the polymorphic regions of pfmsp1 block 2 and pfmsp2 block 3. RESULTS Nine allele types were observed in pfmsp1 block2. The K1-type allele was predominant with 78% (229/293) prevalence, followed by the MAD20-type allele (52%, 152/293) and RO33-type allele (44%, 129/293). Twelve alleles were detected in pfmsp2, and the 3D7-type allele was the most frequent with 84% (256/304) prevalence, followed by the FC27-type allele (66%, 201/304). Polyclonal infections were detected in 63% (95% CI 56, 69) of the samples, and the MOI (SD) was 1.99 (0.97) in P. falciparum single-species infections. MOIs significantly increased in P. falciparum isolates from symptomatic parasite carriers compared with asymptomatic carriers (2.24 versus 1.69, adjusted b: 0.36, (95% CI 0.01, 0.72), p = 0.046) and parasitaemia > 10,000 parasites/µL compared to parasitaemia < 5000 parasites/µL (2.68 versus 1.63, adjusted b: 0.89, (95% CI 0.46, 1.25), p < 0.001). CONCLUSION This survey showed low allelic diversity and MOI of P. falciparum, which reflects a moderate intensity of malaria transmission in the study areas. MOIs were more likely to be common in symptomatic infections and increased with the parasitaemia level. Further studies in different transmission zones are needed to understand the epidemiology and parasite complexity in the DRC.
Collapse
Affiliation(s)
- Shirley V Simpson
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Sabin S Nundu
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan.
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan.
- Institut National de Recherche Biomédicale (INRB), Kinshasa-Gombe, Democratic Republic of Congo.
| | - Hiroaki Arima
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Osamu Kaneko
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Faculty of Medicine, Juntendo University, Tokyo, 113-8421, Japan
| | - Richard Culleton
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
- Division of Molecular Parasitology, Proteo-Science Centre, Ehime University, Ehime, 790-8577, Japan
| | - Taro Yamamoto
- Programme for Nurturing Global Leaders in Tropical and Emerging Communicable Diseases, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 852-8523, Japan
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 852-8523, Japan
| |
Collapse
|
12
|
Measurably recombining malaria parasites. Trends Parasitol 2023; 39:17-25. [PMID: 36435688 PMCID: PMC9893849 DOI: 10.1016/j.pt.2022.11.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/02/2022] [Accepted: 11/02/2022] [Indexed: 11/24/2022]
Abstract
Genomic epidemiology has guided research and policy for various viral pathogens and there has been a parallel effort towards using genomic epidemiology to combat diseases that are caused by eukaryotic pathogens, such as the malaria parasite. However, the central concept of viral genomic epidemiology, namely that of measurably mutating pathogens, does not apply easily to sexually recombining parasites. Here we introduce the related but different concept of measurably recombining malaria parasites to promote convergence around a unifying theoretical framework for malaria genomic epidemiology. Akin to viral phylodynamics, we anticipate that an inferential framework developed around recombination will help guide practical research and thus realize the full public health potential of genomic epidemiology for malaria parasites and other sexually recombining pathogens.
Collapse
|
13
|
Mensah BA, Akyea-Bobi NE, Ghansah A. Genomic approaches for monitoring transmission dynamics of malaria: A case for malaria molecular surveillance in Sub-Saharan Africa. FRONTIERS IN EPIDEMIOLOGY 2022; 2:939291. [PMID: 38455324 PMCID: PMC10911004 DOI: 10.3389/fepid.2022.939291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/10/2022] [Indexed: 03/09/2024]
Abstract
Transmission dynamics is an important indicator for malaria control and elimination. As we move closer to eliminating malaria in Sub-Saharan Africa (sSA), transmission indices with higher resolution (genomic approaches) will complement our current measurements of transmission. Most of the present programmatic knowledge of malaria transmission patterns are derived from assessments of epidemiologic and clinical data, such as case counts, parasitological estimates of parasite prevalence, and Entomological Inoculation Rates (EIR). However, to eliminate malaria from endemic areas, we need to track changes in the parasite population and how they will impact transmission. This is made possible through the evolving field of genomics and genetics, as well as the development of tools for more in-depth studies on the diversity of parasites and the complexity of infections, among other topics. If malaria elimination is to be achieved globally, country-specific elimination activities should be supported by parasite genomic data from regularly collected blood samples for diagnosis, surveillance and possibly from other programmatic interventions. This presents a unique opportunity to track the spread of malaria parasites and shed additional light on intervention efficacy. In this review, various genetic techniques are highlighted along with their significance for an enhanced understanding of transmission patterns in distinct topological settings throughout Sub-Saharan Africa. The importance of these methods and their limitations in malaria surveillance to guide control and elimination strategies, are explored.
Collapse
Affiliation(s)
- Benedicta A. Mensah
- Department of Epidemiology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nukunu E. Akyea-Bobi
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Anita Ghansah
- Department of Parasitology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| |
Collapse
|
14
|
Andrianaranjaka VHI, Ravaoarisoa E, Rakotomanga TA, Ralinoro F, Rakoto DAD, Randrianarivo RH, Jeannoda V, Ratsimbasoa A. DNA recovery from used malaria RDT to detect Plasmodium species and to assess Plasmodium falciparum genetic diversity: a pilot study in Madagascar. Malar J 2022; 21:227. [PMID: 35883089 PMCID: PMC9327223 DOI: 10.1186/s12936-022-04246-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 07/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Rapid diagnostic tests (RDT) are widely used for malaria diagnosis in Madagascar, where Plasmodium falciparum is the predominant species. Molecular diagnosis is essential for malaria surveillance, but requires additional blood samples for DNA extraction. Used RDTs is an attractive alternative that can be used as a source of DNA. Plasmodium falciparum genetic diversity and multiplicity of infection, usually determined by the genotyping of polymorphic regions of merozoite surface proteins 1 and 2 genes (msp1, msp2), and the repeated region RII of the glutamate-rich protein gene (glurp) have been associated with malaria transmission levels and subsequently with the impact of the deployed control strategies. Thus, the study aims to use RDT as DNA source to detect Plasmodium species, to characterize Plasmodium falciparum genetic diversity and determine the multiplicity of infection. Methods A pilot study was conducted in two sites with different epidemiological patterns: Ankazomborona (low transmission area) and Matanga (high transmission area). On May 2018, used RDT (SD BIOLINE Malaria Ag P.f/Pan, 05FK63) were collected as DNA source. Plasmodium DNA was extracted by simple elution with nuclease free water. Nested-PCR were performed to confirm Plasmodium species and to analyse P. falciparum msp1, msp2 and glurp genes polymorphisms. Results Amongst the 170 obtained samples (N = 74 from Ankazomborona and N = 96 from Matanga), Plasmodium positivity rate was 23.5% (40/170) [95% CI 17.5–30.8%] by nested-PCR with 92.2% (37/40) positive to P. falciparum, 5% (2/40) to Plasmodium vivax and 2.5% (1/40) to P. falciparum/P. vivax mixed infection. Results showed high polymorphisms in P. falciparum msp1, msp2 and glurp genes. Multiple infection rate was 28.6% [95% CI 12.2–52.3%]. The mean of MOI was 1.79 ± 0.74. Conclusion This pilot study highlighted that malaria diagnosis and molecular analysis are possible by using used malaria RDT. A large-scale study needs to be conducted to assess more comprehensively malaria parasites transmission levels and provide new data for guiding the implementation of local strategies for malaria control and elimination. Trial registration Retrospectively registered
Collapse
Affiliation(s)
- Voahangy Hanitriniaina I Andrianaranjaka
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar. .,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar.
| | - Elisabeth Ravaoarisoa
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Tovonahary A Rakotomanga
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Fanomezantsoa Ralinoro
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar.,Programme National de Lutte contre le paludisme, Ministère de la Santé Publique, Antananarivo, Madagascar
| | - Danielle A Doll Rakoto
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Ranjàna H Randrianarivo
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Victor Jeannoda
- Mention Biochimie Fondamentale et Appliquée, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | - Arsène Ratsimbasoa
- Faculté de Médecine, Université de Fianarantsoa, Fianarantsoa, Madagascar.,Centre National d'Application de Recherche Pharmaceutique, Antananarivo, Madagascar
| |
Collapse
|
15
|
Mayor A, da Silva C, Rovira-Vallbona E, Roca-Feltrer A, Bonnington C, Wharton-Smith A, Greenhouse B, Bever C, Chidimatembue A, Guinovart C, Proctor JL, Rodrigues M, Canana N, Arnaldo P, Boene S, Aide P, Enosse S, Saute F, Candrinho B. Prospective surveillance study to detect antimalarial drug resistance, gene deletions of diagnostic relevance and genetic diversity of Plasmodium falciparum in Mozambique: protocol. BMJ Open 2022; 12:e063456. [PMID: 35820756 PMCID: PMC9274532 DOI: 10.1136/bmjopen-2022-063456] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
INTRODUCTION Genomic data constitute a valuable adjunct to routine surveillance that can guide programmatic decisions to reduce the burden of infectious diseases. However, genomic capacities remain low in Africa. This study aims to operationalise a functional malaria molecular surveillance system in Mozambique for guiding malaria control and elimination. METHODS AND ANALYSES This prospective surveillance study seeks to generate Plasmodium falciparum genetic data to (1) monitor molecular markers of drug resistance and deletions in rapid diagnostic test targets; (2) characterise transmission sources in low transmission settings and (3) quantify transmission levels and the effectiveness of antimalarial interventions. The study will take place across 19 districts in nine provinces (Maputo city, Maputo, Gaza, Inhambane, Niassa, Manica, Nampula, Zambézia and Sofala) which span a range of transmission strata, geographies and malaria intervention types. Dried blood spot samples and rapid diagnostic tests will be collected across the study districts in 2022 and 2023 through a combination of dense (all malaria clinical cases) and targeted (a selection of malaria clinical cases) sampling. Pregnant women attending their first antenatal care visit will also be included to assess their value for molecular surveillance. We will use a multiplex amplicon-based next-generation sequencing approach targeting informative single nucleotide polymorphisms, gene deletions and microhaplotypes. Genetic data will be incorporated into epidemiological and transmission models to identify the most informative relationship between genetic features, sources of malaria transmission and programmatic effectiveness of new malaria interventions. Strategic genomic information will be ultimately integrated into the national malaria information and surveillance system to improve the use of the genetic information for programmatic decision-making. ETHICS AND DISSEMINATION The protocol was reviewed and approved by the institutional (CISM) and national ethics committees of Mozambique (Comité Nacional de Bioética para Saúde) and Spain (Hospital Clinic of Barcelona). Project results will be presented to all stakeholders and published in open-access journals. TRIAL REGISTRATION NUMBER NCT05306067.
Collapse
Affiliation(s)
- Alfredo Mayor
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Spanish Consortium for Research in Epidemiology and Public Health (CIBERESP), Madrid, Spain
- Department of Physiologic Sciences, Faculty of Medicine, Universidade Eduardo Mondlane, Maputo, Mozambique
| | - Clemente da Silva
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Eduard Rovira-Vallbona
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | - Bryan Greenhouse
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Caitlin Bever
- Bill & Melinda Gates Foundation, Seattle, Washington, USA
| | | | - Caterina Guinovart
- Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | | | | | | | | | - Simone Boene
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
- Instituto Nacional de Saúde, Maputo, Mozambique
| | | | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça, Manhiça, Maputo, Mozambique
| | | |
Collapse
|
16
|
Zhang X, Wei H, Zhang Y, Zhao Y, Wang L, Hu Y, Nguitragool W, Sattabongkot J, Adams J, Cui L, Cao Y, Wang Q. Genetic diversity of Plasmodium vivax reticulocyte binding protein 2b in global parasite populations. Parasit Vectors 2022; 15:205. [PMID: 35698238 PMCID: PMC9191549 DOI: 10.1186/s13071-022-05296-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 04/23/2022] [Indexed: 11/19/2022] Open
Abstract
Background Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) plays a critical role in parasite invasion of reticulocytes by binding the transferrin receptor 1. PvRBP2b is a vaccine candidate based on the negative correlation between antibody titers against PvRBP2b recombinant proteins and parasitemia and risk of vivax malaria. The aim of this study was to analyze the genetic diversity of the PvRBP2b gene in the global P. vivax populations. Methods Near full-length PvRBP2b nucleotide sequences (190–8349 bp) were obtained from 88 P. vivax isolates collected from the China–Myanmar border (n = 44) and Thailand (n = 44). An additional 224 PvRBP2b sequences were retrieved from genome sequences from parasite populations worldwide. The genetic diversity, neutral selection, haplotype distribution and genetic differentiation of PvRBP2b were examined. Results The genetic diversity of PvRBP2b was distributed unevenly, with peak diversity found in the reticulocyte binding region in the N-terminus. Neutrality analysis suggested that this region is subjected to balancing selection or population bottlenecks. Several amino acid variants were found in all or nearly all P. vivax endemic regions. However, the critical residues responsible for reticulocyte binding were highly conserved. There was substantial population differentiation according to the geographical separation. The distribution of haplotypes in the reticulocyte binding region varied among regions; even the two major haplotypes Hap_6 and Hap_8 were found in only five populations. Conclusions Our data show considerable genetic variations of PvRBPb in global parasite populations. The geographic divergence may pose a challenge to PvRBP2b-based vaccine development. Graphical Abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-022-05296-6.
Collapse
Affiliation(s)
- Xuexing Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Haichao Wei
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion Medicine, General Hospital of Northern Theater Command, Shenyang, 110015, Liaoning, China
| | - Yangminghui Zhang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Yan Zhao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China
| | - Lin Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Department of Blood Transfusion, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - Yubing Hu
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.,Central Laboratory, The First Hospital of China Medical University, Shenyang, 110001, Liaoning, China
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - John Adams
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA
| | - Liwang Cui
- College of Public Health, Global Health Infectious Disease Research (GHIDR) Program, Tampa, FL, USA.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, 3720 Spectrum Boulevard, Suite 304, Tampa, FL, 33612, USA
| | - Yaming Cao
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
| | - Qinghui Wang
- Department of Immunology, College of Basic Medical Science, China Medical University, Shenyang, 110122, Liaoning, China.
| |
Collapse
|
17
|
Nair S, Li X, Arya GA, McDew-White M, Ferrari M, Anderson T. Nutrient Limitation Magnifies Fitness Costs of Antimalarial Drug Resistance Mutations. Antimicrob Agents Chemother 2022; 66:e0152921. [PMID: 35465723 PMCID: PMC9112896 DOI: 10.1128/aac.01529-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 02/22/2022] [Indexed: 12/15/2022] Open
Abstract
Drug resistance mutations tend to disrupt key physiological processes and frequently carry fitness costs, which are a central determinant of the rate of spread of these mutations in natural populations. Head-to-head competition assays provide a standard approach to measuring fitness for malaria parasites. These assays typically use a standardized culture medium containing RPMI 1640, which has a 1.4- to 5.5-fold higher concentration of amino acids than human blood. In this rich medium, we predict that fitness costs will be underestimated because resource competition is weak. We tested this prediction using an artemisinin-sensitive parasite edited to contain kelch-C580Y or R561H mutations conferring resistance to artemisinin or synonymous control mutations. We examined the impact of these single amino acid mutations on fitness, using replicated head-to-head competition experiments conducted in media containing (i) normal RPMI, (ii) modified RPMI with reduced amino acid concentration, (iii) RPMI containing only isoleucine, or (iv) 3-fold diluted RPMI. We found a significant 1.3- to 1.4-fold increase in fitness costs measured in modified and isoleucine-only media relative to normal media, while fitness costs were 2.5-fold higher in diluted media. We conclude that fitness costs are strongly affected by media composition and will be significantly underestimated in normal RPMI. Several components differed between media, including pABA and sodium bicarbonate concentrations, so we cannot directly determine which is responsible. Elevated fitness costs in nature will limit spread of artemisinin (ART) resistance but will also promote evolution of compensatory mutations that restore fitness and can be exploited to maximize selection in laboratory experiments.
Collapse
Affiliation(s)
- Shalini Nair
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Xue Li
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Grace A. Arya
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marina McDew-White
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Marco Ferrari
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Tim Anderson
- Disease Intervention and Prevention Program, Texas Biomedical Research Institute, San Antonio, Texas, USA
| |
Collapse
|
18
|
Dharmaratne ADVTT, Dini S, O’Flaherty K, Price DJ, Beeson J, McGready R, Nosten F, Fowkes FJI, Simpson JA, Zaloumis SG. Quantification of the dynamics of antibody response to malaria to inform sero-surveillance in pregnant women. Malar J 2022; 21:75. [PMID: 35248084 PMCID: PMC8897879 DOI: 10.1186/s12936-022-04111-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/28/2022] [Indexed: 12/02/2022] Open
Abstract
Background Malaria remains a major public health threat and tools sensitive to detect infections in low malaria transmission areas are needed to progress elimination efforts. Pregnant women are particularly vulnerable to malaria infections. Throughout pregnancy they access routine antenatal care, presenting a unique sentinel population to apply novel sero-surveillance tools to measure malaria transmission. The aim of this study was to quantify the dynamic antibody responses to multiple antigens during pregnancy so as to identify a single or multiple antibody response of exposure to malaria in pregnancy. Methods This study involved a secondary analysis of antibody responses to six parasite antigens [five commonly studied merozoite antigens and the variant surface antigen 2-chondroitin sulphate A (VAR2CSA), a pregnancy-specific erythrocytic antigen] measured by enzyme-linked immunosorbent assay (ELISA) over the gestation period until delivery (median of 7 measurements/woman) in 250 pregnant women who attended antenatal clinics located at the Thai-Myanmar border. A multivariate mixture linear mixed model was used to cluster the pregnant women into groups that have similar longitudinal antibody responses to all six antigens over the gestational period using a Bayesian approach. The variable-specific entropy was calculated to identify the antibody responses that have the highest influence on the classification of the women into clusters, and subsequent agreement with grouping of women based on exposure to malaria during pregnancy. Results Of the 250 pregnant women, 135 had a Plasmodium infection detected by light microscopy during pregnancy (39% Plasmodium falciparum only, 33% Plasmodium vivax only and 28% mixed/other species), defined as cases. The antibody responses to all six antigens accurately identified the women who did not have a malaria infection detected during pregnancy (93%, 107/115 controls). Antibody responses to P. falciparum merozoite surface protein 3 (PfMSP3) and P. vivax apical membrane antigen 1 (PvAMA1) were the least dynamic. Antibody responses to the antigens P. falciparum apical membrane antigen 1 (PfAMA1) and PfVAR2CSA were able to identify the majority of the cases more accurately (63%, 85/135). Conclusion These findings suggest that the combination of antibodies, PfAMA1 and PfVAR2CSA, may be useful for sero-surveillance of malaria infections in pregnant women, particularly in low malaria transmission settings. Further investigation of other antibody markers is warranted considering these antibodies combined only detected 63% of the malaria infections during pregnancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12936-022-04111-y.
Collapse
|
19
|
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.
Collapse
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.
| |
Collapse
|
20
|
The Rare, the Best: Spread of Antimalarial-Resistant Plasmodium falciparum Parasites by Anopheles Mosquito Vectors. Microbiol Spectr 2021; 9:e0085221. [PMID: 34668767 PMCID: PMC8528099 DOI: 10.1128/spectrum.00852-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The emergence of resistance to antimalarials has prompted the steady switch to novel therapies for decades. Withdrawal of antimalarials, such as chloroquine in sub-Saharan Africa in the late 1990s, led to rapid declines in the prevalence of resistance markers after a few years, raising the possibility of reintroducing them for malaria treatment. Here, we provide evidence that the mosquito vector plays a crucial role in maintaining parasite genetic diversity. We followed the transmission dynamics of Plasmodium falciparum parasites through its vector in natural infections from gametocytes contained in the blood of asymptomatic volunteers until sporozoites subsequently developed in the mosquito salivary glands. We did not find any selection of the mutant or wild-type pfcrt 76 allele during development in the Anopheles mosquito vector. However, microsatellite genotyping indicated that minority genotypes were favored during transmission through the mosquito. The analysis of changes in the proportions of mutant and wild-type pfcrt 76 alleles showed that, regardless of the genotype, the less-represented allele in the gametocyte population was more abundant in mosquito salivary glands, indicating a selective advantage of the minority allele in the vector. Selection of minority genotypes in the vector would explain the persistence of drug-resistant alleles in the absence of drug pressure in areas with high malaria endemicity and high genetic diversity. Our results may have important epidemiological implications, as they predict the rapid re-emergence and spread of resistant genotypes if antimalarials that had previously selected resistant parasites are reintroduced for malaria prevention or treatment. IMPORTANCE Drug selection pressure in malaria patients is the cause of the emergence of resistant parasites. Resistance imposes a fitness cost for parasites in untreated infections, so withdrawal of the drug leads to the return of susceptible parasites. Little is known about the role of the malaria vector in this phenomenon. In an experimental study conducted in Cameroon, an area of high malaria transmission, we showed that the vector did not favor the parasites based on sensitivity or resistance criteria, but it did favor the selection of minority clones. This finding shows that the vector increases the diversity of plasmodial populations and could play an important role in falciparum malaria epidemiology by maintaining resistant clones despite the absence of therapeutic pressure.
Collapse
|
21
|
Abstract
Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.
Collapse
Affiliation(s)
- Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| |
Collapse
|
22
|
Hendry JA, Kwiatkowski D, McVean G. Elucidating relationships between P.falciparum prevalence and measures of genetic diversity with a combined genetic-epidemiological model of malaria. PLoS Comput Biol 2021; 17:e1009287. [PMID: 34411093 PMCID: PMC8407561 DOI: 10.1371/journal.pcbi.1009287] [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: 09/07/2020] [Revised: 08/31/2021] [Accepted: 07/19/2021] [Indexed: 12/05/2022] Open
Abstract
There is an abundance of malaria genetic data being collected from the field, yet using these data to understand the drivers of regional epidemiology remains a challenge. A key issue is the lack of models that relate parasite genetic diversity to epidemiological parameters. Classical models in population genetics characterize changes in genetic diversity in relation to demographic parameters, but fail to account for the unique features of the malaria life cycle. In contrast, epidemiological models, such as the Ross-Macdonald model, capture malaria transmission dynamics but do not consider genetics. Here, we have developed an integrated model encompassing both parasite evolution and regional epidemiology. We achieve this by combining the Ross-Macdonald model with an intra-host continuous-time Moran model, thus explicitly representing the evolution of individual parasite genomes in a traditional epidemiological framework. Implemented as a stochastic simulation, we use the model to explore relationships between measures of parasite genetic diversity and parasite prevalence, a widely-used metric of transmission intensity. First, we explore how varying parasite prevalence influences genetic diversity at equilibrium. We find that multiple genetic diversity statistics are correlated with prevalence, but the strength of the relationships depends on whether variation in prevalence is driven by host- or vector-related factors. Next, we assess the responsiveness of a variety of statistics to malaria control interventions, finding that those related to mixed infections respond quickly (∼months) whereas other statistics, such as nucleotide diversity, may take decades to respond. These findings provide insights into the opportunities and challenges associated with using genetic data to monitor malaria epidemiology.
Collapse
Affiliation(s)
- Jason A. Hendry
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Dominic Kwiatkowski
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
- Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- Medical Research Council Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
Ralinoro F, Rakotomanga TA, Rakotosaona R, Doll Rakoto DA, Menard D, Jeannoda V, Ratsimbasoa A. Genetic diversity of Plasmodium falciparum populations in three malaria transmission settings in Madagascar. Malar J 2021; 20:239. [PMID: 34044837 PMCID: PMC8161981 DOI: 10.1186/s12936-021-03776-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 05/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Assessment of the genetic diversity of Plasmodium falciparum parasites from various malaria transmission settings could help to define tailored local strategies for malaria control and elimination. Such assessments are currently scarce in Madagascar. The study presented here aimed to bridge this gap by investigating the genetic diversity of P. falciparum populations in three epidemiological strata (Equatorial, Tropical and Fringes) in Madagascar. METHODS Two-hundred and sixty-six P. falciparum isolates were obtained from patients with uncomplicated malaria enrolled in clinical drug efficacy studies conducted at health centres in Tsaratanana (Equatorial stratum), Antanimbary (Tropical stratum) and Anjoma Ramartina (Fringes) in 2013 and 2016. Parasite DNA was extracted from blood samples collected before anti-malarial treatment. Plasmodium species were identified by nested PCR targeting the 18 S rRNA gene. The genetic profiles of P. falciparum parasites were defined by allele-specific nested PCR on the polymorphic regions of the msp-1 and msp-2 genes. RESULTS Fifty-eight alleles were detected in the P. falciparum samples tested: 18 alleles for msp-1 and 40 for msp-2. K1 (62.9%, 139/221) and FC27 (69.5%, 114/164) were the principal msp-1 and msp-2 allele families detected, although the proportions of the msp-1 and msp-2 alleles varied significantly between sites. Polyclonal infections were more frequent at sites in the Equatorial stratum (69.8%) than at sites in the Tropical stratum (60.5%) or Fringes (58.1%). Population genetics analyses showed that genetic diversity was similar between sites and that parasite flow within sites was limited. CONCLUSIONS This study provides recent information about the genetic diversity of P. falciparum populations in three transmission strata in Madagascar, and valuable baseline data for further evaluation of the impact of the control measures implemented in Madagascar.
Collapse
Affiliation(s)
- Fanomezantsoa Ralinoro
- National Malaria Control Programme of Madagascar, Androhibe, Antananarivo, Madagascar. .,Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar.
| | - Tovonahary Angelo Rakotomanga
- National Malaria Control Programme of Madagascar, Androhibe, Antananarivo, Madagascar.,Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | | | | | - Didier Menard
- Malaria Genetics and Resistance Unit and INSERM U1201, Institut Pasteur Paris, Paris, France
| | - Victor Jeannoda
- Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar
| | - Arsene Ratsimbasoa
- National Malaria Control Programme of Madagascar, Androhibe, Antananarivo, Madagascar. .,Faculty of Medicine, University of Fianarantsoa, Fianarantsoa, Madagascar.
| |
Collapse
|
25
|
Ajogbasile FV, Kayode AT, Oluniyi PE, Akano KO, Uwanibe JN, Adegboyega BB, Philip C, John OG, Eromon PJ, Emechebe G, Finimo F, Ogbulafor N, Jiya N, Okafor U, Ambe J, Wammanda RD, Oguche S, Mokuolu OA, Sowunmi A, Folarin OA, Happi CT. Genetic diversity and population structure of Plasmodium falciparum in Nigeria: insights from microsatellite loci analysis. Malar J 2021; 20:236. [PMID: 34039364 PMCID: PMC8152046 DOI: 10.1186/s12936-021-03734-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/13/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria remains a public health burden especially in Nigeria. To develop new malaria control and elimination strategies or refine existing ones, understanding parasite population diversity and transmission patterns is crucial. METHODS In this study, characterization of the parasite diversity and structure of Plasmodium falciparum isolates from 633 dried blood spot samples in Nigeria was carried out using 12 microsatellite loci of P. falciparum. These microsatellite loci were amplified via semi-nested polymerase chain reaction (PCR) and fragments were analysed using population genetic tools. RESULTS Estimates of parasite genetic diversity, such as mean number of different alleles (13.52), effective alleles (7.13), allelic richness (11.15) and expected heterozygosity (0.804), were high. Overall linkage disequilibrium was weak (0.006, P < 0.001). Parasite population structure was low (Fst: 0.008-0.105, AMOVA: 0.039). CONCLUSION The high level of parasite genetic diversity and low population structuring in this study suggests that parasite populations circulating in Nigeria are homogenous. However, higher resolution methods, such as the 24 SNP barcode and whole genome sequencing, may capture more specific parasite genetic signatures circulating in the country. The results obtained can be used as a baseline for parasite genetic diversity and structure, aiding in the formulation of appropriate therapeutic and control strategies in Nigeria.
Collapse
Affiliation(s)
- Fehintola V Ajogbasile
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Adeyemi T Kayode
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Paul E Oluniyi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Kazeem O Akano
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Jessica N Uwanibe
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Benjamin B Adegboyega
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - Courage Philip
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | | | - Philomena J Eromon
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria
| | - George Emechebe
- Department of Paediatrics, Imo State University Teaching Hospital, Orlu, Nigeria
| | - Finimo Finimo
- Department of Paediatrics, Federal Medical Centre, Yenagoa, Nigeria
| | - Nnenna Ogbulafor
- Case Management Unit, National Malaria Elimination Programme, Federal Ministry of Health, Abuja, Nigeria
| | - Nma Jiya
- Department of Paediatrics, Uthman Dan Fodio University, Sokoto, Nigeria
| | - Uche Okafor
- Department of Paediatrics, University of Nigeria Teaching Hospital, University of Nigeria, Nsukka, Nigeria
| | - Jose Ambe
- Department of Paediatrics, University of Maiduguri, Maiduguri, Nigeria
| | | | - Stephen Oguche
- Department of Paediatrics, University of Jos Teaching Hospital, University of Jos, Jos, Nigeria
| | - Olugbenga A Mokuolu
- Department of Paediatrics and Child Health, University of Ilorin, Ilorin, Nigeria
| | - Akintunde Sowunmi
- Institute of Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Nigeria.,Department of Pharmacology and Therapeutics, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Onikepe A Folarin
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria.,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Christian T Happi
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria. .,Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Nigeria.
| |
Collapse
|
26
|
Sumner KM, Freedman E, Mangeni JN, Obala AA, Abel L, Edwards JK, Emch M, Meshnick SR, Pence BW, Prudhomme-O'Meara W, Taylor SM. Exposure to diverse Plasmodium falciparum genotypes shapes the risk of symptomatic malaria in incident and persistent infections: A longitudinal molecular epidemiologic study in Kenya. Clin Infect Dis 2021; 73:1176-1184. [PMID: 33904907 DOI: 10.1093/cid/ciab357] [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: 01/15/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Repeated exposure to malaria infections could protect against symptomatic progression, as people develop adaptive immunity to infections acquired over time. METHODS We investigated how new, recurrent, and persistent Plasmodium falciparum infections were associated with the odds of developing symptomatic compared to asymptomatic malaria. Using a 14-month longitudinal cohort in Western Kenya, we used amplicon deep sequencing of two polymorphic genes (pfama1 and pfcsp) to assess overlap of parasite genotypes (represented by haplotypes) acquired within an individual's successive infections. We hypothesized infections with novel haplotypes would increase the odds of symptomatic malaria. RESULTS After excluding initial infections, we observed 534 asymptomatic and 88 symptomatic infections across 186 people. We detected 109 pfcsp haplotypes, and each infection was classified as harboring novel, recurrent or persistent haplotypes. Incident infections with only new haplotypes had higher odds of symptomatic malaria when compared to infections with only recurrent haplotypes [odds ratio (OR): 3.24, 95% confidence interval (CI): 1.20 to 8.78], but infections with both new and recurrent haplotypes [OR: 0.64, 95% CI: 0.15 to 2.65] did not. Assessing persistent infections, those with mixed (persistent with new or recurrent) haplotypes [OR: 0.77, 95% CI: 0.21 to 2.75] had no association with symptomatic malaria compared to infections with only persistent haplotypes. Results were similar for pfama1. CONCLUSIONS These results confirm that incident infections with only novel haplotypes were associated with increased odds of symptomatic malaria compared to infections with only recurrent haplotypes but this relationship was not seen when haplotypes persisted over time in consecutive infections.
Collapse
Affiliation(s)
- Kelsey M Sumner
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Elizabeth Freedman
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA
| | - Judith N Mangeni
- School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Andrew A Obala
- School of Medicine, College of Health Sciences, Moi University, Eldoret, Kenya
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Jessie K Edwards
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Department of Geography, University of North Carolina, Chapel Hill NC, USA
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Brian W Pence
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA
| | - Wendy Prudhomme-O'Meara
- Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,School of Public Health, College of Health Sciences, Moi University, Eldoret, Kenya.,Duke Global Health Institute, Duke University, Durham NC, USA
| | - Steve M Taylor
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill NC, USA.,Division of Infectious Diseases, School of Medicine, Duke University, Durham NC, USA.,Duke Global Health Institute, Duke University, Durham NC, USA
| |
Collapse
|
27
|
Mohammed H, Assefa A, Chernet M, Wuletaw Y, Commons RJ. Genetic polymorphisms of Plasmodium falciparum isolates from Melka-Werer, North East Ethiopia based on the merozoite surface protein-2 (msp-2) gene as a molecular marker. Malar J 2021; 20:85. [PMID: 33579293 PMCID: PMC7881608 DOI: 10.1186/s12936-021-03625-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/04/2021] [Indexed: 11/21/2022] Open
Abstract
Background The characterization of parasite populations circulating in malaria endemic areas is necessary to evaluate the success of ongoing interventions and malaria control strategies. This study was designed to investigate the genetic diversity of Plasmodium falciparum isolates from the semi-arid area in North East Ethiopia, using the highly polymorphic merozoite surface protein-2 (msp2) gene as a molecular marker. Methods Dried blood spot isolates were collected from patients with P. falciparum infection between September 2014 and January 2015 from Melka-Werer, North East Ethiopia. Parasite DNA was extracted and genotyped using allele-specific nested polymerase chain reactions for msp2. Results 52 isolates were collected with msp2 identified in 41 (78.8%) isolates. Allele typing of the msp2 gene detected the 3D7/IC allelic family in 54% and FC27 allelic family in 46%. A total of 14 different msp2 genotypes were detected including 6 belonging to the 3D7/IC family and 8 to the FC27 family. Forty percent of isolates had multiple genotypes and the overall mean multiplicity of infections (MOI) was 1.2 (95%CI 0.96–1.42). The heterozygosity index was 0.50 for the msp2 locus. There was no difference in MOI between age groups. A negative correlation between parasite density and multiplicity of infection was found (p = 0.02). Conclusion Plasmodium falciparum isolates from the semi-arid area of North East Ethiopia are mainly monoclonal with low MOI and limited genetic diversity in the study population.
Collapse
Affiliation(s)
- Hussein Mohammed
- Malaria, Neglected Tropical Diseases Research Team, Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Ashenafi Assefa
- Malaria, Neglected Tropical Diseases Research Team, Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Melkie Chernet
- Malaria, Neglected Tropical Diseases Research Team, Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yonas Wuletaw
- Malaria, Neglected Tropical Diseases Research Team, Bacterial, Parasitic, Zoonotic Diseases Research Directorate, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Robert J Commons
- Global Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia.,Internal Medicine Services, Ballarat Health Services, Ballarat, Australia
| |
Collapse
|
28
|
Watson OJ, Okell LC, Hellewell J, Slater HC, Unwin HJT, Omedo I, Bejon P, Snow RW, Noor AM, Rockett K, Hubbart C, Nankabirwa JI, Greenhouse B, Chang HH, Ghani AC, Verity R. Evaluating the Performance of Malaria Genetics for Inferring Changes in Transmission Intensity Using Transmission Modeling. Mol Biol Evol 2021; 38:274-289. [PMID: 32898225 PMCID: PMC7783189 DOI: 10.1093/molbev/msaa225] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Substantial progress has been made globally to control malaria, however there is a growing need for innovative new tools to ensure continued progress. One approach is to harness genetic sequencing and accompanying methodological approaches as have been used in the control of other infectious diseases. However, to utilize these methodologies for malaria, we first need to extend the methods to capture the complex interactions between parasites, human and vector hosts, and environment, which all impact the level of genetic diversity and relatedness of malaria parasites. We develop an individual-based transmission model to simulate malaria parasite genetics parameterized using estimated relationships between complexity of infection and age from five regions in Uganda and Kenya. We predict that cotransmission and superinfection contribute equally to within-host parasite genetic diversity at 11.5% PCR prevalence, above which superinfections dominate. Finally, we characterize the predictive power of six metrics of parasite genetics for detecting changes in transmission intensity, before grouping them in an ensemble statistical model. The model predicted malaria prevalence with a mean absolute error of 0.055. Different assumptions about the availability of sample metadata were considered, with the most accurate predictions of malaria prevalence made when the clinical status and age of sampled individuals is known. Parasite genetics may provide a novel surveillance tool for estimating the prevalence of malaria in areas in which prevalence surveys are not feasible. However, the findings presented here reinforce the need for patient metadata to be recorded and made available within all future attempts to use parasite genetics for surveillance.
Collapse
Affiliation(s)
- Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Lucy C Okell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Joel Hellewell
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Hannah C Slater
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - H Juliette T Unwin
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Irene Omedo
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Philip Bejon
- KEMRI-Wellcome Trust Research Programme, Centre for Geographic Medicine Research-Coast, Kilifi, Kenya
| | - Robert W Snow
- Population Health Unit, Kenya Medical Research Institute—Wellcome Trust Research Programme, Nairobi, Kenya
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | | | - Kirk Rockett
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Christina Hubbart
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Joaniter I Nankabirwa
- Infectious Diseases Research Collaboration, Kampala, Uganda
- Makerere University College of Health Sciences, Kampala, Uganda
| | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, San Francisco, CA
| | - Hsiao-Han Chang
- Center for Communicable Disease Dynamics, Harvard TH Chan School of Public Health, Boston, MA
| | - Azra C Ghani
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| |
Collapse
|
29
|
Buyon LE, Santamaria AM, Early AM, Quijada M, Barahona I, Lasso J, Avila M, Volkman SK, Marti M, Neafsey DE, Obaldia III N. Population genomics of Plasmodium vivax in Panama to assess the risk of case importation on malaria elimination. PLoS Negl Trop Dis 2020; 14:e0008962. [PMID: 33315861 PMCID: PMC7769613 DOI: 10.1371/journal.pntd.0008962] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/28/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022] Open
Abstract
Malaria incidence in Panama has plateaued in recent years in spite of elimination efforts, with almost all cases caused by Plasmodium vivax. Notwithstanding, overall malaria prevalence remains low (fewer than 1 case per 1000 persons). We used selective whole genome amplification to sequence 59 P. vivax samples from Panama. The P. vivax samples were collected from two periods (2007-2009 and 2017-2019) to study the population structure and transmission dynamics of the parasite. Imported cases resulting from increased levels of human migration could threaten malaria elimination prospects, and four of the samples evaluated came from individuals with travel history. We explored patterns of recent common ancestry among the samples and observed that a highly genetically related lineage (termed CL1) was dominant among the samples (47 out of 59 samples with good sequencing coverage), spanning the entire period of the collection (2007-2019) and all regions of the country. We also found a second, smaller clonal lineage (termed CL2) of four parasites collected between 2017 and 2019. To explore the regional context of Panamanian P. vivax we conducted principal components analysis and constructed a neighbor-joining tree using these samples and samples collected worldwide from a previous study. Three of the four samples with travel history clustered with samples collected from their suspected country of origin (consistent with importation), while one appears to have been a result of local transmission. The small number of Panamanian P. vivax samples not belonging to either CL1 or CL2 clustered with samples collected from Colombia, suggesting they represent the genetically similar ancestral P. vivax population in Panama or were recently imported from Colombia. The low diversity we observe in Panama indicates that this parasite population has been previously subject to a severe bottleneck and may be eligible for elimination. Additionally, while we confirmed that P. vivax is imported to Panama from diverse geographic locations, the lack of impact from imported cases on the overall parasite population genomic profile suggests that onward transmission from such cases is limited and that imported cases may not presently pose a major barrier to elimination.
Collapse
Affiliation(s)
- Lucas E. Buyon
- Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | | | - Angela M. Early
- Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Mario Quijada
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | | | | | | | - Sarah K. Volkman
- Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
- Simmons University, College of Natural, Behavioral and Health Sciences, Boston, Massachusetts, United States of America
| | | | - Daniel E. Neafsey
- Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Nicanor Obaldia III
- Harvard TH Chan School of Public Health, Boston, Massachusetts, United States of America
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
- University of Glasgow, Glasgow, United Kingdom
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Fola AA, Kattenberg E, Razook Z, Lautu-Gumal D, Lee S, Mehra S, Bahlo M, Kazura J, Robinson LJ, Laman M, Mueller I, Barry AE. SNP barcodes provide higher resolution than microsatellite markers to measure Plasmodium vivax population genetics. Malar J 2020; 19:375. [PMID: 33081815 PMCID: PMC7576724 DOI: 10.1186/s12936-020-03440-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Genomic surveillance of malaria parasite populations has the potential to inform control strategies and to monitor the impact of interventions. Barcodes comprising large numbers of single nucleotide polymorphism (SNP) markers are accurate and efficient genotyping tools, however may need to be tailored to specific malaria transmission settings, since 'universal' barcodes can lack resolution at the local scale. A SNP barcode was developed that captures the diversity and structure of Plasmodium vivax populations of Papua New Guinea (PNG) for research and surveillance. METHODS Using 20 high-quality P. vivax genome sequences from PNG, a total of 178 evenly spaced neutral SNPs were selected for development of an amplicon sequencing assay combining a series of multiplex PCRs and sequencing on the Illumina MiSeq platform. For initial testing, 20 SNPs were amplified in a small number of mono- and polyclonal P. vivax infections. The full barcode was then validated by genotyping and population genetic analyses of 94 P. vivax isolates collected between 2012 and 2014 from four distinct catchment areas on the highly endemic north coast of PNG. Diversity and population structure determined from the SNP barcode data was then benchmarked against that of ten microsatellite markers used in previous population genetics studies. RESULTS From a total of 28,934,460 reads generated from the MiSeq Illumina run, 87% mapped to the PvSalI reference genome with deep coverage (median = 563, range 56-7586) per locus across genotyped samples. Of 178 SNPs assayed, 146 produced high-quality genotypes (minimum coverage = 56X) in more than 85% of P. vivax isolates. No amplification bias was introduced due to either polyclonal infection or whole genome amplification (WGA) of samples before genotyping. Compared to the microsatellite panels, the SNP barcode revealed greater variability in genetic diversity between populations and geographical population structure. The SNP barcode also enabled assignment of genotypes according to their geographic origins with a significant association between genetic distance and geographic distance at the sub-provincial level. CONCLUSIONS High-throughput SNP barcoding can be used to map variation of malaria transmission dynamics at sub-national resolution. The low cost per sample and genotyping strategy makes the transfer of this technology to field settings highly feasible.
Collapse
Affiliation(s)
- Abebe A Fola
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Eline Kattenberg
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Malariology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Zahra Razook
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Dulcie Lautu-Gumal
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Stuart Lee
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
| | - Somya Mehra
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
| | - James Kazura
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
- Centre for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, USA
| | - Leanne J Robinson
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Ivo Mueller
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - Alyssa E Barry
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.
- Department of Medical Biology, The University of Melbourne, Melbourne, VIC, Australia.
- Disease Elimination Program, Burnet Institute, Melbourne, VIC, Australia.
- IMPACT Institute for Innovation in Mental and Physical Health and Clinical Translation, Deakin University, 75 Pigdons Road, Waurn Ponds, Geelong, VIC, 3216, Australia.
| |
Collapse
|
33
|
Tessema SK, Hathaway NJ, Teyssier NB, Murphy M, Chen A, Aydemir O, Duarte EM, Simone W, Colborn J, Saute F, Crawford E, Aide P, Bailey JA, Greenhouse B. Sensitive, highly multiplexed sequencing of microhaplotypes from the Plasmodium falciparum heterozygome. J Infect Dis 2020; 225:1227-1237. [PMID: 32840625 PMCID: PMC8974853 DOI: 10.1093/infdis/jiaa527] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 08/24/2020] [Indexed: 01/28/2023] Open
Abstract
Background Targeted next-generation sequencing offers the potential for consistent, deep coverage of information-rich genomic regions to characterize polyclonal Plasmodium falciparum infections. However, methods to identify and sequence these genomic regions are currently limited. Methods A bioinformatic pipeline and multiplex methods were developed to identify and simultaneously sequence 100 targets and applied to dried blood spot (DBS) controls and field isolates from Mozambique. For comparison, whole-genome sequencing data were generated for the same controls. Results Using publicly available genomes, 4465 high-diversity genomic regions suited for targeted sequencing were identified, representing the P. falciparum heterozygome. For this study, 93 microhaplotypes with high diversity (median expected heterozygosity = 0.7) were selected along with 7 drug resistance loci. The sequencing method achieved very high coverage (median 99%), specificity (99.8%), and sensitivity (90% for haplotypes with 5% within sample frequency in dried blood spots with 100 parasites/µL). In silico analyses revealed that microhaplotypes provided much higher resolution to discriminate related from unrelated polyclonal infections than biallelic single-nucleotide polymorphism barcodes. Conclusions The bioinformatic and laboratory methods outlined here provide a flexible tool for efficient, low-cost, high-throughput interrogation of the P. falciparum genome, and can be tailored to simultaneously address multiple questions of interest in various epidemiological settings.
Collapse
Affiliation(s)
- Sofonias K Tessema
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Nicholas J Hathaway
- Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts
| | - Noam B Teyssier
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Maxwell Murphy
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Anna Chen
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Elias M Duarte
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Wilson Simone
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - James Colborn
- Clinton Health Access Initiative, Maputo, Mozambique
| | - Francisco Saute
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Emily Crawford
- Chan Zuckerberg Biohub, San Francisco, California, United States
| | - Pedro Aide
- Centro de Investigação em Saúde de Manhiça (CISM), Manhiça, Mozambique
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Bryan Greenhouse
- EPPIcenter research program, Division of HIV, ID, and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, California, United States
| |
Collapse
|
34
|
Noviyanti R, Miotto O, Barry A, Marfurt J, Siegel S, Thuy-Nhien N, Quang HH, Anggraeni ND, Laihad F, Liu Y, Sumiwi ME, Trimarsanto H, Coutrier F, Fadila N, Ghanchi N, Johora FT, Puspitasari AM, Tavul L, Trianty L, Utami RAS, Wang D, Wangchuck K, Price RN, Auburn S. Implementing parasite genotyping into national surveillance frameworks: feedback from control programmes and researchers in the Asia-Pacific region. Malar J 2020; 19:271. [PMID: 32718342 PMCID: PMC7385952 DOI: 10.1186/s12936-020-03330-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/09/2020] [Indexed: 01/13/2023] Open
Abstract
The Asia-Pacific region faces formidable challenges in achieving malaria elimination by the proposed target in 2030. Molecular surveillance of Plasmodium parasites can provide important information on malaria transmission and adaptation, which can inform national malaria control programmes (NMCPs) in decision-making processes. In November 2019 a parasite genotyping workshop was held in Jakarta, Indonesia, to review molecular approaches for parasite surveillance and explore ways in which these tools can be integrated into public health systems and inform policy. The meeting was attended by 70 participants from 8 malaria-endemic countries and partners of the Asia Pacific Malaria Elimination Network. The participants acknowledged the utility of multiple use cases for parasite genotyping including: quantifying the prevalence of drug resistant parasites, predicting risks of treatment failure, identifying major routes and reservoirs of infection, monitoring imported malaria and its contribution to local transmission, characterizing the origins and dynamics of malaria outbreaks, and estimating the frequency of Plasmodium vivax relapses. However, the priority of each use case varies with different endemic settings. Although a one-size-fits-all approach to molecular surveillance is unlikely to be applicable across the Asia-Pacific region, consensus on the spectrum of added-value activities will help support data sharing across national boundaries. Knowledge exchange is needed to establish local expertise in different laboratory-based methodologies and bioinformatics processes. Collaborative research involving local and international teams will help maximize the impact of analytical outputs on the operational needs of NMCPs. Research is also needed to explore the cost-effectiveness of genetic epidemiology for different use cases to help to leverage funding for wide-scale implementation. Engagement between NMCPs and local researchers will be critical throughout this process.
Collapse
Affiliation(s)
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Centre for Genomics and Global Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Alyssa Barry
- School of Medicine, Deakin University, Geelong, VIC, Australia
- Burnet Institute, Melbourne, VIC, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Sasha Siegel
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
| | - Nguyen Thuy-Nhien
- Centre for Tropical Medicine, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Huynh Hong Quang
- Institute of Malariology, Parasitology and Entomology, Quy Nhon, Vietnam
| | | | | | - Yaobao Liu
- National Health Commission Key Laboratory of Parasitic Disease Control and Prevention, Jiangsu Provincial Key Laboratory on Parasite and Vector Control Technology, Jiangsu Institute of Parasitic Diseases, Wuxi, Jiangsu Province, China
| | | | | | - Farah Coutrier
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Nadia Fadila
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Najia Ghanchi
- Pathology, Aga Khan University Hospital, Karachi, Pakistan
| | - Fatema Tuj Johora
- Infectious Diseases Division, International Centre for Diarrheal Diseases Research, Bangladesh Mohakhali, Dhaka, Bangladesh
| | | | - Livingstone Tavul
- Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | - Duoquan Wang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Kesang Wangchuck
- Royal Center for Disease Control, Department of Public Health, Ministry of Health, Thimphu, Bhutan
| | - Ric N Price
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sarah Auburn
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, NT, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| |
Collapse
|
35
|
Abamecha A, El-Abid H, Yilma D, Addisu W, Ibenthal A, Bayih AG, Noedl H, Yewhalaw D, Moumni M, Abdissa A. Genetic diversity and genotype multiplicity of Plasmodium falciparum infection in patients with uncomplicated malaria in Chewaka district, Ethiopia. Malar J 2020; 19:203. [PMID: 32513191 PMCID: PMC7281928 DOI: 10.1186/s12936-020-03278-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/29/2020] [Indexed: 12/03/2022] Open
Abstract
Background Genetic diversity in Plasmodium falciparum poses a major threat to malaria control and elimination interventions. Characterization of the genetic diversity of P. falciparum strains can be used to assess intensity of parasite transmission and identify potential deficiencies in malaria control programmes, which provides vital information to evaluating malaria elimination efforts. This study investigated the P. falciparum genetic diversity and genotype multiplicity of infection in parasite isolates from cases with uncomplicated P. falciparum malaria in Southwest Ethiopia. Methods A total of 80 P. falciparum microscopy and qPCR positive blood samples were collected from study participants aged 6 months to 60 years, who visited the health facilities during study evaluating the efficacy of artemether-lumefantrine from September–December, 2017. Polymorphic regions of the msp-1 and msp-2 were genotyped by nested polymerase chain reactions (nPCR) followed by gel electrophoresis for fragment analysis. Results Of 80 qPCR-positive samples analysed for polymorphisms on msp-1 and msp-2 genes, the efficiency of msp-1 and msp-2 gene amplification reactions with family-specific primers were 95% and 98.8%, respectively. Allelic variation of 90% (72/80) for msp-1 and 86.2% (69/80) for msp-2 were observed. K1 was the predominant msp-1 allelic family detected in 20.8% (15/72) of the samples followed by MAD20 and RO33. Within msp-2, allelic family FC27 showed a higher frequency (26.1%) compared to IC/3D7 (15.9%). Ten different alleles were observed in msp-1 with 6 alleles for K1, 3 alleles for MAD20 and 1 allele for RO33. In msp-2, 19 individual alleles were detected with 10 alleles for FC27 and 9 alleles for 3D7. Eighty percent (80%) of isolates had multiple genotypes and the overall mean multiplicity of infection was 3.2 (95% CI 2.87–3.46). The heterozygosity indices were 0.43 and 0.85 for msp-1 and msp-2, respectively. There was no significant association between multiplicity of infection and age or parasite density. Conclusions The study revealed high levels of genetic diversity and mixed-strain infections of P. falciparum populations in Chewaka district, Ethiopia, suggesting that both endemicity level and malaria transmission remain high and that strengthened control efforts are needed in Ethiopia.
Collapse
Affiliation(s)
- Abdulhakim Abamecha
- School of Medical Laboratory Science, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia. .,Department of Biomedical, College of Public Health and Medical Science, Mettu University, Mettu, Ethiopia. .,Tropical and Infectious Diseases Research Center (TIDRC), Jimma University, Jimma, Ethiopia.
| | - Hassan El-Abid
- Laboratory of Cellular Genomics and Molecular Techniques for Investigation, Faculty of Sciences, Moulay Ismail University, Meknès, Morocco
| | - Daniel Yilma
- Department of Internal Medicine, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Wondimagegn Addisu
- School of Medical Laboratory Science, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Achim Ibenthal
- Faculty of Science and Art, HAWK University, Gottingen, Germany
| | | | - Harald Noedl
- Malaria Research Initiative Bandarban (MARIB), Vienna, Austria
| | - Delenasaw Yewhalaw
- School of Medical Laboratory Science, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia.,Tropical and Infectious Diseases Research Center (TIDRC), Jimma University, Jimma, Ethiopia
| | - Mohieddine Moumni
- Laboratory of Cellular Genomics and Molecular Techniques for Investigation, Faculty of Sciences, Moulay Ismail University, Meknès, Morocco
| | - Alemseged Abdissa
- School of Medical Laboratory Science, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia.,Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| |
Collapse
|
36
|
Pava Z, Puspitasari AM, Rumaseb A, Handayuni I, Trianty L, Utami RAS, Tirta YK, Burdam F, Kenangalem E, Wirjanata G, Kho S, Trimarsanto H, Anstey NM, Poespoprodjo JR, Noviyanti R, Price RN, Marfurt J, Auburn S. Molecular surveillance over 14 years confirms reduction of Plasmodium vivax and falciparum transmission after implementation of Artemisinin-based combination therapy in Papua, Indonesia. PLoS Negl Trop Dis 2020; 14:e0008295. [PMID: 32379762 PMCID: PMC7237043 DOI: 10.1371/journal.pntd.0008295] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 05/19/2020] [Accepted: 04/15/2020] [Indexed: 01/13/2023] Open
Abstract
Genetic epidemiology can provide important insights into parasite transmission that can inform public health interventions. The current study compared long-term changes in the genetic diversity and structure of co-endemic Plasmodium falciparum and P. vivax populations. The study was conducted in Papua Indonesia, where high-grade chloroquine resistance in P. falciparum and P. vivax led to a universal policy of Artemisinin-based Combination Therapy (ACT) in 2006. Microsatellite typing and population genetic analyses were undertaken on available isolates collected between 2004 and 2017 from patients with uncomplicated malaria (n = 666 P. falciparum and n = 615 P. vivax). The proportion of polyclonal P. falciparum infections fell from 28% (38/135) before policy change (2004-2006) to 18% (22/125) at the end of the study (2015-2017); p<0.001. Over the same period, polyclonal P. vivax infections fell from 67% (80/119) to 35% (33/93); p<0.001. P. falciparum strains persisted for up to 9 years compared to 3 months for P. vivax, reflecting higher rates of outbreeding in the latter. Sub-structure was observed in the P. falciparum population, but not in P. vivax, confirming different patterns of outbreeding. The P. falciparum population exhibited 4 subpopulations that changed in frequency over time. Notably, a sharp rise was observed in the frequency of a minor subpopulation (K2) in the late post-ACT period, accounting for 100% of infections in late 2016-2017. The results confirm epidemiological evidence of reduced P. falciparum and P. vivax transmission over time. The smaller change in P. vivax population structure is consistent with greater outbreeding associated with relapsing infections and highlights the need for radical cure to reduce recurrent infections. The study emphasizes the challenge in disrupting P. vivax transmission and demonstrates the potential of molecular data to inform on the impact of public health interventions.
Collapse
Affiliation(s)
- Zuleima Pava
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | | | - Angela Rumaseb
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Irene Handayuni
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Leily Trianty
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | | | | | - Faustina Burdam
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
| | - Enny Kenangalem
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
| | - Grennady Wirjanata
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Steven Kho
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | | | - Nicholas M. Anstey
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Jeanne Rini Poespoprodjo
- Mimika District Health Authority, Timika, Papua, Indonesia
- Timika Malaria Research Programme, Papuan Health and Community Development Foundation, Timika, Papua, Indonesia
- Pediatric Research Office, Department of Child Health, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | | | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| |
Collapse
|
37
|
Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
Collapse
|
38
|
Li X, Kumar S, McDew-White M, Haile M, Cheeseman IH, Emrich S, Button-Simons K, Nosten F, Kappe SHI, Ferdig MT, Anderson TJC, Vaughan AM. Genetic mapping of fitness determinants across the malaria parasite Plasmodium falciparum life cycle. PLoS Genet 2019; 15:e1008453. [PMID: 31609965 PMCID: PMC6821138 DOI: 10.1371/journal.pgen.1008453] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 10/30/2019] [Accepted: 10/01/2019] [Indexed: 12/14/2022] Open
Abstract
Determining the genetic basis of fitness is central to understanding evolution and transmission of microbial pathogens. In human malaria parasites (Plasmodium falciparum), most experimental work on fitness has focused on asexual blood stage parasites, because this stage can be easily cultured, although the transmission of malaria requires both female Anopheles mosquitoes and vertebrate hosts. We explore a powerful approach to identify the genetic determinants of parasite fitness across both invertebrate and vertebrate life-cycle stages of P. falciparum. This combines experimental genetic crosses using humanized mice, with selective whole genome amplification and pooled sequencing to determine genome-wide allele frequencies and identify genomic regions under selection across multiple lifecycle stages. We applied this approach to genetic crosses between artemisinin resistant (ART-R, kelch13-C580Y) and ART-sensitive (ART-S, kelch13-WT) parasites, recently isolated from Southeast Asian patients. Two striking results emerge: we observed (i) a strong genome-wide skew (>80%) towards alleles from the ART-R parent in the mosquito stage, that dropped to ~50% in the blood stage as selfed ART-R parasites were selected against; and (ii) repeatable allele specific skews in blood stage parasites with particularly strong selection (selection coefficient (s) ≤ 0.18/asexual cycle) against alleles from the ART-R parent at loci on chromosome 12 containing MRP2 and chromosome 14 containing ARPS10. This approach robustly identifies selected loci and has strong potential for identifying parasite genes that interact with the mosquito vector or compensatory loci involved in drug resistance.
Collapse
Affiliation(s)
- Xue Li
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Marina McDew-White
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Meseret Haile
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Ian H. Cheeseman
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Scott Emrich
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
- Electrical Engineering and Computer Science, University of Tennessee, Knoxville, Tennessee, United States of America
| | - Katie Button-Simons
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Stefan H. I. Kappe
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Global Health, University of Washington, Seattle, Washington, United States of America
| | - Michael T. Ferdig
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Tim J. C. Anderson
- Texas Biomedical Research Institute, San Antonio, Texas, United States of America
- * E-mail: (TJCA); (AMV)
| | - Ashley M. Vaughan
- Center for Global Infectious Disease Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- * E-mail: (TJCA); (AMV)
| |
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
Ndiaye T, Sy M, Gaye A, Ndiaye D. Genetic polymorphism of Merozoite Surface Protein 1 (msp1) and 2 (msp2) genes and multiplicity of Plasmodium falciparum infection across various endemic areas in Senegal. Afr Health Sci 2019; 19:2446-2456. [PMID: 32127816 PMCID: PMC7040301 DOI: 10.4314/ahs.v19i3.19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
INTRODUCTION Despite a significant decline in Senegal, malaria remains a burden in various parts of the country. Assessment of multiplicity of Plasmodium falciparum infection and genetic diversity of parasites population could help in monitoring of malaria control. OBJECTIVE To assess genetic diversity and multiplicity of infection in P. falciparum isolates from three areas in Senegal with different malaria transmissions. METHODS 136 blood samples were collected from patients with uncomplicated P. falciparum malaria in Pikine, Kedougou and Thies. Polymorphic loci of msp1 and 2 (Merozoite surface protein-1 and 2) genes were amplified by nested PCR. RESULTS For msp1gene, K1 allelic family was predominant with frequency of 71%. Concerning msp2 gene, IC3D7 allelic family was the most represented with frequency of 83%. Multiclonal isolates found were 36% and 31% for msp1et msp2 genes respectively. The MOI found in all areas was 2.56 and was statistically different between areas (P=0.024). Low to intermediate genetic diversity were found with heterozygosity range (He=0,394-0,637) and low genetic differentiation (Fst msp1= 0.011; Fst msp2=0.017) were observed between P. falciparum population within the country. CONCLUSION Low to moderate genetic diversity of P.falciparum strains and MOI disparities were found in Senegal.
Collapse
Affiliation(s)
- Tolla Ndiaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Mouhamad Sy
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Amy Gaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
| | - Daouda Ndiaye
- Laboratory of Parasitology/Mycology HALD, Cheikh Anta Diop University of Dakar, PO Box 5005, Dakar, Senegal
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA, USA
| |
Collapse
|
41
|
Taylor AR, Jacob PE, Neafsey DE, Buckee CO. Estimating Relatedness Between Malaria Parasites. Genetics 2019; 212:1337-1351. [PMID: 31209105 PMCID: PMC6707449 DOI: 10.1534/genetics.119.302120] [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: 03/12/2019] [Accepted: 06/03/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding the relatedness of individuals within or between populations is a common goal in biology. Increasingly, relatedness features in genetic epidemiology studies of pathogens. These studies are relatively new compared to those in humans and other organisms, but are important for designing interventions and understanding pathogen transmission. Only recently have researchers begun to routinely apply relatedness to apicomplexan eukaryotic malaria parasites, and to date have used a range of different approaches on an ad hoc basis. Therefore, it remains unclear how to compare different studies and which measures to use. Here, we systematically compare measures based on identity-by-state (IBS) and identity-by-descent (IBD) using a globally diverse data set of malaria parasites, Plasmodium falciparum and P. vivax, and provide marker requirements for estimates based on IBD. We formally show that the informativeness of polyallelic markers for relatedness inference is maximized when alleles are equifrequent. Estimates based on IBS are sensitive to allele frequencies, which vary across populations and by experimental design. For portability across studies, we thus recommend estimates based on IBD. To generate estimates with errors below an arbitrary threshold of 0.1, we recommend ∼100 polyallelic or 200 biallelic markers. Marker requirements are immediately applicable to haploid malaria parasites and other haploid eukaryotes. C.I.s facilitate comparison when different marker sets are used. This is the first attempt to provide rigorous analysis of the reliability of, and requirements for, relatedness inference in malaria genetic epidemiology. We hope it will provide a basis for statistically informed prospective study design and surveillance strategies.
Collapse
Affiliation(s)
- Aimee R Taylor
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Pierre E Jacob
- Department of Statistics, Harvard University, Cambridge, Massachusetts 02138
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T. H. Chan School of Public Health, Boston, Massachusetts 02115
| |
Collapse
|
42
|
Lê HG, Kang JM, Jun H, Lee J, Thái TL, Myint MK, Aye KS, Sohn WM, Shin HJ, Kim TS, Na BK. Changing pattern of the genetic diversities of Plasmodium falciparum merozoite surface protein-1 and merozoite surface protein-2 in Myanmar isolates. Malar J 2019; 18:241. [PMID: 31311565 PMCID: PMC6636015 DOI: 10.1186/s12936-019-2879-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/09/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Plasmodium falciparum merozoite surface protein-1 (PfMSP-1) and -2 (PfMSP-2) are major blood-stage vaccine candidate antigens. Understanding the genetic diversity of the genes, pfmsp-1 and pfmsp-2, is important for recognizing the genetic structure of P. falciparum, and the development of an effective vaccine based on the antigens. In this study, the genetic diversities of pfmsp-1 and pfmsp-2 in the Myanmar P. falciparum were analysed. METHODS The pfmsp-1 block 2 and pfmsp-2 block 3 regions were amplified by polymerase chain reaction from blood samples collected from Myanmar patients who were infected with P. falciparum in 2013-2015. The amplified gene fragments were cloned into a T&A vector, and sequenced. Sequence analysis of Myanmar pfmsp-1 block 2 and pfmsp-2 block 3 was performed to identify the genetic diversity of the regions. The temporal genetic changes of both pfmsp-1 and pfmsp-2 in the Myanmar P. falciparum population, as well as the polymorphic diversity in the publicly available global pfmsp-1 and pfmsp-2, were also comparatively analysed. RESULTS High levels of genetic diversity of pfmsp-1 and pfmsp-2 were observed in the Myanmar P. falciparum isolates. Twenty-eight different alleles of pfmsp-1 (8 for K1 type, 14 for MAD20 type, and 6 for RO33 type) and 59 distinct alleles of pfmsp-2 (18 for FC27, and 41 for 3D7 type) were identified in the Myanmar P. falciparum population in amino acid level. Comparative analyses of the genetic diversity of the Myanmar pfmsp-1 and pfmsp-2 alleles in the recent (2013-2015) and past (2004-2006) Myanmar P. falciparum populations indicated the dynamic genetic expansion of the pfmsp-1 and pfmsp-2 in recent years, suggesting that a high level of genetic differentiation and recombination of the two genes may be maintained. Population genetic structure analysis of the global pfmsp-1 and pfmsp-2 also suggested that a high level of genetic diversity of the two genes was found in the global P. falciparum population. CONCLUSION Despite the recent remarkable decline of malaria cases, the Myanmar P. falciparum population still remains of sufficient size to allow the generation and maintenance of genetic diversity. The high level of genetic diversity of pfmsp-1 and pfmsp-2 in the global P. falciparum population emphasizes the necessity for continuous monitoring of the genetic diversity of the genes for better understanding of the genetic make-up and evolutionary aspect of the genes in the global P. falciparum population.
Collapse
Affiliation(s)
- Hương Giang Lê
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Jung-Mi Kang
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Hojong Jun
- Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea
| | - Jinyoung Lee
- Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea
| | - Thị Lam Thái
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea.,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea
| | - Moe Kyaw Myint
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Khin Saw Aye
- Department of Medical Research Pyin Oo Lwin Branch, Pyin Oo Lwin, Myanmar
| | - Woon-Mok Sohn
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea
| | - Ho-Joon Shin
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Tong-Soo Kim
- Department of Tropical Medicine, and Inha Research Institute for Medical Sciences, Inha University College of Medicine, Incheon, 22212, Republic of Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine, and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju, 52727, Republic of Korea. .,BK21Plus Team for Anti-aging Biotechnology and Industry, Department of Convergence Medical Science, Gyeongsang National University, Jinju, 52727, Republic of Korea.
| |
Collapse
|
43
|
Apinjoh TO, Ouattara A, Titanji VPK, Djimde A, Amambua-Ngwa A. Genetic diversity and drug resistance surveillance of Plasmodium falciparum for malaria elimination: is there an ideal tool for resource-limited sub-Saharan Africa? Malar J 2019; 18:217. [PMID: 31242921 PMCID: PMC6595576 DOI: 10.1186/s12936-019-2844-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
The intensification of malaria control interventions has resulted in its global decline, but it remains a significant public health burden especially in sub-Saharan Africa (sSA). Knowledge on the parasite diversity, its transmission dynamics, mechanisms of adaptation to environmental and interventional pressures could help refine or develop new control and elimination strategies. Critical to this is the accurate assessment of the parasite’s genetic diversity and monitoring of genetic markers of anti-malarial resistance across all susceptible populations. Such wide molecular surveillance will require selected tools and approaches from a variety of ever evolving advancements in technology and the changing epidemiology of malaria. The choice of an effective approach for specific endemic settings remains challenging, particularly for countries in sSA with limited access to advanced technologies. This article examines the current strategies and tools for Plasmodium falciparum genetic diversity typing and resistance monitoring and proposes how the different tools could be employed in resource-poor settings. Advanced approaches enabling targeted deep sequencing is valued as a sensitive method for assessing drug resistance and parasite diversity but remains out of the reach of most laboratories in sSA due to the high cost of development and maintenance. It is, however, feasible to equip a limited number of laboratories as Centres of Excellence in Africa (CEA), which will receive and process samples from a network of peripheral laboratories in the continent. Cheaper, sensitive and portable real-time PCR methods can be used in peripheral laboratories to pre-screen and select samples for targeted deep sequence or genome wide analyses at these CEAs.
Collapse
Affiliation(s)
- Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Amed Ouattara
- School of Medicine, University of Maryland, College Park, Baltimore, USA
| | - Vincent P K Titanji
- Faculty of Science, Engineering and Technology, Cameroon Christian University, Bali, Cameroon
| | - Abdoulaye Djimde
- Malaria Research and Training Centre, University of Science, Techniques and Technologies of Bamako, Bamako, Mali
| | | |
Collapse
|
44
|
Shetty AC, Jacob CG, Huang F, Li Y, Agrawal S, Saunders DL, Lon C, Fukuda MM, Ringwald P, Ashley EA, Han KT, Hlaing TM, Nyunt MM, Silva JC, Stewart KE, Plowe CV, O'Connor TD, Takala-Harrison S. Genomic structure and diversity of Plasmodium falciparum in Southeast Asia reveal recent parasite migration patterns. Nat Commun 2019; 10:2665. [PMID: 31209259 PMCID: PMC6572796 DOI: 10.1038/s41467-019-10121-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 04/17/2019] [Indexed: 02/08/2023] Open
Abstract
Estimates of Plasmodium falciparum migration may inform strategies for malaria elimination. Here we elucidate fine-scale parasite population structure and infer recent migration across Southeast Asia using identity-by-descent (IBD) approaches based on genome-wide single nucleotide polymorphisms called in 1722 samples from 54 districts. IBD estimates are consistent with isolation-by-distance. We observe greater sharing of larger IBD segments between artemisinin-resistant parasites versus sensitive parasites, which is consistent with the recent spread of drug resistance. Our IBD analyses reveal actionable patterns, including isolated parasite populations, which may be prioritized for malaria elimination, as well as asymmetrical migration identifying potential sources and sinks of migrating parasites.
Collapse
Affiliation(s)
- Amol C Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | | | - Fang Huang
- National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Beijing, 102206, PR China
| | - Yao Li
- Center for Geospatial Information Science, University of Maryland, College Park, MD, 20742, USA
| | - Sonia Agrawal
- Graduate Program in Epidemiology and Human Genetics, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - David L Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Khan Daun Penh, Phnom Penh, Cambodia
| | - Mark M Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, 10400, Thailand
| | - Pascal Ringwald
- Global Malaria Programme, World Health Organization, Geneva, 1202, Switzerland
| | - Elizabeth A Ashley
- Mahidol-Oxford Tropical Medicine Research Unit (MORU), Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, 11191, Myanmar
| | | | - Myaing M Nyunt
- Duke Global Health Institute, Duke University, Durham, NC, 27710, USA
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Kathleen E Stewart
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK
| | | | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
- Program in Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
| |
Collapse
|
45
|
Redmond SN, MacInnis BM, Bopp S, Bei AK, Ndiaye D, Hartl DL, Wirth DF, Volkman SK, Neafsey DE. De Novo Mutations Resolve Disease Transmission Pathways in Clonal Malaria. Mol Biol Evol 2019; 35:1678-1689. [PMID: 29722884 PMCID: PMC5995194 DOI: 10.1093/molbev/msy059] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Detecting de novo mutations in viral and bacterial pathogens enables researchers to reconstruct detailed networks of disease transmission and is a key technique in genomic epidemiology. However, these techniques have not yet been applied to the malaria parasite, Plasmodium falciparum, in which a larger genome, slower generation times, and a complex life cycle make them difficult to implement. Here, we demonstrate the viability of de novo mutation studies in P. falciparum for the first time. Using a combination of sequencing, library preparation, and genotyping methods that have been optimized for accuracy in low-complexity genomic regions, we have detected de novo mutations that distinguish nominally identical parasites from clonal lineages. Despite its slower evolutionary rate compared with bacterial or viral species, de novo mutation can be detected in P. falciparum across timescales of just 1–2 years and evolutionary rates in low-complexity regions of the genome can be up to twice that detected in the rest of the genome. The increased mutation rate allows the identification of separate clade expansions that cannot be found using previous genomic epidemiology approaches and could be a crucial tool for mapping residual transmission patterns in disease elimination campaigns and reintroduction scenarios.
Collapse
Affiliation(s)
- Seth N Redmond
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Bronwyn M MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Selina Bopp
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Amy K Bei
- Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Daouda Ndiaye
- Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Parasitology, Faculty of Medicine and Pharmacy, Cheikh Anta Diop University, Dakar, Senegal
| | - Daniel L Hartl
- Broad Institute of MIT and Harvard, Cambridge, MA.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA
| | - Dyann F Wirth
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| | - Sarah K Volkman
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA.,Department of Nursing, School of Nursing and Health Sciences, Simmons College, Boston, MA, 02115
| | - Daniel E Neafsey
- Broad Institute of MIT and Harvard, Cambridge, MA.,Harvard T.H. Chan School of Public Health, Boston, MA
| |
Collapse
|
46
|
Low genetic diversity and complexity of submicroscopic Plasmodium falciparum infections among febrile patients in low transmission areas in Senegal. PLoS One 2019; 14:e0215755. [PMID: 31022221 PMCID: PMC6483351 DOI: 10.1371/journal.pone.0215755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/08/2019] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION Submicroscopic Plasmodium infections are common in malaria endemic countries, but very little studies have been done in Senegal. This study investigates the genetic diversity and complexity of submicroscopic P. falciparum infections among febrile patients in low transmission areas in Senegal. MATERIALS AND METHODS Hundred and fifty blood samples were collected from febrile individuals living in Dielmo and Ndiop (Senegal) between August 2014 and January 2015, tested for microscopic and sub-microscopic P. falciparum infections and characterized for their genetic diversity and complexity of infections using msp-1 and msp-2 genotyping. RESULTS Submicroscopic P. falciparum infections were 19.6% and 25% in Dielmo and Ndiop, respectively. K1 and 3D7 were the predominant msp-1 and msp-2 allelic types with respective frequencies of 67.36% and 67.10% in microscopic isolates and 58.24% and 78% in submicroscopic ones. Frequencies of msp-1 allelic types were statistically comparable between the studied groups (p>0.05), and were respectively 93.54% vs 87.5% for K1, 60% vs 54.83% for MAD20 and 41.93% vs 22.5% for RO33 while frequencies of msp-2 allelic types were significantly highest in the microscopy group for FC27 (41.93% vs 10%, Fisher's Exact Test, p = 0.001) and 3D7 (61.29% vs 32.5%, Fisher's Exact Test, p = 0.02). Multiplicities of infection were lowest in submicroscopic P. falciparum isolates. CONCLUSIONS The study revealed a high submicroscopic P. falciparum carriage among patients in the study areas, and that submicroscopic P. falciparum isolates had a lower genetic diversity and complexity of malaria infections.
Collapse
|
47
|
Estimating effective population size for a cestode parasite infecting three-spined sticklebacks. Parasitology 2019; 146:883-896. [PMID: 30720409 DOI: 10.1017/s0031182018002226] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Remarkably few attempts have been made to estimate contemporary effective population size (Ne) for parasitic species, despite the valuable perspectives it can offer on the tempo and pace of parasite evolution as well as coevolutionary dynamics of host-parasite interactions. In this study, we utilized multi-locus microsatellite data to derive single-sample and temporal estimates of contemporary Ne for a cestode parasite (Schistocephalus solidus) as well as three-spined stickleback hosts (Gasterosteus aculeatus) in lakes across Alaska. Consistent with prior studies, both approaches recovered small and highly variable estimates of parasite and host Ne. We also found that estimates of host Ne and parasite Ne were sensitive to assumptions about population genetic structure and connectivity. And, while prior work on the stickleback-cestode system indicates that physiographic factors external to stickleback hosts largely govern genetic variation in S. solidus, our findings indicate that stickleback host attributes and factors internal to the host - namely body length, genetic diversity and infection - shape contemporary Ne of cestode parasites.
Collapse
|
48
|
Sibley CH. A Solid Beginning to Understanding Plasmodium vivax in Africa. J Infect Dis 2019; 220:1716-1718. [DOI: 10.1093/infdis/jiz019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 11/13/2022] Open
|
49
|
Bahk YY, Kim J, Ahn SK, Na BK, Chai JY, Kim TS. Genetic Diversity of Plasmodium vivax Causing Epidemic Malaria in the Republic of Korea. THE KOREAN JOURNAL OF PARASITOLOGY 2018; 56:545-552. [PMID: 30630274 PMCID: PMC6327206 DOI: 10.3347/kjp.2018.56.6.545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 11/23/2022]
Abstract
Plasmodium vivax is more challenging to control and eliminate than P. falciparum due to its more asymptomatic infections with low parasite densities making diagnosis more difficult, in addition to its unique biological characteristics. The potential re-introduction of incidence cases, either through borders or via human migrations, is another major hurdle to sustained control and elimination. The Republic of Korea has experienced re-emergence of vivax malaria in 1993 but is one of the 32 malaria-eliminating countries to-date. Despite achieving successful nationwide control and elimination of vivax malaria, the evolutionary characteristics of vivax malaria isolates in the Republic of Korea have not been fully understood. In this review, we present an overview of the genetic variability of such isolates to increase understanding of the epidemiology, diversity, and dynamics of vivax populations in the Republic of Korea.
Collapse
Affiliation(s)
- Young Yil Bahk
- Department of Biotechnology, College of Biomedical and Health Science, Konkuk University, Chungju 27478,
Korea
| | - Jeonga Kim
- Department of Medicine, Division of Endocrinology, Diabetes, and Metabolism, UAB Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL 35294,
USA
| | - Seong Kyu Ahn
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
| | - Byoung-Kuk Na
- Department of Parasitology and Tropical Medicine and Institute of Health Sciences, Gyeongsang National University College of Medicine, Jinju 52727,
Korea
| | - Jong-Yil Chai
- Korea Association of Health Promotion, Seoul 07653,
Korea
| | - Tong-Soo Kim
- Department of Parasitology and Tropical Medicine, Inha University School of Medicine, Incheon 22212,
Korea
| |
Collapse
|
50
|
Nkhoma SC, Banda RL, Khoswe S, Dzoole-Mwale TJ, Ward SA. Intra-host dynamics of co-infecting parasite genotypes in asymptomatic malaria patients. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 65:414-424. [PMID: 30145390 PMCID: PMC6219893 DOI: 10.1016/j.meegid.2018.08.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/13/2018] [Accepted: 08/20/2018] [Indexed: 11/22/2022]
Abstract
Malaria-infected individuals often harbor mixtures of genetically distinct parasite genotypes. We studied intra-host dynamics of parasite genotypes co-infecting asymptomatic adults in an area of intense malaria transmission in Chikhwawa, Malawi. Serial blood samples (5 ml) were collected over seven consecutive days from 25 adults with asymptomatic Plasmodium falciparum malaria and analyzed to determine whether a single peripheral blood sample accurately captures within-host parasite diversity. Blood samples from three of the participants were also analyzed by limiting dilution cloning and SNP genotyping of the parasite clones isolated to examine both the number and relatedness of co-infecting parasite haplotypes. We observed rapid turnover of co-infecting parasite genotypes in 88% of the individuals sampled (n = 22) such that the genetic composition of parasites infecting these individuals changed dramatically over the course of seven days of follow up. Nineteen of the 25 individuals sampled (76%) carried multiple parasite genotypes at baseline. Analysis of serial blood samples from three of the individuals revealed that they harbored 6, 12 and 17 distinct parasite haplotypes respectively. Approximately 70% of parasite haplotypes recovered from the three extensively sampled individuals were unrelated (proportion of shared alleles <83.3%) and were deemed to have primarily arisen from superinfection (inoculation of unrelated parasite haplotypes through multiple mosquito bites). The rest were related at the half-sib level or greater and were deemed to have been inoculated into individual human hosts via parasite co-transmission from single mosquito bites. These findings add further to the growing weight of evidence indicating that a single blood sample poorly captures within-host parasite diversity and underscore the importance of repeated blood sampling to accurately capture within-host parasite ecology. Our data also demonstrate a more pronounced role for parasite co-transmission in generating within-host parasite diversity in high transmission settings than previously assumed. Taken together, these findings have important implications for understanding the evolution of drug resistance, malaria transmission, parasite virulence, allocation of gametocyte sex ratios and acquisition of malaria immunity.
Collapse
Affiliation(s)
- Standwell C Nkhoma
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK; Wellcome Trust-Liverpool-Glasgow Centre for Global Health Research, 70 Pembroke Place, Liverpool L69 3GF, UK.
| | - Rachel L Banda
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stanley Khoswe
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Tamika J Dzoole-Mwale
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Stephen A Ward
- Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| |
Collapse
|