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Peters MAE, Mideo N, MacPherson A. The maintenance of genetic diversity under host-parasite coevolution in finite, structured populations. J Evol Biol 2023; 36:1328-1341. [PMID: 37610056 DOI: 10.1111/jeb.14207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/12/2023] [Accepted: 06/27/2023] [Indexed: 08/24/2023]
Abstract
As a corollary to the Red Queen hypothesis, host-parasite coevolution has been hypothesized to maintain genetic variation in both species. Recent theoretical work, however, suggests that reciprocal natural selection alone is insufficient to maintain variation at individual loci. As highlighted by our brief review of the theoretical literature, models of host-parasite coevolution often vary along multiple axes (e.g. inclusion of ecological feedbacks or abiotic selection mosaics), complicating a comprehensive understanding of the effects of interacting evolutionary processes on diversity. Here we develop a series of comparable models to explore the effect of interactions between spatial structures and antagonistic coevolution on genetic diversity. Using a matching alleles model in finite populations connected by migration, we find that, in contrast to panmictic populations, coevolution in a spatially structured environment can maintain genetic variation relative to neutral expectations with migration alone. These results demonstrate that geographic structure is essential for understanding the effect of coevolution on biological diversity.
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Affiliation(s)
- Madeline A E Peters
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, USA
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Ailene MacPherson
- Department of Mathematics, Simon Fraser University, Burnaby, British Columbia, Canada
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2
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Topazian HM, Moser KA, Ngasala B, Oluoch PO, Forconi CS, Mhamilawa LE, Aydemir O, Kharabora O, Deutsch-Feldman M, Read AF, Denton M, Lorenzo A, Mideo N, Ogutu B, Moormann AM, Mårtensson A, Odwar B, Bailey JA, Akala H, Ong'echa JM, Juliano JJ. Low Complexity of Infection Is Associated With Molecular Persistence of Plasmodium falciparum in Kenya and Tanzania. Front Epidemiol 2022; 2:852237. [PMID: 38455314 PMCID: PMC10910917 DOI: 10.3389/fepid.2022.852237] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 05/06/2022] [Indexed: 03/09/2024]
Abstract
Background Plasmodium falciparum resistance to artemisinin-based combination therapies (ACTs) is a threat to malaria elimination. ACT-resistance in Asia raises concerns for emergence of resistance in Africa. While most data show high efficacy of ACT regimens in Africa, there have been reports describing declining efficacy, as measured by both clinical failure and prolonged parasite clearance times. Methods Three hundred children aged 2-10 years with uncomplicated P. falciparum infection were enrolled in Kenya and Tanzania after receiving treatment with artemether-lumefantrine. Blood samples were taken at 0, 24, 48, and 72 h, and weekly thereafter until 28 days post-treatment. Parasite and host genetics were assessed, as well as clinical, behavioral, and environmental characteristics, and host anti-malarial serologic response. Results While there was a broad range of clearance rates at both sites, 85% and 96% of Kenyan and Tanzanian samples, respectively, were qPCR-positive but microscopy-negative at 72 h post-treatment. A greater complexity of infection (COI) was negatively associated with qPCR-detectable parasitemia at 72 h (OR: 0.70, 95% CI: 0.53-0.94), and a greater baseline parasitemia was marginally associated with qPCR-detectable parasitemia (1,000 parasites/uL change, OR: 1.02, 95% CI: 1.01-1.03). Demographic, serological, and host genotyping characteristics showed no association with qPCR-detectable parasitemia at 72 h. Parasite haplotype-specific clearance slopes were grouped around the mean with no association detected between specific haplotypes and slower clearance rates. Conclusions Identifying risk factors for slow clearing P. falciparum infections, such as COI, are essential for ongoing surveillance of ACT treatment failure in Kenya, Tanzania, and more broadly in sub-Saharan Africa.
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Affiliation(s)
- Hillary M. Topazian
- Department of Infectious Disease Epidemiology, Imperial College, London, United Kingdom
| | - Kara A. Moser
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Billy Ngasala
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Peter O. Oluoch
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Catherine S. Forconi
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Lwidiko E. Mhamilawa
- Department of Parasitology and Medical Entomology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Ozkan Aydemir
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Oksana Kharabora
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Molly Deutsch-Feldman
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
| | - Andrew F. Read
- Department of Entomology, Penn State University, University Park, PA, United States
| | - Madeline Denton
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
| | - Antonio Lorenzo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Bernhards Ogutu
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Ann M. Moormann
- Department of Medicine, University of Massachusetts Chan Medical School, Worcester, MA, United States
| | - Andreas Mårtensson
- Department of Women's and Children's Health, International Maternal and Child Health, Uppsala University, Uppsala, Sweden
| | - Boaz Odwar
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | - Jeffrey A. Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, United States
| | - Hoseah Akala
- Center for Global Health Research, Kenyan Medical Research Institute, Kisumu, Kenya
| | | | - Jonathan J. Juliano
- Institute for Global Health and Infectious Diseases, University of North Carolina, Chapel Hill, NC, United States
- Department of Epidemiology, Gillings School of Global Public Health, Chapel Hill, NC, United States
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
- Curriculum in Genetics and Molecular Biology, School of Medicine, University of North Carolina, Chapel Hill, NC, United States
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Abstract
Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.
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Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Anna Willoughby
- Odum School of Ecology, University of Georgia, Athens, GA, USA,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Andrew Yates
- University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
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4
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Djidjou-Demasse R, Ducrot A, Mideo N, Texier G. Understanding dynamics of Plasmodium falciparum gametocytes production: Insights from an age-structured model. J Theor Biol 2022; 539:111056. [PMID: 35150720 DOI: 10.1016/j.jtbi.2022.111056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 02/01/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022]
Abstract
Many models of within-host malaria infection dynamics have been formulated since the pioneering work of Anderson et al. in 1989. Biologically, the goal of these models is to understand what governs the severity of infections, the patterns of infectiousness, and the variation thereof across individual hosts. Mathematically, these models are based on dynamical systems, with standard approaches ranging from K-compartments ordinary differential equations (ODEs) to delay differential equations (DDEs), to capture the relatively constant duration of replication and bursting once a parasite infects a host red blood cell. Using malariatherapy data, which offers fine-scale resolution on the dynamics of infection across a number of individual hosts, we compare the fit and robustness of one of these standard approaches (K-compartments ODE) with a partial differential equations (PDEs) model, which explicitly tracks the "age" of an infected cell. While both models perform quite similarly in terms of goodness-of-fit for suitably chosen K, the K-compartments ODE model particularly overestimates parasite densities early on in infections when the number of repeated compartments is not large enough. Finally, the K-compartments ODE model (for suitably chosen K) and the PDE model highlight a strong qualitative connection between the density of transmissible parasite stages (i.e., gametocytes) and the density of host-damaging (and asexually-replicating) parasite stages. This finding provides a simple tool for predicting which hosts are most infectious to mosquitoes -vectors of Plasmodium parasites- which is a crucial component of global efforts to control and eliminate malaria.
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Affiliation(s)
| | - Arnaud Ducrot
- Normandie Univ., UNIHAVRE, LMAH, FR-CNRS-3335 ISCN, 76600 Le Havre, France
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Gaëtan Texier
- Aix Marseille Univ., IRD, AP-HM, SSA, VITROME, IHU Méditerranée Infection, Marseille, France; Centre d'Epidémiologie et de Santé Publique des Armées (CESPA), Marseille, France
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6
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Elderd BD, Mideo N, Duffy MA. Looking across Scales in Disease Ecology and Evolution. Am Nat 2022; 199:51-58. [DOI: 10.1086/717176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Farrell MJ, Park AW, Cressler CE, Dallas T, Huang S, Mideo N, Morales-Castilla I, Davies TJ, Stephens P. The ghost of hosts past: impacts of host extinction on parasite specificity. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200351. [PMID: 34538147 PMCID: PMC8450631 DOI: 10.1098/rstb.2020.0351] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2021] [Indexed: 11/29/2022] Open
Abstract
A growing body of research is focused on the extinction of parasite species in response to host endangerment and declines. Beyond the loss of parasite species richness, host extinction can impact apparent parasite host specificity, as measured by host richness or the phylogenetic distances among hosts. Such impacts on the distribution of parasites across the host phylogeny can have knock-on effects that may reshape the adaptation of both hosts and parasites, ultimately shifting the evolutionary landscape underlying the potential for emergence and the evolution of virulence across hosts. Here, we examine how the reshaping of host phylogenies through extinction may impact the host specificity of parasites, and offer examples from historical extinctions, present-day endangerment, and future projections of biodiversity loss. We suggest that an improved understanding of the impact of host extinction on contemporary host-parasite interactions may shed light on core aspects of disease ecology, including comparative studies of host specificity, virulence evolution in multi-host parasite systems, and future trajectories for host and parasite biodiversity. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
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Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | | | - Clayton E. Cressler
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Tad Dallas
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70806, USA
- Department of Biological Sciences, University of South Carolina, Columbia, SC, 29208, USA
| | - Shan Huang
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Ignacio Morales-Castilla
- Universidad de Alcalá, GloCEE - Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, 28805 Alcalá de Henares, Madrid, Spain
| | - T. Jonathan Davies
- Department of Botany, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, Canada, V6T 1Z4
- Department of Botany and Plant Biotechnology, African Centre for DNA Barcoding, University of Johannesburg, Johannesburg 2092, South Africa
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Kamiya T, Davis NM, Greischar MA, Schneider D, Mideo N. Linking functional and molecular mechanisms of host resilience to malaria infection. eLife 2021; 10:e65846. [PMID: 34636723 PMCID: PMC8510579 DOI: 10.7554/elife.65846] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/16/2021] [Indexed: 12/30/2022] Open
Abstract
It remains challenging to understand why some hosts suffer severe illnesses, while others are unscathed by the same infection. We fitted a mathematical model to longitudinal measurements of parasite and red blood cell density in murine hosts from diverse genetic backgrounds to identify aspects of within-host interactions that explain variation in host resilience and survival during acute malaria infection. Among eight mouse strains that collectively span 90% of the common genetic diversity of laboratory mice, we found that high host mortality was associated with either weak parasite clearance, or a strong, yet imprecise response that inadvertently removes uninfected cells in excess. Subsequent cross-sectional cytokine assays revealed that the two distinct functional mechanisms of poor survival were underpinned by low expression of either pro- or anti-inflammatory cytokines, respectively. By combining mathematical modelling and molecular immunology assays, our study uncovered proximate mechanisms of diverse infection outcomes across multiple host strains and biological scales.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology and Evolutionary Biology, University of TorontoTorontoCanada
| | - Nicole M Davis
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Megan A Greischar
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthacaUnited States
| | - David Schneider
- Department of Microbiology and Immunology, Stanford UniversityStanfordUnited States
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of TorontoTorontoCanada
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McLeod DV, Wahl LM, Mideo N. Mosaic vaccination: How distributing different vaccines across a population could improve epidemic control. Evol Lett 2021; 5:458-471. [PMID: 34621533 PMCID: PMC8484727 DOI: 10.1002/evl3.252] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 07/27/2021] [Indexed: 01/19/2023] Open
Abstract
Although vaccination has been remarkably effective against some pathogens, for others, rapid antigenic evolution results in vaccination conferring only weak and/or short‐lived protection. Consequently, considerable effort has been invested in developing more evolutionarily robust vaccines, either by targeting highly conserved components of the pathogen (universal vaccines) or by including multiple immunological targets within a single vaccine (multi‐epitope vaccines). An unexplored third possibility is to vaccinate individuals with one of a number of qualitatively different vaccines, creating a “mosaic” of individual immunity in the population. Here we explore whether a mosaic vaccination strategy can deliver superior epidemiological outcomes to “conventional” vaccination, in which all individuals receive the same vaccine. We suppose vaccine doses can be distributed between distinct vaccine “targets” (e.g., different surface proteins against which an immune response can be generated) and/or immunologically distinct variants at these targets (e.g., strains); the pathogen can undergo antigenic evolution at both targets. Using simple mathematical models, here we provide a proof‐of‐concept that mosaic vaccination often outperforms conventional vaccination, leading to fewer infected individuals, improved vaccine efficacy, and lower individual risks over the course of the epidemic.
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Affiliation(s)
- David V McLeod
- Centre D'Ecologie Fonctionnelle & Evolutive CNRS Montpellier 34090 France
| | - Lindi M Wahl
- Mathematics Western University London ON N6A 5B7 Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON M5S 3B2 Canada
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10
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Wait LF, Kamiya T, Fairlie-Clarke KJ, Metcalf CJE, Graham AL, Mideo N. Differential drivers of intraspecific and interspecific competition during malaria-helminth co-infection. Parasitology 2021; 148:1030-1039. [PMID: 33971991 PMCID: PMC11010048 DOI: 10.1017/s003118202100072x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/14/2021] [Accepted: 05/04/2021] [Indexed: 11/05/2022]
Abstract
Various host and parasite factors interact to determine the outcome of infection. We investigated the effects of two factors on the within-host dynamics of malaria in mice: initial infectious dose and co-infection with a helminth that limits the availability of red blood cells (RBCs). Using a statistical, time-series approach to model the within-host ‘epidemiology’ of malaria, we found that increasing initial dose reduced the time to peak cell-to-cell parasite propagation, but also reduced its magnitude, while helminth co-infection delayed peak cell-to-cell propagation, except at the highest malaria doses. Using a mechanistic model of within-host infection dynamics, we identified dose-dependence in parameters describing host responses to malaria infection and uncovered a plausible explanation of the observed differences in single vs co-infections. Specifically, in co-infections, our model predicted a higher background death rate of RBCs. However, at the highest dose, when intraspecific competition between malaria parasites would be highest, these effects of co-infection were not observed. Such interactions between initial dose and co-infection, although difficult to predict a priori, are key to understanding variation in the severity of disease experienced by hosts and could inform studies of malaria transmission dynamics in nature, where co-infection and low doses are the norm.
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Affiliation(s)
- L. F. Wait
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - T. Kamiya
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | | | - C. J. E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - A. L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey, USA
| | - N. Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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11
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Whitlock AOB, Juliano JJ, Mideo N. Immune selection suppresses the emergence of drug resistance in malaria parasites but facilitates its spread. PLoS Comput Biol 2021; 17:e1008577. [PMID: 34280179 PMCID: PMC8321109 DOI: 10.1371/journal.pcbi.1008577] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 07/29/2021] [Accepted: 06/04/2021] [Indexed: 12/23/2022] Open
Abstract
Although drug resistance in Plasmodium falciparum typically evolves in regions of low transmission, resistance spreads readily following introduction to regions with a heavier disease burden. This suggests that the origin and the spread of resistance are governed by different processes, and that high transmission intensity specifically impedes the origin. Factors associated with high transmission, such as highly immune hosts and competition within genetically diverse infections, are associated with suppression of resistant lineages within hosts. However, interactions between these factors have rarely been investigated and the specific relationship between adaptive immunity and selection for resistance has not been explored. Here, we developed a multiscale, agent-based model of Plasmodium parasites, hosts, and vectors to examine how host and parasite dynamics shape the evolution of resistance in populations with different transmission intensities. We found that selection for antigenic novelty (“immune selection”) suppressed the evolution of resistance in high transmission settings. We show that high levels of population immunity increased the strength of immune selection relative to selection for resistance. As a result, immune selection delayed the evolution of resistance in high transmission populations by allowing novel, sensitive lineages to remain in circulation at the expense of the spread of a resistant lineage. In contrast, in low transmission settings, we observed that resistant strains were able to sweep to high population prevalence without interference. Additionally, we found that the relationship between immune selection and resistance changed when resistance was widespread. Once resistance was common enough to be found on many antigenic backgrounds, immune selection stably maintained resistant parasites in the population by allowing them to proliferate, even in untreated hosts, when resistance was linked to a novel epitope. Our results suggest that immune selection plays a role in the global pattern of resistance evolution. Drug resistance in the malaria parasite, Plasmodium falciparum, presents an ongoing public health challenge, but aspects of its evolution are poorly understood. Although antimalarial resistance is common worldwide, it can typically be traced to just a handful of evolutionary origins. Counterintuitively, although Sub Saharan Africa bears 90% of the global malaria burden, resistance typically originates in regions where transmission intensity is low. In high transmission regions, infections are genetically diverse, and hosts have significant standing adaptive immunity, both of which are known to suppress the frequency of resistance within infections. However, interactions between immune-driven selection, transmission intensity, and resistance have not been investigated. Using a multiscale, agent-based model, we found that high transmission intensity slowed the evolution of resistance via its effect on host population immunity. High host immunity strengthened selection for antigenic novelty, interfering with selection for resistance and allowing sensitive lineages to suppress resistant lineages in untreated hosts. However, once resistance was common in the circulating parasite population, immune selection maintained it in the population at a high prevalence. Our findings provide a novel explanation for observations about the origin of resistance and suggest that adaptive immunity is a critical component of selection.
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Affiliation(s)
| | - Jonathan J. Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Canada
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12
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Affiliation(s)
- Devin Kirk
- Department of Ecology and Evolutionary Biology University of Toronto Toronto OntarioM5S 1A1Canada
| | - Megan Greischar
- Department of Ecology and Evolutionary Biology University of Toronto Toronto OntarioM5S 1A1Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology University of Toronto Toronto OntarioM5S 1A1Canada
| | - Martin Krkošek
- Department of Ecology and Evolutionary Biology University of Toronto Toronto OntarioM5S 1A1Canada
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13
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Peters MAE, Greischar MA, Mideo N. Challenges in forming inferences from limited data: a case study of malaria parasite maturation. J R Soc Interface 2021; 18:20210065. [PMID: 33906391 DOI: 10.1098/rsif.2021.0065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Inferring biological processes from population dynamics is a common challenge in ecology, particularly when faced with incomplete data. This challenge extends to inferring parasite traits from within-host infection dynamics. We focus on rodent malaria infections (Plasmodium berghei), a system for which previous work inferred an immune-mediated extension in the length of the parasite development cycle within red blood cells. By developing a system of delay-differential equations to describe within-host infection dynamics and simulating data, we demonstrate the potential to obtain biased estimates of parasite (and host) traits when key biological processes are not considered. Despite generating infection dynamics using a fixed parasite developmental cycle length, we find that known sources of measurement bias in parasite stage and abundance data can affect estimates of parasite developmental duration, with stage misclassification driving inferences about extended cycle length. We discuss alternative protocols and statistical methods that can mitigate such misestimation.
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Affiliation(s)
- Madeline A E Peters
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto Ontario, Canada
| | - Megan A Greischar
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, The University of Toronto, Toronto Ontario, Canada
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Krkošek M, Jarvis-Cross M, Wadhawan K, Berry I, Soucy JPR, Bodner K, Greiner A, Krichel L, Penk S, Shea D, Vargas Soto JS, Tekwa EW, Mideo N, Molnár PK. Establishment, contagiousness, and initial spread of SARS-CoV-2 in Canada. Facets (Ott) 2021. [DOI: 10.1139/facets-2020-0055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
This study empirically quantifies dynamics of SARS-CoV-2 establishment and early spread in Canada. We developed a transmission model that was simulation tested and fitted in a Bayesian framework to timeseries of new cases per day prior to physical distancing interventions. A hierarchical version was fitted to all provinces simultaneously to obtain average estimates for Canada. Across scenarios of a latent period of 2–4 d and an infectious period of 5–9 d, the R0 estimate for Canada ranges from a minimum of 3.0 (95% CI: 2.3–3.9) to a maximum of 5.3 (95% CI: 3.9–7.1). Among provinces, the estimated commencement of community transmission ranged from 3 d before to 50 d after the first reported case and from 2 to 25 d before the first reports of community transmission. Among parameter scenarios and provinces, the median reduction in transmission needed to obtain R0 < 1 ranged from 46% (95% CI: 43%–48%) to 89% (95% CI: 88%–90%). Our results indicate that local epidemics of SARS-CoV-2 in Canada entail high levels of stochasticity, contagiousness, and observation delay, which facilitates rapid undetected spread and requires comprehensive testing and contact tracing for its containment.
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Affiliation(s)
- Martin Krkošek
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Madeline Jarvis-Cross
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Kiran Wadhawan
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Isha Berry
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Jean-Paul R. Soucy
- Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, ON M5T 3M7, Canada
| | - Korryn Bodner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Laboratory of Quantitative Global Change Ecology, Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Ariel Greiner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Leila Krichel
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Stephanie Penk
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Laboratory of Quantitative Global Change Ecology, Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Dylan Shea
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Juan S. Vargas Soto
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
- Laboratory of Quantitative Global Change Ecology, Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
| | - Ed W. Tekwa
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901-8551, USA
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Péter K. Molnár
- Laboratory of Quantitative Global Change Ecology, Department of Biological Sciences, University of Toronto Scarborough, 1265 Military Trail, Toronto, ON M1C 1A4, Canada
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15
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Price TAR, Windbichler N, Unckless RL, Sutter A, Runge JN, Ross PA, Pomiankowski A, Nuckolls NL, Montchamp-Moreau C, Mideo N, Martin OY, Manser A, Legros M, Larracuente AM, Holman L, Godwin J, Gemmell N, Courret C, Buchman A, Barrett LG, Lindholm AK. Resistance to natural and synthetic gene drive systems. J Evol Biol 2020; 33:1345-1360. [PMID: 32969551 PMCID: PMC7796552 DOI: 10.1111/jeb.13693] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 08/10/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023]
Abstract
Scientists are rapidly developing synthetic gene drive elements intended for release into natural populations. These are intended to control or eradicate disease vectors and pests, or to spread useful traits through wild populations for disease control or conservation purposes. However, a crucial problem for gene drives is the evolution of resistance against them, preventing their spread. Understanding the mechanisms by which populations might evolve resistance is essential for engineering effective gene drive systems. This review summarizes our current knowledge of drive resistance in both natural and synthetic gene drives. We explore how insights from naturally occurring and synthetic drive systems can be integrated to improve the design of gene drives, better predict the outcome of releases and understand genomic conflict in general.
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Affiliation(s)
- Tom A. R. Price
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | | | - Andreas Sutter
- School of Biological Sciences, Norwich Research Park, University of East Anglia, Norwich NR4 7TJ, UK
| | - Jan-Niklas Runge
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
| | - Perran A. Ross
- Bio21 and the School of Biosciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Andrew Pomiankowski
- Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | | | - Catherine Montchamp-Moreau
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2 Canada
| | - Oliver Y. Martin
- Department of Biology (D-BIOL) & Institute of Integrative Biology (IBZ), ETH Zurich, Universitätsstrasse 16, CH 8092 Zurich, Switzerland
| | - Andri Manser
- Department of Ecology, Evolution and Behaviour, University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthieu Legros
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | | | - Luke Holman
- School of Biosciences, The University of Melbourne, Melbourne, Victoria 3010, Australia
| | - John Godwin
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA
| | - Neil Gemmell
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Cécile Courret
- Evolution Génome Comportement et Ecologie, CNRS, IRD, Université Paris-Saclay, Gif sur Yvette 91190, France
- Department of Biology, University of Rochester, Rochester, New York, USA
| | - Anna Buchman
- University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, CA 94080
| | - Luke G. Barrett
- CSIRO Agriculture and Food, Canberra, Australian Capital Territory, Australia
| | - Anna K. Lindholm
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
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16
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Kamiya T, Greischar MA, Schneider DS, Mideo N. Uncovering drivers of dose-dependence and individual variation in malaria infection outcomes. PLoS Comput Biol 2020; 16:e1008211. [PMID: 33031367 PMCID: PMC7544130 DOI: 10.1371/journal.pcbi.1008211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 07/31/2020] [Indexed: 01/01/2023] Open
Abstract
To understand why some hosts get sicker than others from the same type of infection, it is essential to explain how key processes, such as host responses to infection and parasite growth, are influenced by various biotic and abiotic factors. In many disease systems, the initial infection dose impacts host morbidity and mortality. To explore drivers of dose-dependence and individual variation in infection outcomes, we devised a mathematical model of malaria infection that allowed host and parasite traits to be linear functions (reaction norms) of the initial dose. We fitted the model, using a hierarchical Bayesian approach, to experimental time-series data of acute Plasmodium chabaudi infection across doses spanning seven orders of magnitude. We found evidence for both dose-dependent facilitation and debilitation of host responses. Most importantly, increasing dose reduced the strength of activation of indiscriminate host clearance of red blood cells while increasing the half-life of that response, leading to the maximal response at an intermediate dose. We also explored the causes of diverse infection outcomes across replicate mice receiving the same dose. Besides random noise in the injected dose, we found variation in peak parasite load was due to unobserved individual variation in host responses to clear infected cells. Individual variation in anaemia was likely driven by random variation in parasite burst size, which is linked to the rate of host cells lost to malaria infection. General host vigour in the absence of infection was also correlated with host health during malaria infection. Our work demonstrates that the reaction norm approach provides a useful quantitative framework for examining the impact of a continuous external factor on within-host infection processes.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Megan A. Greischar
- Department of Ecology Evolutionary Biology, Cornell University, United States of America
| | - David S. Schneider
- Program in Immunology, Stanford University, Stanford, California, United States of America
- Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
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17
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Abstract
AbstractRecent years have seen significant progress in understanding the impact of host community assemblage on disease risk, yet diversity in disease vectors has rarely been investigated. Using published malaria and mosquito surveys from Kenya, we analyzed the relationship between malaria prevalence and multiple axes of mosquito diversity: abundance, species richness, and composition. We found a net amplification of malaria prevalence by vector species richness, a result of a strong direct positive association between richness and prevalence alongside a weak indirect negative association between the two, mediated through mosquito community composition. One plausible explanation of these patterns is species niche complementarity, whereby less competent vector species contribute to disease transmission by filling spatial or temporal gaps in transmission left by dominant vectors. A greater understanding of vector community assemblage and function, as well as any interactions between host and vector biodiversity, could offer insights to both fundamental and applied ecology.
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18
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Abstract
Repeated emergence of zoonotic viruses from bat reservoirs into human populations demands predictive approaches to preemptively identify virus-carrying bat species. Here, we use machine learning to examine drivers of viral diversity in bats, determine whether those drivers depend on viral genome type, and predict undetected viral carriers. Our results indicate that bat species with longer life spans, broad geographic distributions in the eastern hemisphere, and large group sizes carry more viruses overall. Life span was a stronger predictor of deoxyribonucleic acid viral diversity, while group size and family were more important for predicting ribonucleic acid viruses, potentially reflecting broad differences in infection duration. Importantly, our models predict 54 bat species as likely carriers of zoonotic viruses, despite not currently being considered reservoirs. Mapping these predictions as a proportion of local bat diversity, we identify global regions where efforts to reduce disease spillover into humans by identifying viral carriers may be most productive.
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Affiliation(s)
- Cylita Guy
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Department of BiologyUniversity of Toronto at MississaugaMississaugaONCanada
| | - John M. Ratcliffe
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
- Department of BiologyUniversity of Toronto at MississaugaMississaugaONCanada
| | - Nicole Mideo
- Department of Ecology and Evolutionary BiologyUniversity of TorontoTorontoONCanada
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19
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Greischar MA, Alexander HK, Bashey F, Bento AI, Bhattacharya A, Bushman M, Childs LM, Daversa DR, Day T, Faust CL, Gallagher ME, Gandon S, Glidden CK, Halliday FW, Hanley KA, Kamiya T, Read AF, Schwabl P, Sweeny AR, Tate AT, Thompson RN, Wale N, Wearing HJ, Yeh PJ, Mideo N. Evolutionary consequences of feedbacks between within-host competition and disease control. Evol Med Public Health 2020; 2020:30-34. [PMID: 32099654 PMCID: PMC7027713 DOI: 10.1093/emph/eoaa004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/14/2022]
Abstract
Lay Summary: Competition often occurs among diverse parasites within a single host, but control efforts could change its strength. We examined how the interplay between competition and control could shape the evolution of parasite traits like drug resistance and disease severity.
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Affiliation(s)
- Megan A Greischar
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Helen K Alexander
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Farrah Bashey
- Department of Biology, Indiana University, 1001 E. 3rd St., Bloomington, IN 47405, USA
| | - Ana I Bento
- Odum School of Ecology and the Center for the Ecology of Infectious Diseases, University of Georgia, 140 E Green St., Athens, GA 30602, USA
| | - Amrita Bhattacharya
- Department of Biology, Indiana University, 1001 E. 3rd St., Bloomington, IN 47405, USA
| | - Mary Bushman
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Lauren M Childs
- Department of Mathematics, McBryde Hall, Virginia Tech, Blacksburg, VA 24061, USA
| | - David R Daversa
- Institute of Integrative Biology, University of Liverpool, Liverpool, L69 3BX, UK.,Institute of Zoology, Zoological Society of London, Regent's Park, NW1 4RY, UK
| | - Troy Day
- Departments of Mathematics & Biology, Jeffery Hall, Queen's University, Kingston, ON K7L 3N6, Canada
| | - Christina L Faust
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Sylvain Gandon
- CEFE UMR 5175, CNRS - Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919, Route de Mende, 34293 Montpellier Cedex 5, France
| | - Caroline K Glidden
- Department of Integrative Biology, Oregon State University, 3029 Cordley Hall Corvallis, OR 97331, USA
| | - Fletcher W Halliday
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, 8057, Switzerland
| | - Kathryn A Hanley
- Department of Biology, New Mexico State University, Foster Hall, Las Cruces, NM 88003, USA
| | - Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Huck Institutes for the Life Sciences; Departments of Biology and Entomology, Pennsylvania State University, University Park, PA 16802, USA
| | - Philipp Schwabl
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Amy R Sweeny
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK
| | - Ann T Tate
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Robin N Thompson
- Department of Zoology, University of Oxford, Zoology Research and Administration Building, 11a Mansfield Road, Oxford OX1 3SZ, UK.,Mathematical Institute, University of Oxford, Woodstock Road, Oxford OX2 6GG, UK.,Christ Church, University of Oxford, St Aldates, Oxford OX1 1DP, UK
| | - Nina Wale
- Department of Ecology & Evolutionary Biology, University of Michigan, 1105 North University Ave, Biological Sciences Building, Ann Arbor, MI 48109, USA
| | - Helen J Wearing
- Departments of Biology and Mathematics & Statistics, The University of New Mexico, Albuquerque, NM 87131, USA
| | - Pamela J Yeh
- Department of Ecology & Evolutionary Biology, University of California, Los Angeles, 621 Charles E Young Dr South, Los Angeles, CA 90095, USA
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
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20
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Kamiya T, Greischar MA, Wadhawan K, Gilbert B, Paaijmans K, Mideo N. Temperature-dependent variation in the extrinsic incubation period elevates the risk of vector-borne disease emergence. Epidemics 2019; 30:100382. [PMID: 32004794 DOI: 10.1016/j.epidem.2019.100382] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying ecological drivers of disease transmission is central to understanding disease risks. For vector-borne diseases, temperature is a major determinant of transmission because vital parameters determining the fitness of parasites and vectors are highly temperature-sensitive, including the extrinsic incubation period required for parasites to develop within the vector. Temperature also underlies dramatic differences in the individual-level variation in the extrinsic incubation period, yet the influence of this variation in disease transmission is largely unexplored. We incorporate empirical estimates of dengue virus extrinsic incubation period and its variation across a range of temperatures into a stochastic model to examine the consequences for disease emergence. We find that such variation impacts the probability of disease emergence because exceptionally rapid, but empirically observed incubation - typically ignored by modelling only the average - increases the chance of disease emergence even at the limits of the temperature range for dengue transmission. We show that variation in the extrinsic incubation period causes the greatest proportional increase in the risk of disease emergence at cooler temperatures where the mean incubation period is long, and associated variation is large. Thus, ignoring EIP variation will likely lead to underestimation of the risk of vector-borne disease emergence in temperate climates.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada.
| | - Megan A Greischar
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Kiran Wadhawan
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Benjamin Gilbert
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
| | - Krijn Paaijmans
- Center for Evolution & Medicine, Biodesign Center for Immunotherapy, Vaccines and Virotherapy, School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, ON M5S 3B2, Canada
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21
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Greischar MA, Beck-Johnson LM, Mideo N. Partitioning the influence of ecology across scales on parasite evolution. Evolution 2019; 73:2175-2188. [PMID: 31495911 DOI: 10.1111/evo.13840] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/31/2019] [Indexed: 11/30/2022]
Abstract
Vector-borne parasites must succeed at three scales to persist: they must proliferate within a host, establish in vectors, and transmit back to hosts. Ecology outside the host undergoes dramatic seasonal and human-induced changes, but predicting parasite evolutionary responses requires integrating their success across scales. We develop a novel, data-driven model to titrate the evolutionary impact of ecology at multiple scales on human malaria parasites. We investigate how parasites invest in transmission versus proliferation, a life-history trait that influences disease severity and spread. We find that transmission investment controls the pattern of host infectiousness over the course of infection: a trade-off emerges between early and late infectiousness, and the optimal resolution of that trade-off depends on ecology outside the host. An expanding epidemic favors rapid proliferation, and can overwhelm the evolutionary influence of host recovery rates and mosquito population dynamics. If transmission investment and recovery rate are positively correlated, then ecology outside the host imposes potent selection for aggressive parasite proliferation at the expense of transmission. Any association between transmission investment and recovery represents a key unknown, one that is likely to influence whether the evolutionary consequences of interventions are beneficial or costly for human health.
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Affiliation(s)
- Megan A Greischar
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
| | | | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, M5S 3B2, Canada
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22
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Hall MD, Mideo N. Linking sex differences to the evolution of infectious disease life-histories. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0431. [PMID: 30150228 DOI: 10.1098/rstb.2017.0431] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/23/2022] Open
Abstract
Sex differences in the prevalence, course and severity of infection are widespread, yet the evolutionary consequences of these differences remain unclear. Understanding how male-female differences affect the trajectory of infectious disease requires connecting the contrasting dynamics that pathogens might experience within each sex to the number of susceptible and infected individuals that are circulating in a population. In this study, we build on theory using genetic covariance functions to link the growth of a pathogen within a host to the evolution and spread of disease between individuals. Using the Daphnia-Pasteuria system as a test case, we show that on the basis of within-host dynamics alone, females seem to be more evolutionarily liable for the pathogen, with higher spore loads and greater divergence among pathogen genotypes as infection progresses. Between-host transmission, however, appears to offset the lower performance of a pathogen within a male host, making even subtle differences between the sexes evolutionarily relevant, as long as the selection generated by the between-host dynamics is sufficiently strong. Our model suggests that relatively simple differences in within-host processes occurring in males and females can lead to complex patterns of genetic constraint on pathogen evolution, particularly during an expanding epidemic.This article is part of the theme issue 'Linking local adaptation with the evolution of sex differences'.
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Affiliation(s)
- Matthew D Hall
- School of Biological Sciences and Centre for Geometric Biology, Monash University, Melbourne, Victoria 3800, Australia
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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23
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Greischar MA, Reece SE, Savill NJ, Mideo N. The Challenge of Quantifying Synchrony in Malaria Parasites. Trends Parasitol 2019; 35:341-355. [PMID: 30952484 DOI: 10.1016/j.pt.2019.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/21/2022]
Abstract
Malaria infection is often accompanied by periodic fevers, triggered by synchronous cycles of parasite replication within the host. The degree of synchrony in parasite development influences the efficacy of drugs and immune defenses and is therefore relevant to host health and infectiousness. Synchrony is thought to vary over the course of infection and across different host-parasite genotype or species combinations, but the evolutionary significance - if any - of this diversity remains elusive. Standardized methods are lacking, but the most common metric for quantifying synchrony is the percentage of parasites in a particular developmental stage. We use a heuristic model to show that this metric is often unacceptably biased. Methodological challenges must be addressed to characterize diverse patterns of synchrony and their consequences for disease severity and spread.
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Affiliation(s)
- Megan A Greischar
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.
| | - Sarah E Reece
- Institute of Evolutionary Biology and Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Nicholas J Savill
- Institute of Evolutionary Biology and Institute of Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
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24
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Guy C, Thiagavel J, Mideo N, Ratcliffe JM. Phylogeny matters: revisiting 'a comparison of bats and rodents as reservoirs of zoonotic viruses'. R Soc Open Sci 2019; 6:181182. [PMID: 30891262 PMCID: PMC6408376 DOI: 10.1098/rsos.181182] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 01/09/2019] [Indexed: 05/21/2023]
Abstract
Diseases emerging from wildlife have been the source of many major human outbreaks. Predicting key sources of these outbreaks requires an understanding of the factors that explain pathogen diversity in reservoir species. Comparative methods are powerful tools for understanding variation in pathogen diversity and rely on correcting for phylogenetic relatedness among reservoir species. We reanalysed a previously published dataset, examining the relative effects of species' traits on patterns of viral diversity in bats and rodents. We expanded on prior work by using more highly resolved phylogenies for bats and rodents and incorporating a phylogenetically controlled principal components analysis. For rodents, sympatry and torpor use were important predictors of viral richness and, as previously reported, phylogeny had minimal impact in models. For bats, in contrast to prior work, we find that phylogeny does have an effect in models. Patterns of viral diversity in bats were related to geographical distribution (i.e. latitude and range size) and life history (i.e. lifespan, body size and birthing frequency). However, the effects of these predictors were marginal relative to citation count, emphasizing that the ability to accurately assess reservoir status largely depends on sampling effort and highlighting the need for additional data in future comparative studies.
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Affiliation(s)
- Cylita Guy
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada L5L 1C6
| | - Jeneni Thiagavel
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada L5L 1C6
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
| | - John M. Ratcliffe
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON, Canada M5S 3B2
- Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, Mississauga, ON, Canada L5L 1C6
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25
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Kamiya T, Mideo N, Alizon S. Coevolution of virulence and immunosuppression in multiple infections. J Evol Biol 2018; 31:995-1005. [DOI: 10.1111/jeb.13280] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/19/2018] [Accepted: 03/29/2018] [Indexed: 12/22/2022]
Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto ON Canada
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology; University of Toronto; Toronto ON Canada
| | - Samuel Alizon
- Laboratoire MIVEGEC (UMR CNRS 5290, UR IRD 224, UM); Montpellier France
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26
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Birget PLG, Greischar MA, Reece SE, Mideo N. Altered life history strategies protect malaria parasites against drugs. Evol Appl 2018; 11:442-455. [PMID: 29636798 PMCID: PMC5891063 DOI: 10.1111/eva.12516] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022] Open
Abstract
Drug resistance has been reported against all antimalarial drugs, and while parasites can evolve classical resistance mechanisms (e.g., efflux pumps), it is also possible that changes in life history traits could help parasites evade the effects of treatment. The life history of malaria parasites is governed by an intrinsic resource allocation problem: specialized stages are required for transmission, but producing these stages comes at the cost of producing fewer of the forms required for within-host survival. Drug treatment, by design, alters the probability of within-host survival, and so should alter the costs and benefits of investing in transmission. Here, we use a within-host model of malaria infection to predict optimal patterns of investment in transmission in the face of different drug treatment regimes and determine the extent to which alternative patterns of investment can buffer the fitness loss due to drugs. We show that over a range of drug doses, parasites are predicted to adopt "reproductive restraint" (investing more in asexual replication and less in transmission) to maximize fitness. By doing so, parasites recoup some of the fitness loss imposed by drugs, though as may be expected, increasing dose reduces the extent to which altered patterns of transmission investment can benefit parasites. We show that adaptation to drug-treated infections could result in more virulent infections in untreated hosts. This work emphasizes that in addition to classical resistance mechanisms, drug treatment generates selection for altered parasite life history. Understanding how any shifts in life history will alter the efficacy of drugs, as well as any limitations on such shifts, is important for evaluating and predicting the consequences of drug treatment.
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Affiliation(s)
- Philip L. G. Birget
- Institutes of Evolutionary Biology, Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
| | - Megan A. Greischar
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Sarah E. Reece
- Institutes of Evolutionary Biology, Immunology and Infection ResearchUniversity of EdinburghEdinburghUK
| | - Nicole Mideo
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoONCanada
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27
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Abstract
Biological rhythms are thought to have evolved to enable organisms to organize their activities according to the earth's predictable cycles, but quantifying the fitness advantages of rhythms is challenging and data revealing their costs and benefits are scarce. More difficult still is explaining why parasites that live exclusively within the bodies of other organisms have biological rhythms. Rhythms exist in the development and traits of parasites, in host immune responses, and in disease susceptibility. This raises the possibility that timing matters for how hosts and parasites interact and, consequently, for the severity and transmission of diseases. Here, we take an evolutionary ecological perspective to examine why parasites exhibit biological rhythms and how their rhythms are regulated. Specifically, we examine the adaptive significance (evolutionary costs and benefits) of rhythms for parasites and explore to what extent interactions between hosts and parasites can drive rhythms in infections. That parasites with altered rhythms can evade the effects of control interventions underscores the urgent need to understand how and why parasites exhibit biological rhythms. Thus, we contend that examining the roles of biological rhythms in disease offers innovative approaches to improve health and opens up a new arena for studying host-parasite (and host-parasite-vector) coevolution.
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Affiliation(s)
- Sarah E. Reece
- Institutes of Evolution, Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
- Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Kimberley F. Prior
- Institutes of Evolution, Immunology and Infection Research, University of Edinburgh, Edinburgh, UK
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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28
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Kamiya T, Greischar MA, Mideo N. Epidemiological consequences of immune sensitisation by pre-exposure to vector saliva. PLoS Negl Trop Dis 2017; 11:e0005956. [PMID: 28991904 PMCID: PMC5648264 DOI: 10.1371/journal.pntd.0005956] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 10/19/2017] [Accepted: 09/12/2017] [Indexed: 11/25/2022] Open
Abstract
Blood-feeding arthropods—like mosquitoes, sand flies, and ticks—transmit many diseases that impose serious public health and economic burdens. When a blood-feeding arthropod bites a mammal, it injects saliva containing immunogenic compounds that facilitate feeding. Evidence from Leishmania, Plasmodium and arboviral infections suggests that the immune responses elicited by pre-exposure to arthropod saliva can alter disease progression if the host later becomes infected. Such pre-sensitisation of host immunity has been reported to both exacerbate and limit infection symptoms, depending on the system in question, with potential implications for recovery. To explore if and how immune pre-sensitisation alters the effects of vector control, we develop a general model of vector-borne disease. We show that the abundance of pre-sensitised infected hosts should increase when control efforts moderately increase vector mortality rates. If immune pre-sensitisation leads to more rapid clearance of infection, increasing vector mortality rates may achieve greater than expected disease control. However, when immune pre-sensitisation prolongs the duration of infection, e.g., through mildly symptomatic cases for which treatment is unlikely to be sought, vector control can actually increase the total number of infected hosts. The rising infections may go unnoticed unless active surveillance methods are used to detect such sub-clinical individuals, who could provide long-lasting reservoirs for transmission and suffer long-term health consequences of those sub-clinical infections. Sensitivity analysis suggests that these negative consequences could be mitigated through integrated vector management. While the effect of saliva pre-exposure on acute symptoms is well-studied for leishmaniasis, the immunological and clinical consequences are largely uncharted for other vector-parasite-host combinations. We find a large range of plausible epidemiological outcomes, positive and negative for public health, underscoring the need to quantify how immune pre-sensitisation modulates recovery and transmission rates in vector-borne diseases. Many diseases of health and economic importance are transmitted by arthropod vectors, like mosquitoes, sand flies, and ticks. When a blood-feeding arthropod bites a mammal, it injects saliva containing compounds that facilitate feeding. The immune responses elicited by previous exposure to vector saliva can alter disease severity if the host later becomes infected. Such pre-sensitisation of host immunity has been linked to either exacerbation or mitigation of symptoms in a number of disease systems. We develop a general model of vector-borne disease to examine how vector control efforts alter the frequency of immune pre-sensitisation and thus change the epidemiological impact of control. We show that the abundance of pre-sensitised infected hosts should increase when control efforts moderately increase vector mortality rates. When immune pre-sensitisation leads to longer infections—by generating sub-clinical cases for which treatment is not rapidly sought—killing vectors can lead to unexpected increases in the number of infected hosts. The rising case burden may go unnoticed unless sub-clinical individuals are tested for infection. Conversely, if immune pre-sensitisation leads to more rapid clearance of infection, increasing vector mortality rates may achieve greater than expected disease control. Our findings highlight the need to quantify how immune pre-sensitisation modulates clinical outcomes and parasite transmission in humans.
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Affiliation(s)
- Tsukushi Kamiya
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Megan A Greischar
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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Wilson AJ, Morgan ER, Booth M, Norman R, Perkins SE, Hauffe HC, Mideo N, Antonovics J, McCallum H, Fenton A. What is a vector? Philos Trans R Soc Lond B Biol Sci 2017; 372:20160085. [PMID: 28289253 PMCID: PMC5352812 DOI: 10.1098/rstb.2016.0085] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/15/2016] [Indexed: 11/18/2022] Open
Abstract
Many important and rapidly emerging pathogens of humans, livestock and wildlife are 'vector-borne'. However, the term 'vector' has been applied to diverse agents in a broad range of epidemiological systems. In this perspective, we briefly review some common definitions, identify the strengths and weaknesses of each and consider the functional differences between vectors and other hosts from a range of ecological, evolutionary and public health perspectives. We then consider how the use of designations can afford insights into our understanding of epidemiological and evolutionary processes that are not otherwise apparent. We conclude that from a medical and veterinary perspective, a combination of the 'haematophagous arthropod' and 'mobility' definitions is most useful because it offers important insights into contact structure and control and emphasizes the opportunities for pathogen shifts among taxonomically similar species with similar feeding modes and internal environments. From a population dynamics and evolutionary perspective, we suggest that a combination of the 'micropredator' and 'sequential' definition is most appropriate because it captures the key aspects of transmission biology and fitness consequences for the pathogen and vector itself. However, we explicitly recognize that the value of a definition always depends on the research question under study.This article is part of the themed issue 'Opening the black box: re-examining the ecology and evolution of parasite transmission'.
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Affiliation(s)
- Anthony James Wilson
- Vector-borne Viral Diseases Programme, The Pirbright Institute, Ash Road, Pirbright, Woking GU24 0NF, UK
| | - Eric René Morgan
- School of Veterinary Sciences, University of Bristol, Life Sciences Building, 24 Tyndall Avenue, Bristol BS8 1TQ, UK
| | - Mark Booth
- School of Medicine, Pharmacy and Health, Durham University, Thornaby TS17 6BH, UK
| | - Rachel Norman
- School of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Sarah Elizabeth Perkins
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
- Department of Biodiversity and Molecular Ecology, Centre for Research and Innovation, Fondazione Edmund Mach, Via E. Mach 1, 38010 S Michele all'Adige (TN), Italy
| | - Heidi Christine Hauffe
- Department of Biodiversity and Molecular Ecology, Centre for Research and Innovation, Fondazione Edmund Mach, Via E. Mach 1, 38010 S Michele all'Adige (TN), Italy
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada M5S 3B2
| | - Janis Antonovics
- Department of Biology, University of Virginia, Charlottesville, VA 22904, USA
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan 4111, Queensland, Australia
| | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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Smith DRM, Mideo N. Modelling the evolution of HIV-1 virulence in response to imperfect therapy and prophylaxis. Evol Appl 2017; 10:297-309. [PMID: 28250813 PMCID: PMC5322411 DOI: 10.1111/eva.12458] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/15/2016] [Indexed: 12/11/2022] Open
Abstract
Average HIV‐1 virulence appears to have evolved in different directions in different host populations since antiretroviral therapy first became available, and models predict that HIV drugs can select for either higher or lower virulence, depending on how treatment is administered. However, HIV virulence evolution in response to “leaky” therapy (treatment that imperfectly suppresses viral replication) and the use of preventive drugs (pre‐exposure prophylaxis) has not been explored. Using adaptive dynamics, we show that higher virulence can evolve when antiretroviral therapy is imperfectly effective and that this evolution erodes some of the long‐term clinical and epidemiological benefits of HIV treatment. The introduction of pre‐exposure prophylaxis greatly reduces infection prevalence, but can further amplify virulence evolution when it, too, is leaky. Increasing the uptake rate of these imperfect interventions increases selection for higher virulence and can lead to counterintuitive increases in infection prevalence in some scenarios. Although populations almost always fare better with access to interventions than without, untreated individuals could experience particularly poor clinical outcomes when virulence evolves. These findings predict that antiretroviral drugs may have underappreciated evolutionary consequences, but that maximizing drug efficacy can prevent this evolutionary response. We suggest that HIV virulence evolution should be closely monitored as access to interventions continues to improve.
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Affiliation(s)
- David R M Smith
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology University of Toronto Toronto ON Canada
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31
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Abstract
The theory that coevolving hosts and parasites create a fluctuating selective environment for one another (i.e., produce Red Queen dynamics) has deep roots in evolutionary biology; yet empirical evidence for Red Queen dynamics remains scarce. Fluctuating coevolutionary dynamics underpin the Red Queen hypothesis for the evolution of sex, as well as hypotheses explaining the persistence of genetic variation under sexual selection, local parasite adaptation, the evolution of mutation rate, and the evolution of nonrandom mating. Coevolutionary models that exhibit Red Queen dynamics typically assume that hosts and parasites encounter one another randomly. However, if related individuals aggregate into family groups or are clustered spatially, related hosts will be more likely to encounter parasites transmitted by genetically similar individuals. Using a model that incorporates familial parasite transmission, we show that a slight degree of familial parasite transmission is sufficient to halt coevolutionary fluctuations. Our results predict that evidence for Red Queen dynamics, and its evolutionary consequences, are most likely to be found in biological systems in which hosts and parasites mix mainly at random, and are less likely to be found in systems with familial aggregation. This presents a challenge to the Red Queen hypothesis and other hypotheses that depend on coevolutionary cycling.
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Affiliation(s)
- Philip B Greenspoon
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada, M5S 3B2
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Ramiro RS, Pollitt LC, Mideo N, Reece SE. Facilitation through altered resource availability in a mixed-species rodent malaria infection. Ecol Lett 2016; 19:1041-50. [PMID: 27364562 PMCID: PMC5025717 DOI: 10.1111/ele.12639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 03/03/2016] [Accepted: 05/13/2016] [Indexed: 12/17/2022]
Abstract
A major challenge in disease ecology is to understand how co-infecting parasite species interact. We manipulate in vivo resources and immunity to explain interactions between two rodent malaria parasites, Plasmodium chabaudi and P. yoelii. These species have analogous resource-use strategies to the human parasites Plasmodium falciparum and P. vivax: P. chabaudi and P. falciparum infect red blood cells (RBC) of all ages (RBC generalist); P. yoelii and P. vivax preferentially infect young RBCs (RBC specialist). We find that: (1) recent infection with the RBC generalist facilitates the RBC specialist (P. yoelii density is enhanced ~10 fold). This occurs because the RBC generalist increases availability of the RBC specialist's preferred resource; (2) co-infections with the RBC generalist and RBC specialist are highly virulent; (3) and the presence of an RBC generalist in a host population can increase the prevalence of an RBC specialist. Thus, we show that resources shape how parasite species interact and have epidemiological consequences.
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Affiliation(s)
- Ricardo S Ramiro
- Institutes of Evolutionary Biology, and Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3JFL, UK
| | - Laura C Pollitt
- Institutes of Evolutionary Biology, and Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3JFL, UK.,Centre for Immunity, Infection & Evolution, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JFL, UK
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Sarah E Reece
- Institutes of Evolutionary Biology, and Immunology and Infection Research, University of Edinburgh, Edinburgh, EH9 3JFL, UK.,Centre for Immunity, Infection & Evolution, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JFL, UK
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33
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Greischar MA, Mideo N, Read AF, Bjørnstad ON. Predicting optimal transmission investment in malaria parasites. Evolution 2016; 70:1542-58. [DOI: 10.1111/evo.12969] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 05/07/2016] [Indexed: 01/07/2023]
Affiliation(s)
- Megan A. Greischar
- Center For Infectious Disease Dynamics, Departments of Entomology and Biology, The Pennsylvania State University; University Park; Pennsylvania 16802
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON M5S 3B2 Canada
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology; University of Toronto; Toronto ON M5S 3B2 Canada
| | - Andrew F. Read
- Center For Infectious Disease Dynamics, Departments of Entomology and Biology, The Pennsylvania State University; University Park; Pennsylvania 16802
- Fogarty International Center; National Institutes of Health; Bethesda Maryland 20892
| | - Ottar N. Bjørnstad
- Center For Infectious Disease Dynamics, Departments of Entomology and Biology, The Pennsylvania State University; University Park; Pennsylvania 16802
- Fogarty International Center; National Institutes of Health; Bethesda Maryland 20892
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Mideo N, Bailey JA, Hathaway NJ, Ngasala B, Saunders DL, Lon C, Kharabora O, Jamnik A, Balasubramanian S, Björkman A, Mårtensson A, Meshnick SR, Read AF, Juliano JJ. A deep sequencing tool for partitioning clearance rates following antimalarial treatment in polyclonal infections. Evol Med Public Health 2016; 2016:21-36. [PMID: 26817485 PMCID: PMC4753362 DOI: 10.1093/emph/eov036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 12/21/2015] [Indexed: 11/14/2022]
Abstract
BACKGROUND AND OBJECTIVES Current tools struggle to detect drug-resistant malaria parasites when infections contain multiple parasite clones, which is the norm in high transmission settings in Africa. Our aim was to develop and apply an approach for detecting resistance that overcomes the challenges of polyclonal infections without requiring a genetic marker for resistance. METHODOLOGY Clinical samples from patients treated with artemisinin combination therapy were collected from Tanzania and Cambodia. By deeply sequencing a hypervariable locus, we quantified the relative abundance of parasite subpopulations (defined by haplotypes of that locus) within infections and revealed evolutionary dynamics during treatment. Slow clearance is a phenotypic, clinical marker of artemisinin resistance; we analyzed variation in clearance rates within infections by fitting parasite clearance curves to subpopulation data. RESULTS In Tanzania, we found substantial variation in clearance rates within individual patients. Some parasite subpopulations cleared as slowly as resistant parasites observed in Cambodia. We evaluated possible explanations for these data, including resistance to drugs. Assuming slow clearance was a stable phenotype of subpopulations, simulations predicted that modest increases in their frequency could substantially increase time to cure. CONCLUSIONS AND IMPLICATIONS By characterizing parasite subpopulations within patients, our method can detect rare, slow clearing parasites in vivo whose phenotypic effects would otherwise be masked. Since our approach can be applied to polyclonal infections even when the genetics underlying resistance are unknown, it could aid in monitoring the emergence of artemisinin resistance. Our application to Tanzanian samples uncovers rare subpopulations with worrying phenotypes for closer examination.
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Affiliation(s)
- Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada;
| | - Jeffrey A Bailey
- Division of Transfusion Medicine, Department of Medicine, University of Massachusetts, Worcester, MA, USA; Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
| | - Nicholas J Hathaway
- Program in Bioinformatics and Integrative Biology, University of Massachusetts, Worcester, MA, USA
| | - Billy Ngasala
- Department of Parasitology, Muhimbili University of Health and Allied Sciences, Dar Es Salaam, Tanzania
| | - David L Saunders
- Division of Immunology and Medicine, USAMC Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Chanthap Lon
- US Army Medical Component, Armed Forces Research Institute of Medical Sciences, Phnom Penh, Cambodia
| | - Oksana Kharabora
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Andrew Jamnik
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Sujata Balasubramanian
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Anders Björkman
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Mårtensson
- Malaria Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden; Centre for Clinical Research Sörmland, Uppsala University, Sweden; Department of Women's and Children's Health, International Maternal and Child Health (IMCH), Uppsala University, Sweden
| | - Steven R Meshnick
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Andrew F Read
- Center for Infectious Disease Dynamics, Department of Biology and Entomology, the Pennsylvania State University, University Park, PA, USA and
| | - Jonathan J Juliano
- Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC, USA; Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
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Kouyos RD, Metcalf CJE, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt LC, Read AF, Smith DL, Standley C, Wale N, Grenfell B. The path of least resistance: aggressive or moderate treatment? Proc Biol Sci 2015; 281:20140566. [PMID: 25253451 DOI: 10.1098/rspb.2014.0566] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The evolution of resistance to antimicrobial chemotherapy is a major and growing cause of human mortality and morbidity. Comparatively little attention has been paid to how different patient treatment strategies shape the evolution of resistance. In particular, it is not clear whether treating individual patients aggressively with high drug dosages and long treatment durations, or moderately with low dosages and short durations can better prevent the evolution and spread of drug resistance. Here, we summarize the very limited available empirical evidence across different pathogens and provide a conceptual framework describing the information required to effectively manage drug pressure to minimize resistance evolution.
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Affiliation(s)
- Roger D Kouyos
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zürich, University of Zürich, Zürich, Switzerland
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Department of Zoology, Oxford University, Oxford, UK
| | - Ruthie Birger
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA
| | - Eili Y Klein
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Center for Advanced Modeling, Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pia Abel zur Wiesch
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Peter Ankomah
- Department of Biology, Emory University, Atlanta, GA, USA
| | - Nimalan Arinaminpathy
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Tiffany L Bogich
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | | | - Charles Brower
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Center for Disease Dynamics, Economics & Policy, Washington, DC, USA
| | - Geoffrey Chi-Johnston
- Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Ted Cohen
- Division of Global Health Equity, Brigham and Women's Hospital and Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
| | - Troy Day
- Departments of Mathematics and Biology, Queen's University, Kingston, Ontario, Canada
| | - Bryan Greenhouse
- Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, VA, USA
| | - Silvie Huijben
- Barcelona Centre for International Health Research, Hospital Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Joshua Metlay
- General Medicine Division, Massachusetts General Hospital, Boston, MA, USA
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Laura C Pollitt
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA Centre for Immunology, Infection and Evolution, University of Edinburgh, Edinburgh, UK
| | - Andrew F Read
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
| | - David L Smith
- Department of Zoology, Oxford University, Oxford, UK
| | - Claire Standley
- Department of Health Policy, George Washington University, Washington, DC, USA
| | - Nina Wale
- Centre for Infectious Disease Dynamics, The Pennsylvania State University, University Park, State College, PA, USA Departments of Biology and Entomology, The Pennsylvania State University, University Park, State College, PA, USA
| | - Bryan Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ, USA Fogarty International Center, National Institutes of Health, Bethesda, MD, USA
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O'Donnell AJ, Mideo N, Reece SE. Disrupting rhythms in Plasmodium chabaudi: costs accrue quickly and independently of how infections are initiated. Malar J 2013; 12:372. [PMID: 24160251 PMCID: PMC3819465 DOI: 10.1186/1475-2875-12-372] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 10/23/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the blood, the synchronous malaria parasite, Plasmodium chabaudi, exhibits a cell-cycle rhythm of approximately 24 hours in which transitions between developmental stages occur at particular times of day in the rodent host. Previous experiments reveal that when the timing of the parasite's cell-cycle rhythm is perturbed relative to the circadian rhythm of the host, parasites suffer a (~50%) reduction in asexual stages and gametocytes. Why it matters for parasites to have developmental schedules in synchronization with the host's rhythm is unknown. The experiment presented here investigates this issue by: (a) validating that the performance of P. chabaudi is negatively affected by mismatch to the host circadian rhythm; (b) testing whether the effect of mismatch depends on the route of infection or the developmental stage of inoculated parasites; and, (c) examining whether the costs of mismatch are due to challenges encountered upon initial infection and/or due to ongoing circadian host processes operating during infection. METHODS The experiment simultaneously perturbed the time of day infections were initiated, the stage of parasite inoculated, and the route of infection. The performance of parasites during the growth phase of infections was compared across the cross-factored treatment groups (i e, all combinations of treatments were represented). RESULTS The data show that mismatch to host rhythms is costly for parasites, reveal that this phenomenon does not depend on the developmental stage of parasites nor the route of infection, and suggest that processes operating at the initial stages of infection are responsible for the costs of mismatch. Furthermore, mismatched parasites are less virulent, in that they cause less anaemia to their hosts. CONCLUSION It is beneficial for parasites to be in synchronization with their host's rhythm, regardless of the route of infection or the parasite stage inoculated. Given that arrested cell-cycle development (quiescence) is implicated in tolerance to drugs, understanding how parasite schedules are established and maintained in the blood is important.
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Affiliation(s)
- Aidan J O'Donnell
- Institutes of Evolution, Immunology and Infection Research, University of Edinburgh, Edinburgh, UK.
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Huijben S, Bell AS, Sim DG, Tomasello D, Mideo N, Day T, Read AF. Aggressive chemotherapy and the selection of drug resistant pathogens. PLoS Pathog 2013; 9:e1003578. [PMID: 24068922 PMCID: PMC3771897 DOI: 10.1371/journal.ppat.1003578] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 07/10/2013] [Indexed: 11/19/2022] Open
Abstract
Drug resistant pathogens are one of the key public health challenges of the 21st century. There is a widespread belief that resistance is best managed by using drugs to rapidly eliminate target pathogens from patients so as to minimize the probability that pathogens acquire resistance de novo. Yet strong drug pressure imposes intense selection in favor of resistance through alleviation of competition with wild-type populations. Aggressive chemotherapy thus generates opposing evolutionary forces which together determine the rate of drug resistance emergence. Identifying treatment regimens which best retard resistance evolution while maximizing health gains and minimizing disease transmission requires empirical analysis of resistance evolution in vivo in conjunction with measures of clinical outcomes and infectiousness. Using rodent malaria in laboratory mice, we found that less aggressive chemotherapeutic regimens substantially reduced the probability of onward transmission of resistance (by >150-fold), without compromising health outcomes. Our experiments suggest that there may be cases where resistance evolution can be managed more effectively with treatment regimens other than those which reduce pathogen burdens as fast as possible. Drug-resistance is a major public health problem. Conventional wisdom on resistance management is to use aggressive chemotherapy to kill pathogens as rapidly as possible so as to prevent them from acquiring resistance. This is the reason why physicians frequently exhort patients to finish drug courses even after they no longer feel sick. However, this approach is based on the notion that we need only prevent new resistant mutants from arising. We hypothesize that in the situation where such mutants are already present at the time of treatment, more aggressive chemotherapy will select for these the fastest by rapidly killing all sensitive competitors. Here we demonstrate in a rodent malaria model that such selection indeed occurs more intensely following aggressive treatment than following less aggressive treatment, without any benefit to host health or infectivity. This suggests that aggressive chemotherapy will not be the best way to retard resistance evolution in some - perhaps many - circumstances. We suggest that an evidence-based approach across a wide range of infectious diseases is needed to manage resistance evolution.
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Affiliation(s)
- Silvie Huijben
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail: (SH); (AFR)
| | - Andrew S. Bell
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Derek G. Sim
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Danielle Tomasello
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Nicole Mideo
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Troy Day
- Departments of Mathematics, Statistics and Biology, Jeffery Hall, Queen's University, Kingston, Ontario, Canada
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania, United States of America
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (SH); (AFR)
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38
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Mideo N, Kennedy DA, Carlton JM, Bailey JA, Juliano JJ, Read AF. Ahead of the curve: next generation estimators of drug resistance in malaria infections. Trends Parasitol 2013; 29:321-8. [PMID: 23746748 PMCID: PMC3694767 DOI: 10.1016/j.pt.2013.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 12/16/2022]
Abstract
Drug resistance is a major obstacle to controlling infectious diseases. A key challenge is detecting the early signs of drug resistance when little is known about its genetic basis. Focusing on malaria parasites, we propose a way to do this. Newly developing or low level resistance at low frequency in patients can be detected through a phenotypic signature: individual parasite variants clearing more slowly following drug treatment. Harnessing the abundance and resolution of deep sequencing data, our 'selection differential' approach addresses some limitations of extant methods of resistance detection, should allow for the earliest detection of resistance in malaria or other multi-clone infections, and has the power to uncover the true scale of the drug resistance problem.
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Affiliation(s)
- Nicole Mideo
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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Read AF, Mideo N. The vector as protector. Nature 2013; 498:177-8. [DOI: 10.1038/nature12252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Abstract
For vector-borne parasites such as malaria, how within- and between-host processes interact to shape transmission is poorly understood. In the host, malaria parasites replicate asexually but for transmission to occur, specialized sexual stages (gametocytes) must be produced. Despite the central role that gametocytes play in disease transmission, explanations of why parasites adjust gametocyte production in response to in-host factors remain controversial. We propose that evolutionary theory developed to explain variation in reproductive effort in multicellular organisms, provides a framework to understand gametocyte investment strategies. We examine why parasites adjust investment in gametocytes according to the impact of changing conditions on their in-host survival. We then outline experiments required to determine whether plasticity in gametocyte investment enables parasites to maintain fitness in a variable environment. Gametocytes are a target for anti-malarial transmission-blocking interventions so understanding plasticity in investment is central to maximizing the success of control measures in the face of parasite evolution.
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Affiliation(s)
- Lucy M. Carter
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
- *Corresponding author. Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3JT, UK. Tel: +44 131 650 7706; Fax: +44 131 650 6564; E-mail:
| | - Björn F.C. Kafsack
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Manuel Llinás
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Nicole Mideo
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Laura C. Pollitt
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | - Sarah E. Reece
- Institute of Evolutionary Biology, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Department of Molecular Biology, 246 Carl Icahn Lab, Washington Road, Princeton University, Princeton, NJ, USA; Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, Millennium Science Complex, University Park, PA, USA and Centre for Immunity, Infection & Evolution. Institutes of Evolution, Immunology and Infection Research, School of Biological Sciences, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
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Mideo N, Reece SE, Smith AL, Metcalf CJE. The Cinderella syndrome: why do malaria-infected cells burst at midnight? Trends Parasitol 2013; 29:10-6. [PMID: 23253515 PMCID: PMC3925801 DOI: 10.1016/j.pt.2012.10.006] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 10/31/2012] [Accepted: 10/31/2012] [Indexed: 11/20/2022]
Abstract
An interesting quirk of many malaria infections is that all parasites within a host – millions of them – progress through their cell cycle synchronously. This surprising coordination has long been recognized, yet there is little understanding of what controls it or why it has evolved. Interestingly, the conventional explanation for coordinated development in other parasite species does not seem to apply here. We argue that for malaria parasites, a critical question has yet to be answered: is the coordination due to parasites bursting at the same time or at a particular time? We explicitly delineate these fundamentally different scenarios, possible underlying mechanistic explanations and evolutionary drivers, and discuss the existing corroborating data and key evidence needed to solve this evolutionary mystery.
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Metcalf CJE, Long GH, Mideo N, Forester JD, Bjørnstad ON, Graham AL. Revealing mechanisms underlying variation in malaria virulence: effective propagation and host control of uninfected red blood cell supply. J R Soc Interface 2012; 9:2804-13. [PMID: 22718989 PMCID: PMC3479917 DOI: 10.1098/rsif.2012.0340] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Malaria parasite clones with the highest transmission rates to mosquitoes also tend to induce the most severe fitness consequences (or virulence) in mammals. This is in accord with expectations from the virulence–transmission trade-off hypothesis. However, the mechanisms underlying how different clones cause virulence are not well understood. Here, using data from eight murine malaria clones, we apply recently developed statistical methods to infer differences in clone characteristics, including induction of differing host-mediated changes in red blood cell (RBC) supply. Our results indicate that the within-host mechanisms underlying similar levels of virulence are variable and that killing of uninfected RBCs by immune effectors and/or retention of RBCs in the spleen may ultimately reduce virulence. Furthermore, the correlation between clone virulence and the degree of host-induced mortality of uninfected RBCs indicates that hosts increasingly restrict their RBC supply with increasing intrinsic virulence of the clone with which they are infected. Our results demonstrate a role for self-harm in self-defence for hosts and highlight the diversity and modes of virulence of malaria.
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Affiliation(s)
- C J E Metcalf
- Department of Zoology, Oxford University, Oxford, UK.
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Abstract
Explaining the contribution of host and pathogen factors in driving infection dynamics is a major ambition in parasitology. There is increasing recognition that analyses based on single summary measures of an infection (e.g., peak parasitaemia) do not adequately capture infection dynamics and so, the appropriate use of statistical techniques to analyse dynamics is necessary to understand infections and, ultimately, control parasites. However, the complexities of within-host environments mean that tracking and analysing pathogen dynamics within infections and among hosts poses considerable statistical challenges. Simple statistical models make assumptions that will rarely be satisfied in data collected on host and parasite parameters. In particular, model residuals (unexplained variance in the data) should not be correlated in time or space. Here we demonstrate how failure to account for such correlations can result in incorrect biological inference from statistical analysis. We then show how mixed effects models can be used as a powerful tool to analyse such repeated measures data in the hope that this will encourage better statistical practices in parasitology.
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Affiliation(s)
- Laura C Pollitt
- Institute of Evolutionary Biology, University of Edinburgh, School of Biological Sciences, Edinburgh, United Kingdom.
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Mideo N, Acosta-Serrano A, Aebischer T, Brown MJF, Fenton A, Friman VP, Restif O, Reece SE, Webster JP, Brown SP. Life in cells, hosts, and vectors: parasite evolution across scales. Infect Genet Evol 2012; 13:344-7. [PMID: 22465537 DOI: 10.1016/j.meegid.2012.03.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/14/2012] [Accepted: 03/17/2012] [Indexed: 12/13/2022]
Abstract
Parasite evolution is increasingly being recognized as one of the most important issues in applied evolutionary biology. Understanding how parasites maximize fitness whilst facing the diverse challenges of living in cells, hosts, and vectors, is central to disease control and offers a novel testing ground for evolutionary theory. The Centre for Immunity, Infection, and Evolution at the University of Edinburgh recently held a symposium to address the question "How do parasites maximise fitness across a range of biological scales?" The symposium brought together researchers whose work looks across scales and environments to understand why and how parasites 'do what they do', tying together mechanism, evolutionary explanations, and public health implications. With a broad range of speakers, our aim was to define and encourage more holistic approaches to studying parasite evolution. Here, we present a synthesis of the current state of affairs in parasite evolution, the research presented at the symposium, and insights gained through our discussions. We demonstrate that such interdisciplinary approaches are possible and identify key areas for future progress.
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Affiliation(s)
- Nicole Mideo
- Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom.
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Abstract
Preventing disease is a major goal of applied bioscience and explaining variation in the harm caused by parasites, and their infectiousness, are major goals of evolutionary biology. The emerging field of evolutionary medicine integrates these two ambitions to inform the development of control strategies that retard or withstand unfavorable parasite evolution. However, as parasites live in hostile and changeable environments – the bodies of other organisms – the success of integrating evolutionary biology with medicine requires a better understanding of how natural selection has solved the problems parasites face. There is increasing appreciation that natural selection shapes parasite strategies to survive in the host and transmit between hosts through facultative (plastic) shifts in parasite traits expressed during infections and in different hosts. This article describes how integrating parasite plasticity into biomedical thinking is central to explaining disease outcomes and transmission patterns, as well as predicting the success of control measures.
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Affiliation(s)
- Nicole Mideo
- Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Sarah E Reece
- Institutes of Evolution, Immunity & Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, UK
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Mideo N, Savill NJ, Chadwick W, Schneider P, Read AF, Day T, Reece SE. Causes of variation in malaria infection dynamics: insights from theory and data. Am Nat 2011; 178:E174-E188. [PMID: 22089879 PMCID: PMC3937740 DOI: 10.1086/662670] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Parasite strategies for exploiting host resources are key determinants of disease severity (i.e., virulence) and infectiousness (i.e., transmission between hosts). By iterating the development of theory and empirical tests, we investigated whether variation in parasite traits across two genetically distinct clones of the rodent malaria parasite, Plasmodium chabaudi, explains differences in within-host infection dynamics and virulence. First, we experimentally tested key predictions of our earlier modeling work. As predicted, the more virulent genotype produced more progeny parasites per infected cell (burst size), but in contrast to predictions, invasion rates of red blood cells (RBCs) did not differ between the genotypes studied. Second, we further developed theory by confronting our earlier model with these new data, testing a new set of models that incorporate more biological realism, and developing novel theoretical tools for identifying differences between parasite genotypes. Overall, we found robust evidence that differences in burst sizes contribute to variation in dynamics and that differential interactions between parasites and host immune responses also play a role. In contrast to previous work, our model predicts that RBC age structure is not important for explaining dynamics. Integrating theory and empirical tests is a potentially powerful way of progressing understanding of disease biology.
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Affiliation(s)
- Nicole Mideo
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Nicholas J. Savill
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Institute of Immunity and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - William Chadwick
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Petra Schneider
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Andrew F. Read
- Center for Infectious Disease Dynamics, Departments of Biology and Entomology, Pennsylvania State University, University Park, Pennsylvania 16802; and Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892
| | - Troy Day
- Departments of Biology and Mathematics and Statistics, Queen’s University, Kingston, Ontario K7L 3N6, Canada
| | - Sarah E. Reece
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Institute of Immunity and Infection Research, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
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Abstract
Within- and between-host disease processes occur on the same timescales, therefore changes in the within-host dynamics of parasites, resources, and immunity can interact with changes in the epidemiological dynamics to affect evolutionary outcomes. Consequently, studies of the evolution of disease life histories, that is, infection-age-specific patterns of transmission and virulence, have been constrained by the need for a mechanistic understanding of within-host disease dynamics. In a companion paper (Day et al. 2011), we develop a novel approach that quantifies the relevant within-host aspects of disease through genetic covariance functions. Here, we demonstrate how to apply this theory to data. Using two previously published datasets from rodent malaria infections, we show how to translate experimental measures into disease life-history traits, and how to quantify the covariance in these traits. Our results show how patterns of covariance can interact with epidemiological dynamics to affect evolutionary predictions for disease life history. We also find that the selective constraints on disease life-history evolution can vary qualitatively, and that "simple" virulence-transmission trade-offs that are often the subject of experimental investigation can be obscured by trade-offs within one trait alone. Finally, we highlight the type and quality of data required for future applications.
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Affiliation(s)
- Nicole Mideo
- Centre for Immunity, Infection, and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
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Pollitt LC, Mideo N, Drew DR, Schneider P, Colegrave N, Reece SE. Competition and the Evolution of Reproductive Restraint in Malaria Parasites. Am Nat 2011; 177:358-67. [DOI: 10.1086/658175] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Competition between parasite species or strains within hosts is a major evolutionary force in infections. In response, parasites exhibit a diverse array of strategies that improve their chances of growth or reproduction over competitors. This Review describes three types of competition that parasites face (exploitation, apparent and interference), identifies successful strategies for confronting these and discusses whether these strategies are true adaptations to competition. Although many studies of multiple infections have focused on disease outcomes (e.g. virulence), rather than on the particular parasite strategies that have adapted in response to the ensuing competitive interactions, these strategies are ultimately responsible for shaping disease outcomes of interest. A better understanding of parasite adaptations to competitive interactions will have important public health implications.
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Affiliation(s)
- Nicole Mideo
- Department of Biology, Queen's University, Kingston, ON K7L 3N6, Canada.
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