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Guo B, Takala-Harrison S, O’Connor TD. Benchmarking and Optimization of Methods for the Detection of Identity-By-Descent in High-Recombining Plasmodium falciparum Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.04.592538. [PMID: 38746392 PMCID: PMC11092787 DOI: 10.1101/2024.05.04.592538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Genomic surveillance is crucial for identifying at-risk populations for targeted malaria control and elimination. Identity-by-descent (IBD) is increasingly being used in Plasmodium population genomics to estimate genetic relatedness, effective population size (N e ), population structure, and signals of positive selection. Despite its potential, a thorough evaluation of IBD segment detection tools for species with high recombination rates, such as P. falciparum, remains absent. Here, we perform comprehensive benchmarking of IBD callers - probabilistic (hmmIBD, isoRelate), identity-by-state-based (hap-IBD, phased IBD) and others (Refined IBD) - using population genetic simulations tailored for high recombination, and IBD quality metrics at both the IBD segment level and the IBD-based downstream inference level. Our results demonstrate that low marker density per genetic unit, related to high recombination relative to mutation, significantly compromises the accuracy of detected IBD segments. In genomes with high recombination rates resembling P. falciparum, most IBD callers exhibit high false negative rates for shorter IBD segments, which can be partially mitigated through optimization of IBD caller parameters, especially those related to marker density. Notably, IBD detected with optimized parameters allows for more accurate capture of selection signals and population structure; IBD-based N e inference is very sensitive to IBD detection errors, with IBD called from hmmIBD uniquely providing less biased estimates of N e in this context. Validation with empirical data from the MalariaGEN Pf 7 database, representing different transmission settings, corroborates these findings. We conclude that context-specific evaluation and parameter optimization are essential for accurate IBD detection in high-recombining species and recommend hmmIBD for quality-sensitive analysis, such as estimation of N e in these species. Our optimization and high-level benchmarking methods not only improve IBD segment detection in high-recombining genomes but also enhance overall genomic analysis, paving the way for more accurate genomic surveillance and targeted intervention strategies for malaria.
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Affiliation(s)
- Bing Guo
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Timothy D. O’Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
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2
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. PLoS Pathog 2024; 20:e1012013. [PMID: 38870266 PMCID: PMC11206942 DOI: 10.1371/journal.ppat.1012013] [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: 02/01/2024] [Revised: 06/26/2024] [Accepted: 05/24/2024] [Indexed: 06/15/2024] Open
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. In low transmission settings, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. We performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n = 1,409) through estimation of identity-by-descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 multi-isolate clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally observed 61 nonsynonymous substitutions that increased markedly in frequency over the study period as well as a novel pfk13 mutation (G718S). However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions, given that clones carrying drug resistance polymorphisms do not demonstrate enhanced persistence or higher abundance than clones carrying polymorphisms of comparable frequency that are unrelated to resistance. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philipp Schwabl
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Angela M. Early
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret Laws
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O. Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Lise Musset
- Laboratoire de Parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Port of Spain, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Daniel E. Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum. Nat Commun 2024; 15:2499. [PMID: 38509066 PMCID: PMC10954658 DOI: 10.1038/s41467-024-46659-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 02/28/2024] [Indexed: 03/22/2024] Open
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD), yet strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we use simulations, a true IBD inference algorithm, and empirical data sets from different malaria transmission settings to investigate the extent of this bias and explore potential correction strategies. We analyze whole genome sequence data generated from 640 new and 3089 publicly available Plasmodium falciparum clinical isolates. We demonstrate that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discover that the removal of IBD peak regions partially restores the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness and extent of inbreeding. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, USA
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (NOVA), Lisbon, Portugal
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
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4
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Vanhove M, Schwabl P, Clementson C, Early AM, Laws M, Anthony F, Florimond C, Mathieu L, James K, Knox C, Singh N, Buckee CO, Musset L, Cox H, Niles-Robin R, Neafsey DE. Temporal and spatial dynamics of Plasmodium falciparum clonal lineages in Guyana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.31.578156. [PMID: 38352461 PMCID: PMC10862847 DOI: 10.1101/2024.01.31.578156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Plasmodium parasites, the causal agents of malaria, are eukaryotic organisms that obligately undergo sexual recombination within mosquitoes. However, in low transmission settings where most mosquitoes become infected with only a single parasite clone, parasites recombine with themselves, and the clonal lineage is propagated rather than broken up by outcrossing. We investigated whether stochastic/neutral factors drive the persistence and abundance of Plasmodium falciparum clonal lineages in Guyana, a country with relatively low malaria transmission, but the only setting in the Americas in which an important artemisinin resistance mutation (pfk13 C580Y) has been observed. To investigate whether this clonality was potentially associated with the persistence and spatial spread of the mutation, we performed whole genome sequencing on 1,727 Plasmodium falciparum samples collected from infected patients across a five-year period (2016-2021). We characterized the relatedness between each pair of monoclonal infections (n=1,409) through estimation of identity by descent (IBD) and also typed each sample for known or candidate drug resistance mutations. A total of 160 clones (mean IBD ≥ 0.90) were circulating in Guyana during the study period, comprising 13 highly related clusters (mean IBD ≥ 0.40). In the five-year study period, we observed a decrease in frequency of a mutation associated with artemisinin partner drug (piperaquine) resistance (pfcrt C350R) and limited co-occurence of pfcrt C350R with duplications of plasmepsin 2/3, an epistatic interaction associated with piperaquine resistance. We additionally report polymorphisms exhibiting evidence of selection for drug resistance or other phenotypes and reported a novel pfk13 mutation (G718S) as well as 61 nonsynonymous substitutions that increased markedly in frequency. However, P. falciparum clonal dynamics in Guyana appear to be largely driven by stochastic factors, in contrast to other geographic regions. The use of multiple artemisinin combination therapies in Guyana may have contributed to the disappearance of the pfk13 C580Y mutation.
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Affiliation(s)
- Mathieu Vanhove
- 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
| | | | - 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
| | - Margaret Laws
- 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
| | - Frank Anthony
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Célia Florimond
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Luana Mathieu
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Kashana James
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Cheyenne Knox
- 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
| | - Narine Singh
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - Caroline O Buckee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Lise Musset
- Laboratoire de parasitologie, World Health Organization Collaborating Center for Surveillance of Antimalarial Drug Resistance, Center Nationale de Référence du Paludisme, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Horace Cox
- National Malaria Program, Ministry of Health, Georgetown, Guyana
- Caribbean Public Health Agency, Trinidad and Tobago
| | - Reza Niles-Robin
- National Malaria Program, Ministry of Health, Georgetown, Guyana
| | - 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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Guo B, Borda V, Laboulaye R, Spring MD, Wojnarski M, Vesely BA, Silva JC, Waters NC, O'Connor TD, Takala-Harrison S. Strong Positive Selection Biases Identity-By-Descent-Based Inferences of Recent Demography and Population Structure in Plasmodium falciparum. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.14.549114. [PMID: 37502843 PMCID: PMC10370022 DOI: 10.1101/2023.07.14.549114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Malaria genomic surveillance often estimates parasite genetic relatedness using metrics such as Identity-By-Decent (IBD). Yet, strong positive selection stemming from antimalarial drug resistance or other interventions may bias IBD-based estimates. In this study, we utilized simulations, a true IBD inference algorithm, and empirical datasets from different malaria transmission settings to investigate the extent of such bias and explore potential correction strategies. We analyzed whole genome sequence data generated from 640 new and 4,026 publicly available Plasmodium falciparum clinical isolates. Our findings demonstrated that positive selection distorts IBD distributions, leading to underestimated effective population size and blurred population structure. Additionally, we discovered that the removal of IBD peak regions partially restored the accuracy of IBD-based inferences, with this effect contingent on the population's background genetic relatedness. Consequently, we advocate for selection correction for parasite populations undergoing strong, recent positive selection, particularly in high malaria transmission settings.
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Affiliation(s)
- Bing Guo
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
| | - Victor Borda
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Roland Laboulaye
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Michele D Spring
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mariusz Wojnarski
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Brian A Vesely
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Norman C Waters
- Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Timothy D O'Connor
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD USA
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Carrasquilla M, Early AM, Taylor AR, Knudson Ospina A, Echeverry DF, Anderson TJC, Mancilla E, Aponte S, Cárdenas P, Buckee CO, Rayner JC, Sáenz FE, Neafsey DE, Corredor V. Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis. PLoS Pathog 2022; 18:e1010993. [PMID: 36542676 PMCID: PMC9815574 DOI: 10.1371/journal.ppat.1010993] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 01/05/2023] [Accepted: 11/09/2022] [Indexed: 12/24/2022] Open
Abstract
The human malaria parasite Plasmodium falciparum is globally widespread, but its prevalence varies significantly between and even within countries. Most population genetic studies in P. falciparum focus on regions of high transmission where parasite populations are large and genetically diverse, such as sub-Saharan Africa. Understanding population dynamics in low transmission settings, however, is of particular importance as these are often where drug resistance first evolves. Here, we use the Pacific Coast of Colombia and Ecuador as a model for understanding the population structure and evolution of Plasmodium parasites in small populations harboring less genetic diversity. The combination of low transmission and a high proportion of monoclonal infections means there are few outcrossing events and clonal lineages persist for long periods of time. Yet despite this, the population is evolutionarily labile and has successfully adapted to changes in drug regime. Using newly sequenced whole genomes, we measure relatedness between 166 parasites, calculated as identity by descent (IBD), and find 17 distinct but highly related clonal lineages, six of which have persisted in the region for at least a decade. This inbred population structure is captured in more detail with IBD than with other common population structure analyses like PCA, ADMIXTURE, and distance-based trees. We additionally use patterns of intra-chromosomal IBD and an analysis of haplotypic variation to explore past selection events in the region. Two genes associated with chloroquine resistance, crt and aat1, show evidence of hard selective sweeps, while selection appears soft and/or incomplete at three other key resistance loci (dhps, mdr1, and dhfr). Overall, this work highlights the strength of IBD analyses for studying parasite population structure and resistance evolution in regions of low transmission, and emphasizes that drug resistance can evolve and spread in small populations, as will occur in any region nearing malaria elimination.
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Affiliation(s)
- Manuela Carrasquilla
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Angela M. Early
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Aimee R. Taylor
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Center for Communicable Disease Dynamics, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Angélica Knudson Ospina
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Diego F. Echeverry
- Departamento de Microbiología, Facultad de Salud, Universidad del Valle, Cali, Colombia
- Centro Internacional de Entrenamiento e Investigaciones Médicas (CIDEIM), Cali, Colombia
| | - Timothy J. C. Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institution, San Antonio, Texas, United States of America
| | - Elvira Mancilla
- Secretaría Departamental de Salud del Cauca, Popayán, Colombia
| | - Samanda Aponte
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Pablo Cárdenas
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 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
| | - Julian C. Rayner
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, United Kingdom
| | - Fabián E. Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Daniel E. Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H.Chan School of Public Health, Boston, Massachusetts, United States of America
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Vladimir Corredor
- Departamento de Salud Pública, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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