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Pepey A, Souris M, Kim S, Obadia T, Chy S, Ea M, Ouk S, Remoue F, Sovannaroth S, Mueller I, Witkowski B, Vantaux A. Comparing malaria risk exposure in rural Cambodia population using GPS tracking and questionnaires. Malar J 2024; 23:75. [PMID: 38475843 DOI: 10.1186/s12936-024-04890-6] [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: 07/03/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The Great Mekong Subregion has attained a major decline in malaria cases and fatalities over the last years, but residual transmission hotspots remain, supposedly fueled by forest workers and migrant populations. This study aimed to: (i) characterize the fine-scale mobility of forest-goers and understand links between their daily movement patterns and malaria transmission, using parasites detection via real time polymerase chain reaction (RT PCR) and the individual exposure to Anopheles bites by quantification of anti-Anopheles saliva antibodies via enzyme-linked immunosorbent assay; (ii) assess the concordance of questionnaires and Global Positioning System (GPS) data loggers for measuring mobility. METHODS Two 28 day follow-ups during dry and rainy seasons, including a GPS tracking, questionnaires and health examinations, were performed on male forest goers representing the population at highest risk of infection. Their time spent in different land use categories and demographic data were analyzed in order to understand the risk factors driving malaria in the study area. RESULTS Malaria risk varied with village forest cover and at a resolution of only a few kilometers: participants from villages outside the forest had the highest malaria prevalence compared to participants from forest fringe's villages. The time spent in a specific environment did not modulate the risk of malaria, in particular the time spent in forest was not associated with a higher probability to detect malaria among forest-goers. The levels of antibody response to Anopheles salivary peptide among participants were significantly higher during the rainy season, in accordance with Anopheles mosquito density variation, but was not affected by sociodemographic and mobility factors. The agreement between GPS and self-reported data was only 61.9% in reporting each kind of visited environment. CONCLUSIONS In a context of residual malaria transmission which was mainly depicted by P. vivax asymptomatic infections, the implementation of questionnaires, GPS data-loggers and quantification of anti-saliva Anopheles antibodies on the high-risk group were not powerful enough to detect malaria risk factors associated with different mobility behaviours or time spent in various environments. The joint implementation of GPS trackers and questionnaires allowed to highlight the limitations of both methodologies and the benefits of using them together. New detection and follow-up strategies are still called for.
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Affiliation(s)
- Anaïs Pepey
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia.
| | - Marc Souris
- UMR Unité des Virus Emergents, UVE: Aix-Marseille Univ-IRD 190-Inserm 1207-IHU 5 Méditerranée Infection, 13005, Marseille, France
| | - Saorin Kim
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
| | - Thomas Obadia
- Institut Pasteur, G5 Infectious Disease Epidemiology and Analytics, Université Paris Cité, 75015, Paris, France
- Institut Pasteur, Bioinformatics and Biostatistics Hub, Université Paris Cité, 75015, Paris, France
| | - Sophy Chy
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
| | - Malen Ea
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
| | - Sivkeng Ouk
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
| | - Franck Remoue
- UMR MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Siv Sovannaroth
- National Centre for Parasitology Entomology and Malaria Control (CNM), Phnom Penh 120 801, Phnom Penh, Cambodia
| | - Ivo Mueller
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, VIC, Australia
| | - Benoit Witkowski
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
- Genetic and Biology of Plasmodium Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
| | - Amélie Vantaux
- Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, 5 Blvd Monivong, Phnom Penh 120 210, Phnom Penh, BP983, Cambodia
- Genetic and Biology of Plasmodium Unit, Institut Pasteur de Madagascar, Antananarivo, Madagascar
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2
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetic metrics for inferring National Malaria Control Programme reported incidence in Senegal. Malar J 2024; 23:68. [PMID: 38443939 PMCID: PMC10916253 DOI: 10.1186/s12936-024-04897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/29/2024] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programmes (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. METHODS This study examined parasites from 3147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, a series of Poisson generalized linear mixed-effects models were constructed to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. RESULTS Model-predicted incidence was compared with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (< 10/1000/annual [‰]). CONCLUSIONS When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence > 10‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was < 10‰, many of the correlations between parasite genetics and incidence were reversed, which may reflect the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
- Wesley Wong
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Stephen F Schaffner
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Julie Thwing
- Malaria Branch, Division of Parasitic Diseases and Malaria, Global Health Center, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic, Thies, Senegal
| | - Medoune Ndiop
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Fatou Ba
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Ibrahima Diallo
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Doudou Sene
- Programme National de Lutte contre le Paludisme (PNLP), Dakar, Senegal
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Jessica Ribado
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua Suresh
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Albert Lee
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Katherine E Battle
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Joshua L Proctor
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Caitlin A Bever
- Institute for Disease Modeling at the Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Bronwyn MacInnis
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS), Dakar, Senegal
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Dyann F Wirth
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA
| | - Sarah K Volkman
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, The Broad Institute, Cambridge, MA, USA.
- College of Natural, Behavioral, and Health Sciences, Simmons University, Boston, MA, USA.
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3
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Holzschuh A, Ewnetu Y, Carlier L, Lerch A, Gerlovina I, Baker SC, Yewhalaw D, Haileselassie W, Berhane N, Lemma W, Koepfli C. Plasmodium falciparum transmission in the highlands of Ethiopia is driven by closely related and clonal parasites. Mol Ecol 2024; 33:e17292. [PMID: 38339833 DOI: 10.1111/mec.17292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 12/28/2023] [Accepted: 01/30/2024] [Indexed: 02/12/2024]
Abstract
Malaria cases are frequently recorded in the Ethiopian highlands even at altitudes above 2000 m. The epidemiology of malaria in the Ethiopian highlands, and, in particular, the role of importation by human migration from the highly endemic lowlands is not well understood. We sequenced 187 Plasmodium falciparum samples from two sites in the Ethiopian highlands, Gondar (n = 159) and Ziway (n = 28), using a multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug resistance loci. Here, we characterize the parasite population structure and genetic relatedness. We identify moderate parasite diversity (mean HE : 0.54) and low infection complexity (74.9% monoclonal). A significant percentage of infections share microhaplotypes, even across transmission seasons and sites, indicating persistent local transmission. We identify multiple clusters of clonal or near-clonal infections, highlighting high genetic relatedness. Only 6.3% of individuals diagnosed with P. falciparum reported recent travel. Yet, in clonal or near-clonal clusters, infections of travellers were frequently observed first in time, suggesting that parasites may have been imported and then transmitted locally. 31.1% of infections are pfhrp2-deleted and 84.4% pfhrp3-deleted, and 28.7% have pfhrp2/3 double deletions. Parasites with pfhrp2/3 deletions and wild-type parasites are genetically distinct. Mutations associated with resistance to sulphadoxine-pyrimethamine or suggested to reduce sensitivity to lumefantrine are observed at near-fixation. In conclusion, genomic data corroborate local transmission and the importance of intensified control in the Ethiopian highlands.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Yalemwork Ewnetu
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Lise Carlier
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
- Noul Inc., Seoul, Republic of Korea
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
| | - Inna Gerlovina
- Department of Medicine, Division of HIV, ID and Global Medicine, EPPIcenter Research Program, University of California, San Francisco, California, USA
| | - Sarah Cate Baker
- Trinity Centre for Global Health, Trinity College Dublin, Dublin, Ireland
| | - Delenasaw Yewhalaw
- Tropical and Infectious Disease Research Center, Jimma University, Jimma, Ethiopia
| | | | - Nega Berhane
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Wossenseged Lemma
- Department of Medical Biotechnology, University of Gondar, Gondar, Ethiopia
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana, USA
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4
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Connelly SV, Brazeau NF, Msellem M, Ngasala BE, Aydemir Ö, Goel V, Niaré K, Giesbrecht DJ, Popkin-Hall ZR, Hennelly CM, Park Z, Moormann AM, Ong'echa JM, Verity R, Mohammed S, Shija SJ, Mhamilawa LE, Morris U, Mårtensson A, Lin JT, Björkman A, Juliano JJ, Bailey JA. Strong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2023.02.15.23285960. [PMID: 36865135 PMCID: PMC9980253 DOI: 10.1101/2023.02.15.23285960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania, and continued local transmission. To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo District on the coastal mainland from 2016-2018. Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes. Our data support importation as a main source of genetic diversity and contribution to the parasite population on Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive for malaria reemergence due to susceptible hosts and competent vectors.
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Affiliation(s)
- Sean V Connelly
- MD-PhD Program, University of North Carolina, Chapel Hill, NC 27599
| | | | - Mwinyi Msellem
- Research Division, Ministry of Health, Zanzibar, Tanzania
| | - Billy E Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Özkan Aydemir
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, NC 27599
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - David J Giesbrecht
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
| | - Zachary R Popkin-Hall
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Christopher M Hennelly
- Institute for Global Health and Infectious Diseases, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Zackary Park
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Ann M Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA
| | | | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Imperial College, London
| | - Safia Mohammed
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Shija J Shija
- Zanzibar Malaria Elimination Program (ZAMEP), Zanzibar, Tanzania
| | - Lwidiko E Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Ulrika Morris
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Andreas Mårtensson
- Global Health and Migration Unit, Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Jessica T Lin
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
| | - Anders Björkman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Jonathan J Juliano
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599 USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, 27599 USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912 USA
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5
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Kebede AM, Sutanto E, Trimarsanto H, Benavente ED, Barnes M, Pearson RD, Siegel SV, Erko B, Assefa A, Getachew S, Aseffa A, Petros B, Lo E, Mohammed R, Yilma D, Rumaseb A, Nosten F, Noviyanti R, Rayner JC, Kwiatkowski DP, Price RN, Golassa L, Auburn S. Genomic analysis of Plasmodium vivax describes patterns of connectivity and putative drivers of adaptation in Ethiopia. Sci Rep 2023; 13:20788. [PMID: 38012191 PMCID: PMC10682486 DOI: 10.1038/s41598-023-47889-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 11/20/2023] [Indexed: 11/29/2023] Open
Abstract
Ethiopia has the greatest burden of Plasmodium vivax in Africa, but little is known about the epidemiological landscape of parasites across the country. We analysed the genomic diversity of 137 P. vivax isolates collected nine Ethiopian districts from 2012 to 2016. Signatures of selection were detected by cross-country comparisons with isolates from Thailand (n = 104) and Indonesia (n = 111), representing regions with low and high chloroquine resistance respectively. 26% (35/137) of Ethiopian infections were polyclonal, and 48.5% (17/35) of these comprised highly related clones (within-host identity-by-descent > 25%), indicating frequent co-transmission and superinfection. Parasite gene flow between districts could not be explained entirely by geographic distance, with economic and cultural factors hypothesised to have an impact on connectivity. Amplification of the duffy binding protein gene (pvdbp1) was prevalent across all districts (16-75%). Cross-population haplotype homozygosity revealed positive selection in a region proximal to the putative chloroquine resistance transporter gene (pvcrt-o). An S25P variant in amino acid transporter 1 (pvaat1), whose homologue has recently been implicated in P. falciparum chloroquine resistance evolution, was prevalent in Ethiopia (96%) but not Thailand or Indonesia (35-53%). The genomic architecture in Ethiopia highlights circulating variants of potential public health concern in an endemic setting with evidence of stable transmission.
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Affiliation(s)
| | | | - Hidayat Trimarsanto
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Ernest Diez Benavente
- Laboratory of Experimental Cardiology, Department of Cardiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Mariana Barnes
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
| | | | | | - Berhanu Erko
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Ashenafi Assefa
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- School of Public Health, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sisay Getachew
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
- Addis Ababa University, Addis Ababa, Ethiopia
- Millipore Sigma (Bioreliance), Rockville, USA
| | - Abraham Aseffa
- Armauer Hansen Research Unit (AHRI), Addis Ababa, Ethiopia
| | | | - Eugenia Lo
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, USA
| | | | - Daniel Yilma
- Jimma University Clinical Trial Unit, Department of Internal Medicine, Jimma University, Jimma, Ethiopia
| | - Angela Rumaseb
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
| | - Francois Nosten
- Shoklo Malaria Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | | | - Ric N Price
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Sarah Auburn
- Menzies School of Health Research and Charles Darwin University, Casuarina, PO Box 41096, Darwin, NT, 0811, Australia.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
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6
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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.
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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
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7
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Wong W, Schaffner SF, Thwing J, Seck MC, Gomis J, Diedhiou Y, Sy N, Ndiop M, Ba F, Diallo I, Sene D, Diallo MA, Ndiaye YD, Sy M, Sene A, Sow D, Dieye B, Tine A, Ribado J, Suresh J, Lee A, Battle KE, Proctor JL, Bever CA, MacInnis B, Ndiaye D, Hartl DL, Wirth DF, Volkman SK. Evaluating the performance of Plasmodium falciparum genetics for inferring National Malaria Control Program reported incidence in Senegal. RESEARCH SQUARE 2023:rs.3.rs-3516287. [PMID: 37961451 PMCID: PMC10635402 DOI: 10.21203/rs.3.rs-3516287/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Genetic surveillance of the Plasmodium falciparum parasite shows great promise for helping National Malaria Control Programs (NMCPs) assess parasite transmission. Genetic metrics such as the frequency of polygenomic (multiple strain) infections, genetic clones, and the complexity of infection (COI, number of strains per infection) are correlated with transmission intensity. However, despite these correlations, it is unclear whether genetic metrics alone are sufficient to estimate clinical incidence. Here, we examined parasites from 3,147 clinical infections sampled between the years 2012-2020 through passive case detection (PCD) across 16 clinic sites spread throughout Senegal. Samples were genotyped with a 24 single nucleotide polymorphism (SNP) molecular barcode that detects parasite strains, distinguishes polygenomic (multiple strain) from monogenomic (single strain) infections, and identifies clonal infections. To determine whether genetic signals can predict incidence, we constructed a series of Poisson generalized linear mixed-effects models to predict the incidence level at each clinical site from a set of genetic metrics designed to measure parasite clonality, superinfection, and co-transmission rates. We compared the model-predicted incidence with the reported standard incidence data determined by the NMCP for each clinic and found that parasite genetic metrics generally correlated with reported incidence, with departures from expected values at very low annual incidence (<10/1000/annual [‰]). When transmission is greater than 10 cases per 1000 annual parasite incidence (annual incidence >10 ‰), parasite genetics can be used to accurately infer incidence and is consistent with superinfection-based hypotheses of malaria transmission. When transmission was <10 ‰, we found that many of the correlations between parasite genetics and incidence were reversed, which we hypothesize reflects the disproportionate impact of importation and focal transmission on parasite genetics when local transmission levels are low.
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Affiliation(s)
| | | | | | - Mame Cheikh Seck
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jules Gomis
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Younouss Diedhiou
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Ngayo Sy
- Section de Lutte Anti-Parasitaire (SLAP) Clinic
| | | | - Fatou Ba
- Programme National de Lutte Contre le Paludisme
| | - Ibrahima Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Doudou Sene
- Programme National de Lutte Contre le Paludisme
| | - Mamadou Alpha Diallo
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Yaye Die Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Mouhamad Sy
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Aita Sene
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Djiby Sow
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Baba Dieye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Abdoulaye Tine
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
| | - Jessica Ribado
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Joshua Suresh
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Albert Lee
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Joshua L Proctor
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | - Caitlin A Bever
- Institute for Disease Modeling, Bill and Melinda Gates Foundation
| | | | - Daouda Ndiaye
- Centre International de recherche, de formation en Genomique Appliquee et de Surveillance Sanitaire (CIGASS)
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Haldar K, Alam MS, Koepfli C, Lobo NF, Phru CS, Islam MN, Faiz A, Khan WA, Haque R. Bangladesh in the era of malaria elimination. Trends Parasitol 2023; 39:760-773. [PMID: 37500334 DOI: 10.1016/j.pt.2023.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/06/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023]
Abstract
Bangladesh has dramatically reduced malaria by 93% from 2008 to 2020. The strategy has been district-wise, phased elimination; however, the last districts targeted for elimination include remote, forested regions which present several challenges for prevention, detection, and treatment of malaria. These districts border Myanmar which harbors Plasmodium falciparum malaria parasites resistant to artemisinins, key drugs used in artemisinin-based combination therapies (ACTs) that have been vital for control programs. Challenges in monitoring emergence of artemisinin resistance (AR), tracking parasite reservoirs, changes in vector behavior and responses to insecticides, as well as other environmental and host factors (including the migration of Forcibly Displaced Myanmar Nationals; FDMNs) may pose added hazards in the final phase of eliminating malaria in Bangladesh.
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Affiliation(s)
- Kasturi Haldar
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA.
| | - Mohammed Shafiul Alam
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | - Cristian Koepfli
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA
| | - Neil F Lobo
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, IN, USA; Eck Institute of Global Health, University of Notre Dame, Notre Dame, Indiana, IN, USA
| | - Ching Shwe Phru
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | | | - Abul Faiz
- Dev Care Foundation, Dhaka, Bangladesh
| | - Wasif Ali Khan
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
| | - Rashidul Haque
- Infectious Disease Division, International Center of Diarrheal Diseases, Bangladesh, (icddr, b), Dhaka, Bangladesh
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9
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Fakih BS, Holzschuh A, Ross A, Stuck L, Abdul R, Al-Mafazy AWH, Irema I, Mbena A, Thawer SG, Shija SJ, Aliy SM, Ali A, Fink G, Yukich J, Hetzel MW. Risk of imported malaria infections in Zanzibar: a cross-sectional study. Infect Dis Poverty 2023; 12:80. [PMID: 37641152 PMCID: PMC10464242 DOI: 10.1186/s40249-023-01129-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/11/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Zanzibar has made substantial progress in malaria control with vector control, improved diagnosis, and artemisinin-based combination therapy. Parasite prevalence in the population has remained around 1% but imported infections from mainland Tanzania contribute to sustained local transmission. Understanding travel patterns between mainland Tanzania and Zanzibar, and the risk of malaria infection, may help to control malaria importation to Zanzibar. METHODS A rolling cross-sectional survey linked to routine reactive case detection of malaria was carried out in Zanzibar between May 2017 and October 2018. Households of patients diagnosed with malaria at health facilities were surveyed and household members were tested for malaria using rapid diagnostic tests and a sub-sample by quantitative PCR (qPCR). Interviews elicited a detailed travel history of all household members who had travelled within the past two months, including trips within and outside of Zanzibar. We estimated the association of malaria infection with travel destinations in pre-defined malaria endemicity categories, trip duration, and other co-variates using logistic regression. RESULTS Of 17,891 survey participants, 1177 (7%) reported a recent trip, of which 769 (65%) visited mainland Tanzania. Among travellers to mainland Tanzania with travel destination details and a qPCR result available, 241/378 (64%) reported traveling to districts with a 'high' malaria endemicity and for 12% the highest endemicity category was 'moderate'. Travelers to the mainland were more likely to be infected with malaria parasites (29%, 108/378) than those traveling within Zanzibar (8%, 16/206) or to other countries (6%, 2/17). Among travellers to mainland Tanzania, those visiting highly endemic districts had a higher odds of being qPCR-positive than those who travelled only to districts where malaria-endemicity was classified as low or very low (adjusted odd ratio = 7.0, 95% confidence interval: 1.9-25.5). Among travellers to the mainland, 110/378 (29%) never or only sometimes used a mosquito net during their travel. CONCLUSIONS Strategies to reduce malaria importation to Zanzibar may benefit from identifying population groups traveling to highly endemic areas in mainland Tanzania. Targeted interventions to prevent and clear infections in these groups may be more feasible than attempting to screen and treat all travellers upon arrival in Zanzibar.
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Affiliation(s)
- Bakar S Fakih
- Ifakara Health Institute, Dar es Salaam, Tanzania.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Aurel Holzschuh
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Notre Dame, USA
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Logan Stuck
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | - Ramadhan Abdul
- Ifakara Health Institute, Dar es Salaam, Tanzania
- Amsterdam Institute for Global Health and Development, Amsterdam, Netherlands
| | | | - Imani Irema
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | | | - Sumaiyya G Thawer
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Shija J Shija
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Safia M Aliy
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Günther Fink
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Joshua Yukich
- Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
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10
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Holzschuh A, Lerch A, Gerlovina I, Fakih BS, Al-Mafazy AWH, Reaves EJ, Ali A, Abbas F, Ali MH, Ali MA, Hetzel MW, Yukich J, Koepfli C. Multiplexed ddPCR-amplicon sequencing reveals isolated Plasmodium falciparum populations amenable to local elimination in Zanzibar, Tanzania. Nat Commun 2023; 14:3699. [PMID: 37349311 PMCID: PMC10287761 DOI: 10.1038/s41467-023-39417-1] [Citation(s) in RCA: 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: 01/05/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
Zanzibar has made significant progress toward malaria elimination, but recent stagnation requires novel approaches. We developed a highly multiplexed droplet digital PCR (ddPCR)-based amplicon sequencing method targeting 35 microhaplotypes and drug-resistance loci, and successfully sequenced 290 samples from five districts covering both main islands. Here, we elucidate fine-scale Plasmodium falciparum population structure and infer relatedness and connectivity of infections using an identity-by-descent (IBD) approach. Despite high genetic diversity, we observe pronounced fine-scale spatial and temporal parasite genetic structure. Clusters of near-clonal infections on Pemba indicate persistent local transmission with limited parasite importation, presenting an opportunity for local elimination efforts. Furthermore, we observe an admixed parasite population on Unguja and detect a substantial fraction (2.9%) of significantly related infection pairs between Zanzibar and the mainland, suggesting recent importation. Our study provides a high-resolution view of parasite genetic structure across the Zanzibar archipelago and provides actionable insights for prioritizing malaria elimination efforts.
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Affiliation(s)
- Aurel Holzschuh
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
| | - Anita Lerch
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA
| | - Inna Gerlovina
- EPPIcenter Research Program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, CA, USA
| | - Bakar S Fakih
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Ifakara Health Institute, Dar es Salaam, United Republic of Tanzania
| | | | - Erik J Reaves
- U.S. Centers for Disease Control and Prevention, President's Malaria Initiative, Dar es Salaam, United Republic of Tanzania
| | - Abdullah Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Faiza Abbas
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Haji Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Mohamed Ali Ali
- Zanzibar Malaria Elimination Programme, Zanzibar, United Republic of Tanzania
| | - Manuel W Hetzel
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Joshua Yukich
- School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, University of Notre Dame, Indiana, IN, USA.
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11
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Li Y, Stewart K, Han KT, Han ZY, Aung PP, Thein ZW, Htay T, Chen D, Nyunt MM, Plowe CV. Understanding Spatiotemporal Human Mobility Patterns for Malaria Control Using a Multiagent Mobility Simulation Model. Clin Infect Dis 2023; 76:e867-e874. [PMID: 35851600 PMCID: PMC10169429 DOI: 10.1093/cid/ciac568] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND More details about human movement patterns are needed to evaluate relationships between daily travel and malaria risk at finer scales. A multiagent mobility simulation model was built to simulate the movements of villagers between home and their workplaces in 2 townships in Myanmar. METHODS An agent-based model (ABM) was built to simulate daily travel to and from work based on responses to a travel survey. Key elements for the ABM were land cover, travel time, travel mode, occupation, malaria prevalence, and a detailed road network. Most visited network segments for different occupations and for malaria-positive cases were extracted and compared. Data from a separate survey were used to validate the simulation. RESULTS Mobility characteristics for different occupation groups showed that while certain patterns were shared among some groups, there were also patterns that were unique to an occupation group. Forest workers were estimated to be the most mobile occupation group, and also had the highest potential malaria exposure associated with their daily travel in Ann Township. In Singu Township, forest workers were not the most mobile group; however, they were estimated to visit regions that had higher prevalence of malaria infection over other occupation groups. CONCLUSIONS Using an ABM to simulate daily travel generated mobility patterns for different occupation groups. These spatial patterns varied by occupation. Our simulation identified occupations at a higher risk of being exposed to malaria and where these exposures were more likely to occur.
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Affiliation(s)
- Yao Li
- Department of Geographical Sciences, Center for Geospatial Information Science, University of Maryland, College Park, Maryland, USA
| | - Kathleen Stewart
- Department of Geographical Sciences, Center for Geospatial Information Science, University of Maryland, College Park, Maryland, USA
| | - Kay Thwe Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar
| | - Zay Yar Han
- Department of Medical Research, Ministry of Health and Sports, Yangon, Myanmar.,Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Poe P Aung
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Zaw W Thein
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Thura Htay
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Dong Chen
- Department of Geographical Sciences, University of Maryland, College Park, Maryland, USA
| | - Myaing M Nyunt
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Christopher V Plowe
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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12
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Okmi M, Por LY, Ang TF, Ku CS. Mobile Phone Data: A Survey of Techniques, Features, and Applications. SENSORS (BASEL, SWITZERLAND) 2023; 23:s23020908. [PMID: 36679703 PMCID: PMC9865984 DOI: 10.3390/s23020908] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 05/27/2023]
Abstract
Due to the rapid growth in the use of smartphones, the digital traces (e.g., mobile phone data, call detail records) left by the use of these devices have been widely employed to assess and predict human communication behaviors and mobility patterns in various disciplines and domains, such as urban sensing, epidemiology, public transportation, data protection, and criminology. These digital traces provide significant spatiotemporal (geospatial and time-related) data, revealing people's mobility patterns as well as communication (incoming and outgoing calls) data, revealing people's social networks and interactions. Thus, service providers collect smartphone data by recording the details of every user activity or interaction (e.g., making a phone call, sending a text message, or accessing the internet) done using a smartphone and storing these details on their databases. This paper surveys different methods and approaches for assessing and predicting human communication behaviors and mobility patterns from mobile phone data and differentiates them in terms of their strengths and weaknesses. It also gives information about spatial, temporal, and call characteristics that have been extracted from mobile phone data and used to model how people communicate and move. We survey mobile phone data research published between 2013 and 2021 from eight main databases, namely, the ACM Digital Library, IEEE Xplore, MDPI, SAGE, Science Direct, Scopus, SpringerLink, and Web of Science. Based on our inclusion and exclusion criteria, 148 studies were selected.
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Affiliation(s)
- Mohammed Okmi
- Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur 50603, Malaysia
- Department of Information Technology and Security, Jazan University, Jazan 45142, Saudi Arabia
| | - Lip Yee Por
- Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Tan Fong Ang
- Faculty of Computer Science and Information Technology, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Chin Soon Ku
- Department of Computer Science, Universiti Tunku Abdul Rahman, Kampar 31900, Malaysia
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13
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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.
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14
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Brown TS, Robinson DA, Buckee CO, Mathema B. Connecting the dots: understanding how human mobility shapes TB epidemics. Trends Microbiol 2022; 30:1036-1044. [PMID: 35597716 PMCID: PMC10068677 DOI: 10.1016/j.tim.2022.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/18/2022] [Accepted: 04/19/2022] [Indexed: 01/13/2023]
Abstract
Tuberculosis (TB) remains a leading infectious cause of death worldwide. Reducing TB infections and TB-related deaths rests ultimately on stopping forward transmission from infectious to susceptible individuals. Critical to this effort is understanding how human host mobility shapes the transmission and dispersal of new or existing strains of Mycobacterium tuberculosis (Mtb). Important questions remain unanswered. What kinds of mobility, over what temporal and spatial scales, facilitate TB transmission? How do human mobility patterns influence the dispersal of novel Mtb strains, including emergent drug-resistant strains? This review summarizes the current state of knowledge on mobility and TB epidemic dynamics, using examples from three topic areas, including inference of genetic and spatial clustering of infections, delineating source-sink dynamics, and mapping the dispersal of novel TB strains, to examine scientific questions and methodological issues within this topic. We also review new data sources for measuring human mobility, including mobile phone-associated movement data, and discuss important limitations on their use in TB epidemiology.
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Affiliation(s)
- Tyler S Brown
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Infectious Diseases Division, Massachusetts General Hospital, Boston, MA, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, MS, USA
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
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15
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Arisco NJ, Peterka C, Castro MC. Imported malaria definition and minimum data for surveillance. Sci Rep 2022; 12:17982. [PMID: 36289250 PMCID: PMC9605982 DOI: 10.1038/s41598-022-22590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 10/17/2022] [Indexed: 01/24/2023] Open
Abstract
The mobility of malaria-infected individuals poses challenges to elimination campaigns by way of spreading parasite drug resistance, straining country-to-country collaboration, and making routine data collection difficult, especially in resource-poor settings. Nevertheless, no concerted effort has been made to develop a common framework to define the spatial and temporal components of an imported malaria case and recommend the minimum data needed to identify it. We conducted a scoping review of imported malaria literature from 2010 to 2020 which showed that definitions vary widely, and local capabilities of detecting importation are often restricted in low-income countries. Following this, we propose a common definition for imported malaria and the minimum data required to identify a case, depending on the country's capability of conducting an epidemiological investigation. Lastly, we utilize the proposed definition using data from Brazil to demonstrate both the feasibility and the importance of tracking imported cases. The case of Brazil highlights the capabilities of regular surveillance systems to monitor importation, but also the need to regularly use these data for informing local responses. Supporting countries to use regularly collected data and adopt a common definition is paramount to tackling the importation of malaria cases and achieving elimination goals set forth by the World Health Organization.
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Affiliation(s)
- Nicholas J Arisco
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Cassio Peterka
- Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, DF, Brazil
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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16
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Gerlovina I, Gerlovin B, Rodríguez-Barraquer I, Greenhouse B. Dcifer: an IBD-based method to calculate genetic distance between polyclonal infections. Genetics 2022; 222:6674513. [PMID: 36000888 PMCID: PMC9526043 DOI: 10.1093/genetics/iyac126] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/04/2022] [Indexed: 11/23/2022] Open
Abstract
An essential step toward reconstructing pathogen transmission and answering epidemiologically relevant questions from genomic data is obtaining pairwise genetic distance between infections. For recombining organisms such as malaria parasites, relatedness measures quantifying recent shared ancestry would provide a meaningful distance, suggesting methods based on identity by descent (IBD). While the concept of relatedness and consequently an IBD approach is fairly straightforward for individual parasites, the distance between polyclonal infections, which are prevalent in malaria, presents specific challenges, and awaits a general solution that could be applied to infections of any clonality and accommodate multiallelic (e.g. microsatellite or microhaplotype) and biallelic [single nucleotide polymorphism (SNP)] data. Filling this methodological gap, we present Dcifer (Distance for complex infections: fast estimation of relatedness), a method for calculating genetic distance between polyclonal infections, which is designed for unphased data, explicitly accounts for population allele frequencies and complexity of infection, and provides reliable inference. Dcifer’s IBD-based framework allows us to define model parameters that represent interhost relatedness and to propose corresponding estimators with attractive statistical properties. By using combinatorics to account for unobserved phased haplotypes, Dcifer is able to quickly process large datasets and estimate pairwise relatedness along with measures of uncertainty. We show that Dcifer delivers accurate and interpretable results and detects related infections with statistical power that is 2–4 times greater than that of approaches based on identity by state. Applications to real data indicate that relatedness structure aligns with geographic locations. Dcifer is implemented in a comprehensive publicly available software package.
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Affiliation(s)
- Inna Gerlovina
- EPPIcenter research program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Boris Gerlovin
- EPPIcenter research program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Isabel Rodríguez-Barraquer
- EPPIcenter research program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Bryan Greenhouse
- EPPIcenter research program, Division of HIV, ID and Global Medicine, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
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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.
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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
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18
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Carrasco-Escobar G, Matta-Chuquisapon J, Manrique E, Ruiz-Cabrejos J, Barboza JL, Wong D, Henostroza G, Llanos-Cuentas A, Benmarhnia T. Quantifying the effect of human population mobility on malaria risk in the Peruvian Amazon. ROYAL SOCIETY OPEN SCIENCE 2022; 9:211611. [PMID: 35875474 PMCID: PMC9297009 DOI: 10.1098/rsos.211611] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
The impact of human population movement (HPM) on the epidemiology of vector-borne diseases, such as malaria, has been described. However, there are limited data on the use of new technologies for the study of HPM in endemic areas with difficult access such as the Amazon. In this study conducted in rural Peruvian Amazon, we used self-reported travel surveys and GPS trackers coupled with a Bayesian spatial model to quantify the role of HPM on malaria risk. By using a densely sampled population cohort, this study highlighted the elevated malaria transmission in a riverine community of the Peruvian Amazon. We also found that the high connectivity between Amazon communities for reasons such as work, trading or family plausibly sustains such transmission levels. Finally, by using multiple human mobility metrics including GPS trackers, and adapted causal inference methods we identified for the first time the effect of human mobility patterns on malaria risk in rural Peruvian Amazon. This study provides evidence of the causal effect of HPM on malaria that may help to adapt current malaria control programmes in the Amazon.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Jose Matta-Chuquisapon
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Edgar Manrique
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jorge Ruiz-Cabrejos
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Jose Luis Barboza
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Daniel Wong
- Health Innovation Lab, Institute of Tropical Medicine ‘Alexander von Humboldt’, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Alejandro Llanos-Cuentas
- Instituto de Medicinal Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Tarik Benmarhnia
- Scripps Institution of Oceanography, University of California, San Diego, CA, USA
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19
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Baird JK, Warsame M, Recht J. Survey and Analysis of Chemoprophylaxis Policies for Domestic Travel in Malaria-Endemic Countries. Trop Med Infect Dis 2022; 7:tropicalmed7070121. [PMID: 35878133 PMCID: PMC9325288 DOI: 10.3390/tropicalmed7070121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/23/2022] [Accepted: 05/31/2022] [Indexed: 02/04/2023] Open
Abstract
The prevention of malaria in travelers with the use of antimalarials often occurs in connection with international travel to areas of significant risk of infection. Although these travelers sometimes cause outbreaks in their malaria-free home countries, the cardinal objective of prescribed chemoprophylaxis is to protect the traveler from patent malaria during travel. Here we consider the chemoprophylaxis of domestic travelers from malaria-free but -receptive areas within malaria-endemic countries. The main objective in this setting is the protection of those areas from reintroduced malaria transmission. In order to better understand policy and practices in this regard, we surveyed malaria prevention and treatment guidelines of 36 malaria-endemic countries and 2 that have recently eliminated malaria (Sri Lanka, China) for recommendations regarding malaria chemoprophylaxis for domestic travel. Among them, just 8 provided specific and positive recommendations, 1 recommended without specific guidance, and 4 advised against the practice. Most nations (25/38; 66%) did not mention chemoprophylaxis for domestic travel, though many of those did offer guidance for international travel. The few positive recommendations for domestic travel were dominated by the suppressive prophylaxis options of daily doxycycline or atovaquone-proguanil or weekly mefloquine. The incomplete protection afforded by these strategies, along with impractical dosing in connection with the typically brief domestic travel, may in part explain the broad lack of policies and practices across malaria-endemic nations regarding chemoprophylaxis.
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Affiliation(s)
- John Kevin Baird
- Eijkman-Oxford Clinical Research Unit, Eijkman Institute of Molecular Biology, Jakarta 10430, Indonesia
- The Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
- Correspondence:
| | - Marian Warsame
- School of Public Health and Social Medicine, Institute of Medicine, Gothenburg University, 41390 Gothenburg, Sweden;
| | - Judith Recht
- Independent Researcher, North Bethesda, MD 20852, USA;
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20
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Berry I, Rahman M, Flora MS, Shirin T, Alamgir ASM, Khan MH, Anwar R, Lisa M, Chowdhury F, Islam MA, Osmani MG, Dunkle S, Brum E, Greer AL, Morris SK, Mangtani P, Fisman DN. Seasonality of influenza and coseasonality with avian influenza in Bangladesh, 2010–19: a retrospective, time-series analysis. Lancet Glob Health 2022; 10:e1150-e1158. [DOI: 10.1016/s2214-109x(22)00212-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/22/2022] [Accepted: 04/11/2022] [Indexed: 10/18/2022]
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21
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LaVerriere E, Schwabl P, Carrasquilla M, Taylor AR, Johnson ZM, Shieh M, Panchal R, Straub TJ, Kuzma R, Watson S, Buckee CO, Andrade CM, Portugal S, Crompton PD, Traore B, Rayner JC, Corredor V, James K, Cox H, Early AM, MacInnis BL, Neafsey DE. Design and implementation of multiplexed amplicon sequencing panels to serve genomic epidemiology of infectious disease: a malaria case study. Mol Ecol Resour 2022; 22:2285-2303. [PMID: 35437908 DOI: 10.1111/1755-0998.13622] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022]
Abstract
Multiplexed PCR amplicon sequencing (AmpSeq) is an increasingly popular application for cost-effective monitoring of threatened species and managed wildlife populations, and shows strong potential for genomic epidemiology of infectious disease. AmpSeq data from infectious microbes can inform disease control in multiple ways, including measuring drug resistance marker prevalence, distinguishing imported from local cases, and determining the effectiveness of therapeutics. We describe the design and comparative evaluation of two new AmpSeq assays for Plasmodium falciparum malaria parasites: a four-locus panel ('4CAST') composed of highly diverse antigens, and a 129-locus panel ('AMPLseq') composed of drug resistance markers, highly diverse loci for inferring relatedness, and a locus to detect Plasmodium vivax co-infection. We explore the performance of each panel in various public health use cases with in silico simulations as well as empirical experiments. The 4CAST panel appears highly suitable for evaluating the number of distinct parasite strains within samples (complexity of infection), showing strong performance across a wide range of parasitemia levels without a DNA pre-amplification step. For relatedness inference, the larger AMPLseq panel performs similarly to two existing panels of comparable size, despite differences in the data and approach used for designing each panel. Finally, we describe an R package (paneljudge) that facilitates the design and comparative evaluation of genetic panels for relatedness estimation, and we provide general guidance on the design and implementation of AmpSeq panels for genomic epidemiology of infectious disease.
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Affiliation(s)
- Emily LaVerriere
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Max Planck Institute for Infection Biology, Berlin, Germany
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Zachary M Johnson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Meg Shieh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ruchit Panchal
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Timothy J Straub
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Rebecca Kuzma
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Sean Watson
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Caroline O Buckee
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Carolina M Andrade
- Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Silvia Portugal
- Max Planck Institute for Infection Biology, Berlin, Germany.,Centre of Infectious Diseases, Parasitology, Heidelberg University Hospital, Heidelberg, Germany
| | - Peter D Crompton
- Malaria Infection Biology and Immunity Section, Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, 20852, USA
| | - Boubacar Traore
- Mali International Center of Excellence in Research, University of Sciences, Technique and Technology of Bamako, BP 1805, Point G, Bamako, Mali
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Kashana James
- Guyana National Malaria Control Program, Ministry of Health, 0592, Georgetown, Guyana
| | - Horace Cox
- Guyana Vector Control Services, Ministry of Health, 0592, Georgetown, Guyana
| | - Angela M Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - 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 of MIT and Harvard, Cambridge, MA, USA
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22
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Huber JH, Hsiang MS, Dlamini N, Murphy M, Vilakati S, Nhlabathi N, Lerch A, Nielsen R, Ntshalintshali N, Greenhouse B, Perkins TA. Inferring person-to-person networks of Plasmodium falciparum transmission: are analyses of routine surveillance data up to the task? Malar J 2022; 21:58. [PMID: 35189905 PMCID: PMC8860266 DOI: 10.1186/s12936-022-04072-2] [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: 07/17/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Inference of person-to-person transmission networks using surveillance data is increasingly used to estimate spatiotemporal patterns of pathogen transmission. Several data types can be used to inform transmission network inferences, yet the sensitivity of those inferences to different data types is not routinely evaluated. METHODS The influence of different combinations of spatial, temporal, and travel-history data on transmission network inferences for Plasmodium falciparum malaria were evaluated. RESULTS The information content of these data types may be limited for inferring person-to-person transmission networks and may lead to an overestimate of transmission. Only when outbreaks were temporally focal or travel histories were accurate was the algorithm able to accurately estimate the reproduction number under control, Rc. Applying this approach to data from Eswatini indicated that inferences of Rc and spatiotemporal patterns therein depend upon the choice of data types and assumptions about travel-history data. CONCLUSIONS These results suggest that transmission network inferences made with routine malaria surveillance data should be interpreted with caution.
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Affiliation(s)
- John H Huber
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
| | - Michelle S Hsiang
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Malaria Elimination Initiative, Global Health Group, University of California, San Francisco, CA, USA.,Department of Pediatrics, University of California, San Francisco,, CA, USA
| | - Nomcebo Dlamini
- National Malaria Elimination Programme, Ministry of Health, Manzini, Eswatini
| | - Maxwell Murphy
- Department of Medicine, University of California, San Francisco, CA, USA
| | | | - Nomcebo Nhlabathi
- National Malaria Elimination Programme, Ministry of Health, Manzini, Eswatini
| | - Anita Lerch
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Rasmus Nielsen
- Department of Integrative Biology and Statistics, University of California, Berkeley, CA, USA
| | | | - Bryan Greenhouse
- Department of Medicine, University of California, San Francisco, CA, USA.,Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - T Alex Perkins
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA.
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23
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Gumbo A, Topazian HM, Mwanza A, Mitchell CL, Puerto-Meredith S, Njiko R, Kayange M, Mwalilino D, Mvula B, Tegha G, Mvalo T, Hoffman I, Juliano JJ. Occurrence and Distribution of Nonfalciparum Malaria Parasite Species Among Adolescents and Adults in Malawi. J Infect Dis 2022; 225:257-268. [PMID: 34244739 PMCID: PMC8763954 DOI: 10.1093/infdis/jiab353] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 07/08/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Plasmodium falciparum malaria dominates throughout sub-Saharan Africa, but the prevalence of Plasmodium malariae, Plasmodium ovale spp., and Plasmodium vivax increasingly contribute to infection in countries that control malaria using P. falciparum-specific diagnostic and treatment strategies. METHODS We performed quantitative polymerase chain reaction (qPCR) on 2987 dried blood spots from the 2015-2016 Malawi Demographic and Health Survey to identify presence and distribution of nonfalciparum infection. Bivariate models were used to determine species-specific associations with demographic and environmental risk factors. RESULTS Nonfalciparum infections had broad spatial distributions. Weighted prevalence was 0.025 (SE, 0.004) for P. malariae, 0.097 (SE, 0.008) for P. ovale spp., and 0.001 (SE, 0.0005) for P. vivax. Most infections (85.6%) had low-density parasitemias ≤ 10 parasites/µL, and 66.7% of P. malariae, 34.6% of P. ovale spp., and 40.0% of P. vivax infections were coinfected with P. falciparum. Risk factors for P. malariae were like those known for P. falciparum; however, there were few risk factors recognized for P. ovale spp. and P. vivax, perhaps due to the potential for relapsing episodes. CONCLUSIONS The prevalence of any nonfalciparum infection was 11.7%, with infections distributed across Malawi. Continued monitoring of Plasmodium spp. becomes critical as nonfalciparum infections become important sources of ongoing transmission.
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Affiliation(s)
- Austin Gumbo
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | - Hillary M Topazian
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexis Mwanza
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Cedar L Mitchell
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Sydney Puerto-Meredith
- Department of Epidemiology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Ruth Njiko
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Michael Kayange
- National Malaria Control Programme, Malawi Ministry of Health, Lilongwe, Malawi
| | - David Mwalilino
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Bernard Mvula
- National HIV Reference Laboratory, Malawi Ministry of Health, Lilongwe, Malawi
| | - Gerald Tegha
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - Tisungane Mvalo
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Irving Hoffman
- University of North Carolina Project-Malawi, Lilongwe, Malawi
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
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24
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Markwalter CF, Menya D, Wesolowski A, Esimit D, Lokoel G, Kipkoech J, Freedman E, Sumner KM, Abel L, Ambani G, Meredith HR, Taylor SM, Obala AA, O'Meara WP. Plasmodium falciparum importation does not sustain malaria transmission in a semi-arid region of Kenya. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000807. [PMID: 36962553 PMCID: PMC10021402 DOI: 10.1371/journal.pgph.0000807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/17/2022] [Indexed: 11/19/2022]
Abstract
Human movement impacts the spread and transmission of infectious diseases. Recently, a large reservoir of Plasmodium falciparum malaria was identified in a semi-arid region of northwestern Kenya historically considered unsuitable for malaria transmission. Understanding the sources and patterns of transmission attributable to human movement would aid in designing and targeting interventions to decrease the unexpectedly high malaria burden in the region. Toward this goal, polymorphic parasite genes (ama1, csp) in residents and passengers traveling to Central Turkana were genotyped by amplicon deep sequencing. Genotyping and epidemiological data were combined to assess parasite importation. The contribution of travel to malaria transmission was estimated by modelling case reproductive numbers inclusive and exclusive of travelers. P. falciparum was detected in 6.7% (127/1891) of inbound passengers, including new haplotypes which were later detected in locally-transmitted infections. Case reproductive numbers approximated 1 and did not change when travelers were removed from transmission networks, suggesting that transmission is not fueled by travel to the region but locally endemic. Thus, malaria is not only prevalent in Central Turkana but also sustained by local transmission. As such, interrupting importation is unlikely to be an effective malaria control strategy on its own, but targeting interventions locally has the potential to drive down transmission.
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Affiliation(s)
| | - Diana Menya
- School of Public Health, Moi University College of Health Sciences, Eldoret, Kenya
| | - Amy Wesolowski
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Daniel Esimit
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Gilchrist Lokoel
- Department of Health Services and Sanitation, Turkana County, Kenya
| | - Joseph Kipkoech
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Elizabeth Freedman
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Kelsey M Sumner
- Duke University School of Medicine, Durham, North Carolina, United States of America
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Lucy Abel
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - George Ambani
- Academic Model Providing Access to Healthcare, Eldoret, Kenya
| | - Hannah R Meredith
- Duke Global Health Institute, Durham, North Carolina, United States of America
| | - Steve M Taylor
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Andrew A Obala
- School of Medicine, Moi University College of Health Sciences, Eldoret, Kenya
| | - Wendy P O'Meara
- Duke Global Health Institute, Durham, North Carolina, United States of America
- Duke University School of Medicine, Durham, North Carolina, United States of America
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25
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Brown TS, Arogbokun O, Buckee CO, Chang HH. Distinguishing gene flow between malaria parasite populations. PLoS Genet 2021; 17:e1009335. [PMID: 34928954 PMCID: PMC8726502 DOI: 10.1371/journal.pgen.1009335] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/04/2022] [Accepted: 10/12/2021] [Indexed: 11/19/2022] Open
Abstract
Measuring gene flow between malaria parasite populations in different geographic locations can provide strategic information for malaria control interventions. Multiple important questions pertaining to the design of such studies remain unanswered, limiting efforts to operationalize genomic surveillance tools for routine public health use. This report examines the use of population-level summaries of genetic divergence (FST) and relatedness (identity-by-descent) to distinguish levels of gene flow between malaria populations, focused on field-relevant questions about data size, sampling, and interpretability of observations from genomic surveillance studies. To do this, we use P. falciparum whole genome sequence data and simulated sequence data approximating malaria populations evolving under different current and historical epidemiological conditions. We employ mobile-phone associated mobility data to estimate parasite migration rates over different spatial scales and use this to inform our analysis. This analysis underscores the complementary nature of divergence- and relatedness-based metrics for distinguishing gene flow over different temporal and spatial scales and characterizes the data requirements for using these metrics in different contexts. Our results have implications for the design and implementation of malaria genomic surveillance studies. Malaria is a leading infectious cause of illness and death worldwide. Understanding how malaria parasites are spread between different geographic locations can provide useful information for disease control efforts. Examples include identifying source locations for imported infections in lower-incidence “sink” locations and delineating the routes over which drug-resistant malaria strains disperse across geographic space. Genomic surveillance methods use geolocated genetic sequence data from malaria infections to estimate gene flow and connectivity between parasites populations in different locations. This approach has yielded important insights into patterns of connectivity between malaria populations over local, national, and global scales. However, there are multiple unresolved questions about the design and interpretation of these studies. This study evaluates how much data is needed to distinguish different levels of gene flow between parasite populations (“Are the malaria populations in locations i and j linked by higher or lower connectivity than those in locations k and l?”). We examine data size requirements (including the number of genetic markers and number of individual infections analyzed) for this important, implementation-relevant task across multiple epidemiological scenarios, providing practical guidance for the design and interpretation of similar studies.
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Affiliation(s)
- Tyler S. Brown
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Diseases Division, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail: (TSB); (H-HC)
| | - Olufunmilayo Arogbokun
- Infectious Disease Epidemiology and Ecology Lab, University of North Carolina School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Caroline O. Buckee
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Hsiao-Han Chang
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu City, Taiwan
- * E-mail: (TSB); (H-HC)
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26
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Chang HH, Chang MC, Kiang M, Mahmud AS, Ekapirat N, Engø-Monsen K, Sudathip P, Buckee CO, Maude RJ. Low parasite connectivity among three malaria hotspots in Thailand. Sci Rep 2021; 11:23348. [PMID: 34857842 PMCID: PMC8640040 DOI: 10.1038/s41598-021-02746-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 11/17/2021] [Indexed: 12/25/2022] Open
Abstract
Identifying sources and sinks of malaria transmission is critical for designing effective intervention strategies particularly as countries approach elimination. The number of malaria cases in Thailand decreased 90% between 2012 and 2020, yet elimination has remained a major public health challenge with persistent transmission foci and ongoing importation. There are three main hotspots of malaria transmission in Thailand: Ubon Ratchathani and Sisaket in the Northeast; Tak in the West; and Yala in the South. However, the degree to which these hotspots are connected via travel and importation has not been well characterized. Here, we develop a metapopulation model parameterized by mobile phone call detail record data to estimate parasite flow among these regions. We show that parasite connectivity among these regions was limited, and that each of these provinces independently drove the malaria transmission in nearby provinces. Overall, our results suggest that due to the low probability of domestic importation between the transmission hotspots, control and elimination strategies can be considered separately for each region.
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Affiliation(s)
- Hsiao-Han Chang
- grid.38348.340000 0004 0532 0580Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Meng-Chun Chang
- grid.38348.340000 0004 0532 0580Institute of Bioinformatics and Structural Biology and Department of Life Science, National Tsing Hua University, Hsinchu, Taiwan
| | - Mathew Kiang
- grid.168010.e0000000419368956Department of Epidemiology and Population Health, Stanford University, Stanford, CA USA
| | - Ayesha S. Mahmud
- grid.47840.3f0000 0001 2181 7878Department of Demography, University of California, Berkeley, USA
| | - Nattwut Ekapirat
- grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Prayuth Sudathip
- grid.415836.d0000 0004 0576 2573Division of Vector Borne Diseases, Ministry of Public Health, Nonthaburi, Thailand
| | - Caroline O. Buckee
- grid.38142.3c000000041936754XHarvard TH Chan School of Public Health, Harvard University, Boston, USA
| | - Richard J. Maude
- grid.10223.320000 0004 1937 0490Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand ,grid.38142.3c000000041936754XHarvard TH Chan School of Public Health, Harvard University, Boston, USA ,grid.4991.50000 0004 1936 8948Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
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27
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Schwabl P, Neafsey DE. Molecular surveillance of malaria scales up. Trends Parasitol 2021; 37:1020-1021. [PMID: 34625343 DOI: 10.1016/j.pt.2021.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 09/25/2021] [Indexed: 11/26/2022]
Abstract
Parasite and vector genetic data can guide malaria control, and technological advances are enabling more informative genetic data generation at unprecedented scales. Jacob et al. employ multiplexed amplicon sequencing to profile parasite genetic diversity from thousands of malaria samples, illuminating spatiotemporal patterns of drug resistance to inform regional drug policy change.
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Affiliation(s)
- Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - 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 of MIT and Harvard, Cambridge, MA, USA.
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28
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Citron DT, Guerra CA, García GA, Wu SL, Battle KE, Gibson HS, Smith DL. Quantifying malaria acquired during travel and its role in malaria elimination on Bioko Island. Malar J 2021; 20:359. [PMID: 34461902 PMCID: PMC8404405 DOI: 10.1186/s12936-021-03893-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 08/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Malaria elimination is the goal for Bioko Island, Equatorial Guinea. Intensive interventions implemented since 2004 have reduced prevalence, but progress has stalled in recent years. A challenge for elimination has been malaria infections in residents acquired during travel to mainland Equatorial Guinea. The present article quantifies how off-island contributes to remaining malaria prevalence on Bioko Island, and investigates the potential role of a pre-erythrocytic vaccine in making further progress towards elimination. METHODS Malaria transmission on Bioko Island was simulated using a model calibrated based on data from the Malaria Indicator Surveys (MIS) from 2015 to 2018, including detailed travel histories and malaria positivity by rapid-diagnostic tests (RDTs), as well as geospatial estimates of malaria prevalence. Mosquito population density was adjusted to fit local transmission, conditional on importation rates under current levels of control and within-island mobility. The simulations were then used to evaluate the impact of two pre-erythrocytic vaccine distribution strategies: mass treat and vaccinate, and prophylactic vaccination for off-island travellers. Lastly, a sensitivity analysis was performed through an ensemble of simulations fit to the Bayesian joint posterior probability distribution of the geospatial prevalence estimates. RESULTS The simulations suggest that in Malabo, an urban city containing 80% of the population, there are some pockets of residual transmission, but a large proportion of infections are acquired off-island by travellers to the mainland. Outside of Malabo, prevalence was mainly attributable to local transmission. The uncertainty in the local transmission vs. importation is lowest within Malabo and highest outside. Using a pre-erythrocytic vaccine to protect travellers would have larger benefits than using the vaccine to protect residents of Bioko Island from local transmission. In simulations, mass treatment and vaccination had short-lived benefits, as malaria prevalence returned to current levels as the vaccine's efficacy waned. Prophylactic vaccination of travellers resulted in longer-lasting reductions in prevalence. These projections were robust to underlying uncertainty in prevalence estimates. CONCLUSIONS The modelled outcomes suggest that the volume of malaria cases imported from the mainland is a partial driver of continued endemic malaria on Bioko Island, and that continued elimination efforts on must account for human travel activity.
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Affiliation(s)
- Daniel T Citron
- Institute for Health Metrics and Evaluation, University of Washington, Population Health Building/Hans Rosling Center, 3980 15th Ave NE, Seattle, WA, 98195, USA.
| | - Carlos A Guerra
- Medical Care Development International, 8401 Colesville Road Suite 425, Silver Spring, MD, 20910, USA
| | - Guillermo A García
- Medical Care Development International, 8401 Colesville Road Suite 425, Silver Spring, MD, 20910, USA
| | - Sean L Wu
- Division of Epidemiology and Biostatistics, University of California, 2121 Berkeley Way, Berkeley, CA, 94720, USA
| | - Katherine E Battle
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, 15 Hospital Avenue, WA, 6009, Nedlands, Australia
- Institute for Disease Modeling, 500 5th Ave N, Seattle, WA, 98109, USA
| | - Harry S Gibson
- Malaria Atlas Project, Telethon Kids Institute, Perth Children's Hospital, 15 Hospital Avenue, WA, 6009, Nedlands, Australia
| | - David L Smith
- Institute for Health Metrics and Evaluation, University of Washington, Population Health Building/Hans Rosling Center, 3980 15th Ave NE, Seattle, WA, 98195, USA
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29
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Jacob CG, Thuy-Nhien N, Mayxay M, Maude RJ, Quang HH, Hongvanthong B, Vanisaveth V, Ngo Duc T, Rekol H, van der Pluijm R, von Seidlein L, Fairhurst R, Nosten F, Hossain MA, Park N, Goodwin S, Ringwald P, Chindavongsa K, Newton P, Ashley E, Phalivong S, Maude R, Leang R, Huch C, Dong LT, Nguyen KT, Nhat TM, Hien TT, Nguyen H, Zdrojewski N, Canavati S, Sayeed AA, Uddin D, Buckee C, Fanello CI, Onyamboko M, Peto T, Tripura R, Amaratunga C, Myint Thu A, Delmas G, Landier J, Parker DM, Chau NH, Lek D, Suon S, Callery J, Jittamala P, Hanboonkunupakarn B, Pukrittayakamee S, Phyo AP, Smithuis F, Lin K, Thant M, Hlaing TM, Satpathi P, Satpathi S, Behera PK, Tripura A, Baidya S, Valecha N, Anvikar AR, Ul Islam A, Faiz A, Kunasol C, Drury E, Kekre M, Ali M, Love K, Rajatileka S, Jeffreys AE, Rowlands K, Hubbart CS, Dhorda M, Vongpromek R, Kotanan N, Wongnak P, Almagro Garcia J, Pearson RD, Ariani CV, Chookajorn T, Malangone C, Nguyen T, Stalker J, Jeffery B, Keatley J, Johnson KJ, Muddyman D, Chan XHS, Sillitoe J, Amato R, Simpson V, Gonçalves S, Rockett K, Day NP, Dondorp AM, Kwiatkowski DP, Miotto O. Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination. eLife 2021; 10:e62997. [PMID: 34372970 PMCID: PMC8354633 DOI: 10.7554/elife.62997] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 06/30/2021] [Indexed: 02/04/2023] Open
Abstract
Background National Malaria Control Programmes (NMCPs) currently make limited use of parasite genetic data. We have developed GenRe-Mekong, a platform for genetic surveillance of malaria in the Greater Mekong Subregion (GMS) that enables NMCPs to implement large-scale surveillance projects by integrating simple sample collection procedures in routine public health procedures. Methods Samples from symptomatic patients are processed by SpotMalaria, a high-throughput system that produces a comprehensive set of genotypes comprising several drug resistance markers, species markers and a genomic barcode. GenRe-Mekong delivers Genetic Report Cards, a compendium of genotypes and phenotype predictions used to map prevalence of resistance to multiple drugs. Results GenRe-Mekong has worked with NMCPs and research projects in eight countries, processing 9623 samples from clinical cases. Monitoring resistance markers has been valuable for tracking the rapid spread of parasites resistant to the dihydroartemisinin-piperaquine combination therapy. In Vietnam and Laos, GenRe-Mekong data have provided novel knowledge about the spread of these resistant strains into previously unaffected provinces, informing decision-making by NMCPs. Conclusions GenRe-Mekong provides detailed knowledge about drug resistance at a local level, and facilitates data sharing at a regional level, enabling cross-border resistance monitoring and providing the public health community with valuable insights. The project provides a rich open data resource to benefit the entire malaria community. Funding The GenRe-Mekong project is funded by the Bill and Melinda Gates Foundation (OPP11188166, OPP1204268). Genotyping and sequencing were funded by the Wellcome Trust (098051, 206194, 203141, 090770, 204911, 106698/B/14/Z) and Medical Research Council (G0600718). A proportion of samples were collected with the support of the UK Department for International Development (201900, M006212), and Intramural Research Program of the National Institute of Allergy and Infectious Diseases.
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Affiliation(s)
| | | | - Mayfong Mayxay
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Institute of Research and Education Development (IRED), University of Health Sciences, Ministry of HealthVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Richard J Maude
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Huynh Hong Quang
- Institute of Malariology, Parasitology and Entomology (IMPE-QN)Quy NhonViet Nam
| | - Bouasy Hongvanthong
- Centre of Malariology, Parasitology, and EntomologyVientianeLao People's Democratic Republic
| | - Viengxay Vanisaveth
- Centre of Malariology, Parasitology, and EntomologyVientianeLao People's Democratic Republic
| | - Thang Ngo Duc
- National Institute of Malariology, Parasitology and Entomology (NIMPE)HanoiViet Nam
| | - Huy Rekol
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Rob van der Pluijm
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Lorenz von Seidlein
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Rick Fairhurst
- National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - François Nosten
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | | | - Naomi Park
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | | | | | - Paul Newton
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Elizabeth Ashley
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
| | - Sonexay Phalivong
- Lao-Oxford-Mahosot Hospital-Wellcome Research Unit (LOMWRU), Microbiology Laboratory, Mahosot HospitalVientianeLao People's Democratic Republic
| | - Rapeephan Maude
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Faculty of Medicine, Ramathibodi Hospital, Mahidol UniversityBangkokThailand
| | - Rithea Leang
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Cheah Huch
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Le Thanh Dong
- Institute of Malariology, Parasitology and Entomology (IMPEHCM)Ho Chi Minh CityViet Nam
| | - Kim-Tuyen Nguyen
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tran Minh Nhat
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | - Tran Tinh Hien
- Oxford University Clinical Research UnitHo Chi Minh CityViet Nam
| | | | | | | | | | - Didar Uddin
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Caroline Buckee
- Harvard TH Chan School of Public Health, Harvard UniversityBostonUnited States
| | - Caterina I Fanello
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Marie Onyamboko
- Kinshasa School of Public Health, University of KinshasaKinshasaDemocratic Republic of the Congo
| | - Thomas Peto
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Rupam Tripura
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Chanaki Amaratunga
- National Institute of Allergy and Infectious Diseases, National Institutes of HealthRockvilleUnited States
| | - Aung Myint Thu
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | - Gilles Delmas
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Shoklo Malaria Research UnitMae SotThailand
| | - Jordi Landier
- Shoklo Malaria Research UnitMae SotThailand
- Aix-Marseille Université, INSERM, IRD, SESSTIM, Aix Marseille Institute of Public Health, ISSPAMMarseilleFrance
| | - Daniel M Parker
- Shoklo Malaria Research UnitMae SotThailand
- Susan and Henry Samueli College of Health Sciences, University of California, IrvineIrvineUnited States
| | | | - Dysoley Lek
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria ControlPhnom PenhCambodia
| | - James Callery
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | | | - Sasithon Pukrittayakamee
- Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
- The Royal Society of ThailandBangkokThailand
| | - Aung Pyae Phyo
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Myanmar-Oxford Clinical Research UnitYangonMyanmar
| | - Frank Smithuis
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Myanmar-Oxford Clinical Research UnitYangonMyanmar
| | - Khin Lin
- Department of Medical ResearchPyin Oo LwinMyanmar
| | - Myo Thant
- Defence Services Medical Research CentreYangonMyanmar
| | | | | | | | | | | | | | - Neena Valecha
- National Institute of Malaria Research, Indian Council of Medical ResearchNew DelhiIndia
| | - Anupkumar R Anvikar
- National Institute of Malaria Research, Indian Council of Medical ResearchNew DelhiIndia
| | | | - Abul Faiz
- Malaria Research Group and Dev Care FoundationDhakaBangladesh
| | - Chanon Kunasol
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | - Mihir Kekre
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Mozam Ali
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Katie Love
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | | | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Christina S Hubbart
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Mehul Dhorda
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Worldwide Antimalarial Resistance Network (WWARN), Asia Regional CentreBangkokThailand
| | - Ranitha Vongpromek
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- Worldwide Antimalarial Resistance Network (WWARN), Asia Regional CentreBangkokThailand
| | - Namfon Kotanan
- Faculty of Tropical Medicine, Mahidol UniversityBangkokThailand
| | - Phrutsamon Wongnak
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Jacob Almagro Garcia
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | - Richard D Pearson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | | | | | - T Nguyen
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Jim Stalker
- Wellcome Sanger InstituteHinxtonUnited Kingdom
| | - Ben Jeffery
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Kimberly J Johnson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Xin Hui S Chan
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | | | | | - Victoria Simpson
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | | | - Kirk Rockett
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Wellcome Trust Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Nicholas P Day
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Arjen M Dondorp
- Centre for Tropical Medicine and Global Health, University of OxfordOxfordUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Dominic P Kwiatkowski
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
| | - Olivo Miotto
- Wellcome Sanger InstituteHinxtonUnited Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
- MRC Centre for Genomics and Global Health, Big Data Institute, Oxford UniversityOxfordUnited Kingdom
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30
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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.
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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.
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31
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Thinking clearly about social aspects of infectious disease transmission. Nature 2021; 595:205-213. [PMID: 34194045 DOI: 10.1038/s41586-021-03694-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Social and cultural forces shape almost every aspect of infectious disease transmission in human populations, as well as our ability to measure, understand, and respond to epidemics. For directly transmitted infections, pathogen transmission relies on human-to-human contact, with kinship, household, and societal structures shaping contact patterns that in turn determine epidemic dynamics. Social, economic, and cultural forces also shape patterns of exposure, health-seeking behaviour, infection outcomes, the likelihood of diagnosis and reporting of cases, and the uptake of interventions. Although these social aspects of epidemiology are hard to quantify and have limited the generalizability of modelling frameworks in a policy context, new sources of data on relevant aspects of human behaviour are increasingly available. Researchers have begun to embrace data from mobile devices and other technologies as useful proxies for behavioural drivers of disease transmission, but there is much work to be done to measure and validate these approaches, particularly for policy-making. Here we discuss how integrating local knowledge in the design of model frameworks and the interpretation of new data streams offers the possibility of policy-relevant models for public health decision-making as well as the development of robust, generalizable theories about human behaviour in relation to infectious diseases.
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32
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Buchwald AG, Grover E, Van Dyke J, Kechris K, Lu D, Liu Y, Zhong B, Carlton EJ. Human Mobility Associated With Risk of Schistosoma japonicum Infection in Sichuan, China. Am J Epidemiol 2021; 190:1243-1252. [PMID: 33438003 DOI: 10.1093/aje/kwaa292] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 12/15/2020] [Accepted: 12/29/2020] [Indexed: 11/12/2022] Open
Abstract
Urbanization increases human mobility in ways that can alter the transmission of classically rural, vector-borne diseases like schistosomiasis. The impact of human mobility on individual-level Schistosoma risk is poorly characterized. Travel outside endemic areas may protect against infection by reducing exposure opportunities, whereas travel to other endemic regions may increase risk. Using detailed monthly travel- and water-contact surveys from 27 rural communities in Sichuan, China, in 2008, we aimed to describe human mobility and to identify mobility-related predictors of S. japonicum infection. Candidate predictors included timing, frequency, distance, duration, and purpose of recent travel as well as water-contact measures. Random forests machine learning was used to detect key predictors of individual infection status. Logistic regression was used to assess the strength and direction of associations. Key mobility-related predictors include frequent travel and travel during July-both associated with decreased probability of infection and less time engaged in risky water-contact behavior, suggesting travel may remove opportunities for schistosome exposure. The importance of July travel and July water contact suggests a high-risk window for cercarial exposure. The frequency and timing of human movement out of endemic areas should be considered when assessing potential drivers of rural infectious diseases.
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33
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Tam G, Cowling BJ, Maude RJ. Analysing human population movement data for malaria control and elimination. Malar J 2021; 20:294. [PMID: 34193167 PMCID: PMC8247220 DOI: 10.1186/s12936-021-03828-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Human population movement poses a major obstacle to malaria control and elimination. With recent technological advances, a wide variety of data sources and analytical methods have been used to quantify human population movement (HPM) relevant to control and elimination of malaria. METHODS The relevant literature and selected studies that had policy implications that could help to design or target malaria control and elimination interventions were reviewed. These studies were categorized according to spatiotemporal scales of human mobility and the main method of analysis. RESULTS Evidence gaps exist for tracking routine cross-border HPM and HPM at a regional scale. Few studies accounted for seasonality. Out of twenty included studies, two studies which tracked daily neighbourhood HPM used descriptive analyses as the main method, while the remaining studies used statistical analyses or mathematical modelling. CONCLUSION Although studies quantified varying types of human population movement covering different spatial and temporal scales, methodological gaps remain that warrant further studies related to malaria control and elimination.
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Affiliation(s)
- Greta Tam
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China.,Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Benjamin J Cowling
- WHO Collaborating Centre for Infectious Disease Epidemiology and Control, School of Public Health, Li Ka Shing, Faculty of Medicine, The University of Hong Kong, Hong Kong, China
| | - Richard J Maude
- Mahidol-Oxford Tropical Medicine Research Unit, 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 7LG, UK. .,The Open University, Milton Keynes, MK7 6AA, UK. .,Harvard TH Chan School of Public Health, Harvard University, Boston, MA, 02115, USA.
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34
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Comparing metapopulation dynamics of infectious diseases under different models of human movement. Proc Natl Acad Sci U S A 2021; 118:2007488118. [PMID: 33926962 PMCID: PMC8106338 DOI: 10.1073/pnas.2007488118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Newly available datasets present exciting opportunities to investigate how human population movement contributes to the spread of infectious diseases across large geographical distances. It is now possible to construct realistic models of infectious disease dynamics for the purposes of understanding global-scale epidemics. Nevertheless, a remaining unanswered question is how best to leverage the new data to parameterize models of movement, and whether one's choice of movement model impacts modeled disease outcomes. We adapt three well-studied models of infectious disease dynamics, the susceptible-infected-recovered model, the susceptible-infected-susceptible model, and the Ross-Macdonald model, to incorporate either of two candidate movement models. We describe the effect that the choice of movement model has on each disease model's results, finding that in all cases, there are parameter regimes where choosing one movement model instead of another has a profound impact on epidemiological outcomes. We further demonstrate the importance of choosing an appropriate movement model using the applied case of malaria transmission and importation on Bioko Island, Equatorial Guinea, finding that one model produces intelligible predictions of R 0, whereas the other produces nonsensical results.
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35
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Auburn S, Cheng Q, Marfurt J, Price RN. The changing epidemiology of Plasmodium vivax: Insights from conventional and novel surveillance tools. PLoS Med 2021; 18:e1003560. [PMID: 33891580 PMCID: PMC8064506 DOI: 10.1371/journal.pmed.1003560] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Sarah Auburn and co-authors discuss the unique biology and epidemiology of P. vivax and current evidence on conventional and new approaches to surveillance.
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Affiliation(s)
- Sarah Auburn
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Qin Cheng
- Department of Drug Resistance and Diagnostics, Australian Defence Force Malaria and Infectious Disease Institute, Brisbane, Australia
- The Australian Defence Force Malaria and Infectious Disease Institute Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jutta Marfurt
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
| | - Ric N. Price
- Global and Tropical Health Division, Menzies School of Health Research and Charles Darwin University, Darwin, Australia
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
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36
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Johora FT, Elahi R, Nima MK, Hossain MS, Rashid H, Kibria MG, Mohon AN, Khan WA, Haque R, Alam MS. Persistence of Markers of Chloroquine Resistance in Plasmodium falciparum in Bangladesh. Am J Trop Med Hyg 2021; 104:276-282. [PMID: 33146120 DOI: 10.4269/ajtmh.20-0415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The control of malaria, in terms of drug resistance, remains a significant global challenge, with Bangladesh, a malaria-endemic country, being no exception. The aim of this study was to explore antimalarial resistance in Bangladesh by molecular analysis of Plasmodium falciparum chloroquine resistance transporter (pfcrt) and P. falciparum multidrug resistance transporter 1 (pfmdr1) genetic markers of P. falciparum. Samples were obtained from uncomplicated malaria patients between 2009 and 2014 from six malaria-endemic districts. Based on parasite transmission intensity, the endemic districts were divided into high-transmission (Chittagong Hill Tracts [CHT]) and low-transmission (non-CHT) regions. Falciparum malaria-positive isolates were genotyped for K76T of the pfcrt gene, and N86Y and Y184F of the pfmdr1 gene: in total, 262 P. falciparum clinical isolates were analyzed. In CHT areas, the prevalence of polymorphisms was 70.6% for 76T, 14.4% for 86Y, and 7.8% for 184F. In non-CHT areas, 76T and 86Y mutations were found in 78.0% and 19.5% of the samples, respectively, whereas no 184F mutations were observed. We compared our data with previous similar molecular observations, which shows a significant decrease in pfcrt 76T mutation prevalence. No pfmdr1 amplification was observed in any of the samples suggesting an unaltered susceptibility to amino alcohol drugs such as mefloquine and lumefantrine. This study provides an updated assessment of the current status of pfcrt and pfmdr1 gene mutations in Bangladesh, and suggests there is persistent high prevalence of markers of resistance to aminoquinoline drugs.
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Affiliation(s)
- Fatema Tuj Johora
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rubayet Elahi
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,2Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Maisha Khair Nima
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,3Department of Biological Sciences, Boler-Parseghian Center for Rare and Neglected Diseases, University of Notre Dame, Notre Dame, Indiana
| | - Mohammad Sharif Hossain
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Humaira Rashid
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Golam Kibria
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Abu Naser Mohon
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh.,4Department of Microbiology, Immunology and Infectious Disease, University of Calgary, Alberta, Canada
| | - Wasif A Khan
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Rashidul Haque
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Mohammad Shafiul Alam
- 1Infectious Diseases Division, International Centre for Diarrhoeal Diseases Research, Bangladesh (icddr,b), Dhaka, Bangladesh
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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.
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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
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Childs LM, Larremore DB. Network Models for Malaria: Antigens, Dynamics, and Evolution Over Space and Time. SYSTEMS MEDICINE 2021. [DOI: 10.1016/b978-0-12-801238-3.11512-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
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39
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Moser KA, Madebe RA, Aydemir O, Chiduo MG, Mandara CI, Rumisha SF, Chaky F, Denton M, Marsh PW, Verity R, Watson OJ, Ngasala B, Mkude S, Molteni F, Njau R, Warsame M, Mandike R, Kabanywanyi AM, Mahende MK, Kamugisha E, Ahmed M, Kavishe RA, Greer G, Kitojo CA, Reaves EJ, Mlunde L, Bishanga D, Mohamed A, Juliano JJ, Ishengoma DS, Bailey JA. Describing the current status of Plasmodium falciparum population structure and drug resistance within mainland Tanzania using molecular inversion probes. Mol Ecol 2020; 30:100-113. [PMID: 33107096 DOI: 10.1111/mec.15706] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/25/2020] [Accepted: 10/13/2020] [Indexed: 02/05/2023]
Abstract
High-throughput Plasmodium genomic data is increasingly useful in assessing prevalence of clinically important mutations and malaria transmission patterns. Understanding parasite diversity is important for identification of specific human or parasite populations that can be targeted by control programmes, and to monitor the spread of mutations associated with drug resistance. An up-to-date understanding of regional parasite population dynamics is also critical to monitor the impact of control efforts. However, this data is largely absent from high-burden nations in Africa, and to date, no such analysis has been conducted for malaria parasites in Tanzania countrywide. To this end, over 1,000 P. falciparum clinical isolates were collected in 2017 from 13 sites in seven administrative regions across Tanzania, and parasites were genotyped at 1,800 variable positions genome-wide using molecular inversion probes. Population structure was detectable among Tanzanian P. falciparum parasites, approximately separating parasites from the northern and southern districts and identifying genetically admixed populations in the north. Isolates from nearby districts were more likely to be genetically related compared to parasites sampled from more distant districts. Known drug resistance mutations were seen at increased frequency in northern districts (including two infections carrying pfk13-R561H), and additional variants with undetermined significance for antimalarial resistance also varied by geography. Malaria Indicator Survey (2017) data corresponded with genetic findings, including average region-level complexity-of-infection and malaria prevalence estimates. The parasite populations identified here provide important information on extant spatial patterns of genetic diversity of Tanzanian parasites, to which future surveys of genetic relatedness can be compared.
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Affiliation(s)
- Kara A Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | | | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Mercy G Chiduo
- National Institute for Medical Research, Tanga, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Tanga, Tanzania.,Kilimanjaro Christian Medical Centre/Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - Susan F Rumisha
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Frank Chaky
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA
| | - Patrick W Marsh
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Robert Verity
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J Watson
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.,MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Billy Ngasala
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Sigsbert Mkude
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | - Ritha Njau
- World Health Organization Country Office, Dar es Salaam, Tanzania
| | - Marian Warsame
- Gothenburg University, Gothenburg, Sweden.,Global Malaria Programme, World Health Organization, Geneva, Switzerland
| | - Renata Mandike
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | | | | | - Erasmus Kamugisha
- Catholic University of Health and Allied Sciences/Bugando Medical Centre, Mwanza, Tanzania
| | - Maimuna Ahmed
- Catholic University of Health and Allied Sciences/Bugando Medical Centre, Mwanza, Tanzania
| | - Reginald A Kavishe
- Kilimanjaro Christian Medical Centre/Kilimanjaro Christian Medical University College, Moshi, Tanzania
| | - George Greer
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Chonge A Kitojo
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Erik J Reaves
- U.S. President's Malaria Initiative, U.S. Agency for International Development, U.S. Embassy, Dar es Salaam, Tanzania
| | - Linda Mlunde
- Jhpiego/Boresha Afya Project, Dar es Salaam, Tanzania
| | | | - Ally Mohamed
- National Malaria Control Program (NMCP), Dodoma, Tanzania
| | - Jonathan J Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina Chapel Hill, Chapel Hill, NC, USA.,Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Deus S Ishengoma
- National Institute for Medical Research, 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
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
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40
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Daniels RF, Schaffner SF, Dieye Y, Dieng G, Hainsworth M, Fall FB, Diouf CN, Ndiop M, Cisse M, Gueye AB, Sarr O, Guinot P, Deme AB, Bei AK, Sy M, Thwing J, MacInnis B, Earle D, Guinovart C, Sene D, Hartl DL, Ndiaye D, Steketee RW, Wirth DF, Volkman SK. Genetic evidence for imported malaria and local transmission in Richard Toll, Senegal. Malar J 2020; 19:276. [PMID: 32746830 PMCID: PMC7397603 DOI: 10.1186/s12936-020-03346-x] [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: 02/21/2020] [Accepted: 07/25/2020] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Malaria elimination efforts can be undermined by imported malaria infections. Imported infections are classified based on travel history. METHODS A genetic strategy was applied to better understand the contribution of imported infections and to test for local transmission in the very low prevalence region of Richard Toll, Senegal. RESULTS Genetic relatedness analysis, based upon molecular barcode genotyping data derived from diagnostic material, provided evidence for both imported infections and ongoing local transmission in Richard Toll. Evidence for imported malaria included finding that a large proportion of Richard Toll parasites were genetically related to parasites from Thiès, Senegal, a region of moderate transmission with extensive available genotyping data. Evidence for ongoing local transmission included finding parasites of identical genotype that persisted across multiple transmission seasons as well as enrichment of highly related infections within the households of non-travellers compared to travellers. CONCLUSIONS These data indicate that, while a large number of infections may have been imported, there remains ongoing local malaria transmission in Richard Toll. These proof-of-concept findings underscore the value of genetic data to identify parasite relatedness and patterns of transmission to inform optimal intervention selection and placement.
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Affiliation(s)
- Rachel F. Daniels
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA
| | | | | | | | | | - Fatou B. Fall
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | - Medoune Ndiop
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | | | - Oumar Sarr
- Senegal National Malaria Control Programme, Dakar, Senegal
| | | | - Awa B. Deme
- Dantec Teaching and Research Hospital, Dakar, Senegal
| | - Amy K. Bei
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA
| | - Mouhamad Sy
- Dantec Teaching and Research Hospital, Dakar, Senegal
| | - Julie Thwing
- grid.416738.f0000 0001 2163 0069Centers for Disease Control and Prevention, Atlanta, GA USA
| | | | | | | | - Doudou Sene
- Senegal National Malaria Control Programme, Dakar, Senegal
| | - Daniel L. Hartl
- grid.38142.3c000000041936754XHarvard University, Cambridge, MA USA
| | - Daouda Ndiaye
- grid.8191.10000 0001 2186 9619Cheikh Anta Diop University, Dakar, Senegal
| | | | - Dyann F. Wirth
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA
| | - Sarah K. Volkman
- grid.38142.3c000000041936754XHarvard T.H. Chan School of Public Health, Boston, MA USA ,grid.66859.34Broad Institute, Cambridge, MA USA ,grid.28203.3b0000 0004 0378 6053Simmons University, Boston, MA USA
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41
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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.
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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.
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42
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Li Y, Shetty AC, Lon C, Spring M, Saunders DL, Fukuda MM, Hien TT, Pukrittayakamee S, Fairhurst RM, Dondorp AM, Plowe CV, O’Connor TD, Takala-Harrison S, Stewart K. Detecting geospatial patterns of Plasmodium falciparum parasite migration in Cambodia using optimized estimated effective migration surfaces. Int J Health Geogr 2020; 19:13. [PMID: 32276636 PMCID: PMC7149848 DOI: 10.1186/s12942-020-00207-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 04/01/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Understanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam. METHODS The optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns. RESULTS Optimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns. CONCLUSIONS Optimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.
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Affiliation(s)
- Yao Li
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
| | - Amol C. Shetty
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Chanthap Lon
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Michele Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - David L. Saunders
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mark M. Fukuda
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Arjen M. Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | | | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, 21201 MD USA
| | - Kathleen Stewart
- Center for Geospatial Information Science, Department of Geographical Sciences, University of Maryland, College Park, 20742 MD USA
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43
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Corder RM, Ferreira MU, Gomes MGM. Modelling the epidemiology of residual Plasmodium vivax malaria in a heterogeneous host population: A case study in the Amazon Basin. PLoS Comput Biol 2020; 16:e1007377. [PMID: 32168349 PMCID: PMC7108741 DOI: 10.1371/journal.pcbi.1007377] [Citation(s) in RCA: 12] [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: 08/31/2019] [Revised: 03/31/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
The overall malaria burden in the Americas has decreased dramatically over the past two decades, but residual transmission pockets persist across the Amazon Basin, where Plasmodium vivax is the predominant infecting species. Current elimination efforts require a better quantitative understanding of malaria transmission dynamics for planning, monitoring, and evaluating interventions at the community level. This can be achieved with mathematical models that properly account for risk heterogeneity in communities approaching elimination, where few individuals disproportionately contribute to overall malaria prevalence, morbidity, and onwards transmission. Here we analyse demographic information combined with routinely collected malaria morbidity data from the town of Mâncio Lima, the main urban transmission hotspot of Brazil. We estimate the proportion of high-risk subjects in the host population by fitting compartmental susceptible-infected-susceptible (SIS) transmission models simultaneously to age-stratified vivax malaria incidence densities and the frequency distribution of P. vivax malaria attacks experienced by each individual over 12 months. Simulations with the best-fitting SIS model indicate that 20% of the hosts contribute 86% of the overall vivax malaria burden. Despite the low overall force of infection typically found in the Amazon, about one order of magnitude lower than that in rural Africa, high-risk individuals gradually develop clinical immunity following repeated infections and eventually constitute a substantial infectious reservoir comprised of asymptomatic parasite carriers that is overlooked by routine surveillance but likely fuels onwards malaria transmission. High-risk individuals therefore represent a priority target for more intensive and effective interventions that may not be readily delivered to the entire community.
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Affiliation(s)
- Rodrigo M. Corder
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail: (RMC); (MGMG)
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Gabriela M. Gomes
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, and CMUP, Centro de Matemática da Universidade do Porto, Porto, Portugal
- * E-mail: (RMC); (MGMG)
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Sinha I, Sayeed AA, Uddin D, Wesolowski A, Zaman SI, Faiz MA, Ghose A, Rahman MR, Islam A, Karim MJ, Saha A, Rezwan MK, Shamsuzzaman AKM, Jhora ST, Aktaruzzaman MM, Chang HH, Miotto O, Kwiatkowski D, Dondorp AM, Day NPJ, Hossain MA, Buckee C, Maude RJ. Mapping the travel patterns of people with malaria in Bangladesh. BMC Med 2020; 18:45. [PMID: 32127002 PMCID: PMC7055101 DOI: 10.1186/s12916-020-1512-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 02/05/2020] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Spread of malaria and antimalarial resistance through human movement present major threats to current goals to eliminate the disease. Bordering the Greater Mekong Subregion, southeast Bangladesh is a potentially important route of spread to India and beyond, but information on travel patterns in this area are lacking. METHODS Using a standardised short survey tool, 2090 patients with malaria were interviewed at 57 study sites in 2015-2016 about their demographics and travel patterns in the preceding 2 months. RESULTS Most travel was in the south of the study region between Cox's Bazar district (coastal region) to forested areas in Bandarban (31% by days and 45% by nights), forming a source-sink route. Less than 1% of travel reported was between the north and south forested areas of the study area. Farmers (21%) and students (19%) were the top two occupations recorded, with 67 and 47% reporting travel to the forest respectively. Males aged 25-49 years accounted for 43% of cases visiting forests but only 24% of the study population. Children did not travel. Women, forest dwellers and farmers did not travel beyond union boundaries. Military personnel travelled the furthest especially to remote forested areas. CONCLUSIONS The approach demonstrated here provides a framework for identifying key traveller groups and their origins and destinations of travel in combination with knowledge of local epidemiology to inform malaria control and elimination efforts. Working with the NMEP, the findings were used to derive a set of policy recommendations to guide targeting of interventions for elimination.
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Affiliation(s)
- Ipsita Sinha
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | | | - Didar Uddin
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Amy Wesolowski
- John Hopkins Bloomberg School of Public Health, Baltimore, USA
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Sazid Ibna Zaman
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- BRAC (Building Resources Across Communities), BRAC Centre, Mohakhali, Dhaka, Bangladesh
| | - M Abul Faiz
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Dev Care Foundation, Dhaka, Bangladesh
| | - Aniruddha Ghose
- Chittagong Medical College and Hospital, Chittagong, Bangladesh
| | | | - Akramul Islam
- BRAC (Building Resources Across Communities), BRAC Centre, Mohakhali, Dhaka, Bangladesh
| | - Mohammad Jahirul Karim
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Communicable Disease Control, Directorate General of Health Services, Dhaka, Bangladesh
- Filariasis Elimination, STH Control, Dhaka, Bangladesh
| | - Anjan Saha
- National Malaria Elimination Programme, Dhaka, Bangladesh
| | - M Kamar Rezwan
- Vector-Borne Disease Control, World Health Organization, Dhaka, Bangladesh
| | | | - Sanya Tahmina Jhora
- Communicable Disease Control, Directorate General of Health Services, Dhaka, Bangladesh
| | - M M Aktaruzzaman
- Communicable Disease Control, Directorate General of Health Services, Dhaka, Bangladesh
- National Malaria Elimination Programme, Dhaka, Bangladesh
| | - Hsiao-Han Chang
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Olivo Miotto
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Big Data Institute, University of Oxford, Oxford, UK
| | - Dominic Kwiatkowski
- Big Data Institute, University of Oxford, Oxford, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Arjen M Dondorp
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nicholas P J Day
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - M Amir Hossain
- Chittagong Medical College and Hospital, Chittagong, Bangladesh
| | - Caroline Buckee
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
| | - Richard J Maude
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Harvard T.H. Chan School of Public Health, Harvard University, Boston, USA
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Routledge I, Lai S, Battle KE, Ghani AC, Gomez-Rodriguez M, Gustafson KB, Mishra S, Unwin J, Proctor JL, Tatem AJ, Li Z, Bhatt S. Tracking progress towards malaria elimination in China: Individual-level estimates of transmission and its spatiotemporal variation using a diffusion network approach. PLoS Comput Biol 2020; 16:e1007707. [PMID: 32203520 PMCID: PMC7117777 DOI: 10.1371/journal.pcbi.1007707] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 04/02/2020] [Accepted: 02/03/2020] [Indexed: 01/02/2023] Open
Abstract
In order to monitor progress towards malaria elimination, it is crucial to be able to measure changes in spatio-temporal transmission. However, common metrics of malaria transmission such as parasite prevalence are under powered in elimination contexts. China has achieved major reductions in malaria incidence and is on track to eliminate, having reporting zero locally-acquired malaria cases in 2017 and 2018. Understanding the spatio-temporal pattern underlying this decline, especially the relationship between locally-acquired and imported cases, can inform efforts to maintain elimination and prevent re-emergence. This is particularly pertinent in Yunnan province, where the potential for local transmission is highest. Using a geo-located individual-level dataset of cases recorded in Yunnan province between 2011 and 2016, we introduce a novel Bayesian framework to model a latent diffusion process and estimate the joint likelihood of transmission between cases and the number of cases with unobserved sources of infection. This is used to estimate the case reproduction number, Rc. We use these estimates within spatio-temporal geostatistical models to map how transmission varied over time and space, estimate the timeline to elimination and the risk of resurgence. We estimate the mean Rc between 2011 and 2016 to be 0.171 (95% CI = 0.165, 0.178) for P. vivax cases and 0.089 (95% CI = 0.076, 0.103) for P. falciparum cases. From 2014 onwards, no cases were estimated to have a Rc value above one. An unobserved source of infection was estimated to be moderately likely (p>0.5) for 19/ 611 cases and high (p>0.8) for 2 cases, suggesting very high levels of case ascertainment. Our estimates suggest that, maintaining current intervention efforts, Yunnan is unlikely to experience sustained local transmission up to 2020. However, even with a mean of 0.005 projected up to 2020, locally-acquired cases are possible due to high levels of importation.
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Affiliation(s)
| | - Shengjie Lai
- University of Southampton, Southampton, United Kingdom
| | | | | | | | - Kyle B. Gustafson
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | | | - Joshua L. Proctor
- Institute for Disease Modelling, Bellevue, Washington, United States of America
| | | | - Zhongjie Li
- Chinese Centers for Disease Control and Prevention, Beijing, China
| | - Samir Bhatt
- Imperial College London, London, United Kingom
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47
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Guerra CA, Citron DT, García GA, Smith DL. Characterising malaria connectivity using malaria indicator survey data. Malar J 2019; 18:440. [PMID: 31870353 PMCID: PMC6929427 DOI: 10.1186/s12936-019-3078-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 12/14/2019] [Indexed: 12/13/2022] Open
Abstract
Malaria connectivity describes the flow of parasites among transmission sources and sinks within a given landscape. Because of the spatial and temporal scales at which parasites are transported by their hosts, malaria sub-populations are largely defined by mosquito movement and malaria connectivity among them is largely driven by human movement. Characterising malaria connectivity thus requires characterising human travel between areas with differing levels of exposure to malaria. Whilst understanding malaria connectivity is fundamental for optimising interventions, particularly in areas seeking or sustaining elimination, there is a dearth of human movement data required to achieve this goal. Malaria indicator surveys (MIS) are a generally under utilised but potentially rich source of travel data that provide a unique opportunity to study simple associations between malaria infection and human travel in large population samples. This paper shares the experience working with MIS data from Bioko Island that revealed programmatically useful information regarding malaria importation through human travel. Simple additions to MIS questionnaires greatly augmented the level of detail of the travel data, which can be used to characterise human travel patterns and malaria connectivity to assist targeting interventions. It is argued that MIS potentially represent very important and timely sources of travel data that need to be further exploited.
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Affiliation(s)
- Carlos A Guerra
- Medical Care Development International, 8401 Colesville Road, Suite 425, Silver Spring, MD, 20910, USA.
| | - Daniel T Citron
- Institute for Health Metrics and Evaluation, University of Washington, 2301 Fifth Avenue, Seattle, 98121, USA
| | - Guillermo A García
- Medical Care Development International, 8401 Colesville Road, Suite 425, Silver Spring, MD, 20910, USA
| | - David L Smith
- Institute for Health Metrics and Evaluation, University of Washington, 2301 Fifth Avenue, Seattle, 98121, USA
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Malinga J, Mogeni P, Omedo I, Rockett K, Hubbart C, Jeffreys A, Williams TN, Kwiatkowski D, Bejon P, Ross A. Investigating the drivers of the spatio-temporal patterns of genetic differences between Plasmodium falciparum malaria infections in Kilifi County, Kenya. Sci Rep 2019; 9:19018. [PMID: 31836742 PMCID: PMC6911066 DOI: 10.1038/s41598-019-54348-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 11/12/2019] [Indexed: 01/17/2023] Open
Abstract
Knowledge of how malaria infections spread locally is important both for the design of targeted interventions aiming to interrupt malaria transmission and the design of trials to assess the interventions. A previous analysis of 1602 genotyped Plasmodium falciparum parasites in Kilifi, Kenya collected over 12 years found an interaction between time and geographic distance: the mean number of single nucleotide polymorphism (SNP) differences was lower for pairs of infections which were both a shorter time interval and shorter geographic distance apart. We determine whether the empiric pattern could be reproduced by a simple model, and what mean geographic distances between parent and offspring infections and hypotheses about genotype-specific immunity or a limit on the number of infections would be consistent with the data. We developed an individual-based stochastic simulation model of households, people and infections. We parameterized the model for the total number of infections, and population and household density observed in Kilifi. The acquisition of new infections, mutation, recombination, geographic location and clearance were included. We fit the model to the observed numbers of SNP differences between pairs of parasite genotypes. The patterns observed in the empiric data could be reproduced. Although we cannot rule out genotype-specific immunity or a limit on the number of infections per individual, they are not necessary to account for the observed patterns. The mean geographic distance between parent and offspring malaria infections for the base model was 0.4 km (95% CI 0.24, 1.20), for a distribution with 58% of distances shorter than the mean. Very short mean distances did not fit well, but mixtures of distributions were also consistent with the data. For a pathogen which undergoes meiosis in a setting with moderate transmission and a low coverage of infections, analytic methods are limited but an individual-based model can be used with genotyping data to estimate parameter values and investigate hypotheses about underlying processes.
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Affiliation(s)
- Josephine Malinga
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Polycarp Mogeni
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Irene Omedo
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Kirk Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Anne Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas N Williams
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Department of Medicine, South Kensington Campus, Imperial College London, London, UK
| | - Dominic Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Philip Bejon
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine & Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Amanda Ross
- Swiss Tropical and Public Health Institute, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
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Diakité SAS, Traoré K, Sanogo I, Clark TG, Campino S, Sangaré M, Dabitao D, Dara A, Konaté DS, Doucouré F, Cissé A, Keita B, Doumbouya M, Guindo MA, Toure MB, Sogoba N, Doumbia S, Awandare GA, Diakité M. A comprehensive analysis of drug resistance molecular markers and Plasmodium falciparum genetic diversity in two malaria endemic sites in Mali. Malar J 2019; 18:361. [PMID: 31718631 PMCID: PMC6849310 DOI: 10.1186/s12936-019-2986-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/24/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Drug resistance is one of the greatest challenges of malaria control programme in Mali. Recent advances in next-generation sequencing (NGS) technologies provide new and effective ways of tracking drug-resistant malaria parasites in Africa. The diversity and the prevalence of Plasmodium falciparum drug-resistance molecular markers were assessed in Dangassa and Nioro-du-Sahel in Mali, two sites with distinct malaria transmission patterns. Dangassa has an intense seasonal malaria transmission, whereas Nioro-du-Sahel has an unstable and short seasonal malaria transmission. METHODS Up to 270 dried blood spot samples (214 in Dangassa and 56 in Nioro-du-Sahel) were collected from P. falciparum positive patients in 2016. Samples were analysed on the Agena MassARRAY® iPLEX platform. Specific codons were targeted in Pfcrt, Pfmdr1, Pfdhfr, and Pfdhps, Pfarps10, Pfferredoxin, Pfexonuclease and Pfmdr2 genes. The Sanger's 101-SNPs-barcode method was used to assess the genetic diversity of P. falciparum and to determine the parasite species. RESULTS The Pfcrt_76T chloroquine-resistance genotype was found at a rate of 64.4% in Dangassa and 45.2% in Nioro-du-Sahel (p = 0.025). The Pfdhfr_51I-59R-108N pyrimethamine-resistance genotype was 14.1% and 19.6%, respectively in Dangassa and Nioro-du-Sahel. Mutations in the Pfdhps_S436-A437-K540-A581-613A sulfadoxine-resistance gene was significantly more prevalent in Dangassa as compared to Nioro-du-Sahel (p = 0.035). Up to 17.8% of the isolates from Dangassa vs 7% from Nioro-du-Sahel harboured at least two codon substitutions in this haplotype. The amodiaquine-resistance Pfmdr1_N86Y mutation was identified in only three samples (two in Dangassa and one in Nioro-du-Sahel). The lumefantrine-reduced susceptibility Pfmdr1_Y184F mutation was found in 39.9% and 48.2% of samples in Dangassa and Nioro-du-Sahel, respectively. One piperaquine-resistance Exo_E415G mutation was found in Dangassa, while no artemisinin resistance genetic-background were identified. A high P. falciparum diversity was observed, but no clear genetic aggregation was found at either study sites. Higher multiplicity of infection was observed in Dangassa with both COIL (p = 0.04) and Real McCOIL (p = 0.02) methods relative to Nioro-du-Sahel. CONCLUSIONS This study reveals high prevalence of chloroquine and pyrimethamine-resistance markers as well as high codon substitution rate in the sulfadoxine-resistance gene. High genetic diversity of P. falciparum was observed. These observations suggest that the use of artemisinins is relevant in both Dangassa and Nioro-du-Sahel.
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Affiliation(s)
- Seidina A S Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali.
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.
| | - Karim Traoré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ibrahim Sanogo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Modibo Sangaré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Djeneba Dabitao
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Antoine Dara
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa S Konaté
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fousseyni Doucouré
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Amadou Cissé
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourama Keita
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mory Doumbouya
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Merepen A Guindo
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mahamoudou B Toure
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Nafomon Sogoba
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seydou Doumbia
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
| | - Gordon A Awandare
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Mahamadou Diakité
- Malaria Research and Training Center, University of Sciences, Technics and Technologies of Bamako (USTTB), Bamako, Mali
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Bedford J, Farrar J, Ihekweazu C, Kang G, Koopmans M, Nkengasong J. A new twenty-first century science for effective epidemic response. Nature 2019; 575:130-136. [PMID: 31695207 PMCID: PMC7095334 DOI: 10.1038/s41586-019-1717-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 09/24/2019] [Indexed: 12/20/2022]
Abstract
With rapidly changing ecology, urbanization, climate change, increased travel and fragile public health systems, epidemics will become more frequent, more complex and harder to prevent and contain. Here we argue that our concept of epidemics must evolve from crisis response during discrete outbreaks to an integrated cycle of preparation, response and recovery. This is an opportunity to combine knowledge and skills from all over the world-especially at-risk and affected communities. Many disciplines need to be integrated, including not only epidemiology but also social sciences, research and development, diplomacy, logistics and crisis management. This requires a new approach to training tomorrow's leaders in epidemic prevention and response.
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Affiliation(s)
| | | | | | - Gagandeep Kang
- Translational Health Science and Technology Institute, Faridabad, India
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John Nkengasong
- Africa Centres for Disease Control and Prevention, African Union, Addis Ababa, Ethiopia
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