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Sharp PM, Plenderleith LJ, Culleton RL, Hahn BH. Origin of the human malaria parasite Plasmodium vivax. Trends Parasitol 2024; 40:562-572. [PMID: 38806300 DOI: 10.1016/j.pt.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/30/2024]
Abstract
The geographic origin of Plasmodium vivax, a leading cause of human malaria, has been the subject of much speculation. Here we review the evolutionary history of P. vivax and P. vivax-like parasites in humans and non-human primates on three continents, providing overwhelming evidence for an African origin. This conclusion is consistent with recent reports showing that Duffy-negative humans in Africa are, in fact, susceptible to P. vivax, with parasites invading Duffy-antigen-expressing erythroid precursors. Thus, the African origin of P. vivax not only explains the distribution of the Duffy-negative genotype but also provides new insight into the history and status of P. vivax malaria in Africa and efforts geared toward its eradication.
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Affiliation(s)
- Paul M Sharp
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK; Centre for Immunity, Infection, and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | | | - Richard L Culleton
- Division of Parasitology, Proteo-Science Centre, Ehime University, 454 Shitsukawa, Toon, Ehime 791-0295, Japan
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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2
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Houldcroft CJ, Underdown S. Infectious disease in the Pleistocene: Old friends or old foes? AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 182:513-531. [PMID: 38006200 DOI: 10.1002/ajpa.24737] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 03/01/2023] [Accepted: 03/14/2023] [Indexed: 11/26/2023]
Abstract
The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.
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Affiliation(s)
| | - Simon Underdown
- Human Origins and Palaeoenvironmental Research Group, School of Social Sciences, Oxford Brookes University, Oxford, UK
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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3
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Rifkin RF, Vikram S, Alcorta J, Ramond JB, Cowan DA, Jakobsson M, Schlebusch CM, Lombard M. Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. Commun Biol 2023; 6:240. [PMID: 36869137 PMCID: PMC9984395 DOI: 10.1038/s42003-023-04582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.
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Affiliation(s)
- Riaan F Rifkin
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Marlize Lombard
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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4
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Arisue N, Palacpac NMQ, Ntege EH, Yeka A, Balikagala B, Kanoi BN, Bougouma EC, Tiono AB, Nebie I, Diarra A, Houard S, D’Alessio F, Leroy O, Sirima SB, Egwang TG, Horii T. African-specific polymorphisms in Plasmodium falciparum serine repeat antigen 5 in Uganda and Burkina Faso clinical samples do not interfere with antibody response to BK-SE36 vaccination. Front Cell Infect Microbiol 2022; 12:1058081. [PMID: 36590593 PMCID: PMC9802637 DOI: 10.3389/fcimb.2022.1058081] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/17/2022] [Indexed: 12/23/2022] Open
Abstract
BK-SE36, based on Plasmodium falciparum serine repeat antigen 5 (SERA5), is a blood-stage malaria vaccine candidate currently being evaluated in clinical trials. Phase 1 trials in Uganda and Burkina Faso have demonstrated promising safety and immunogenicity profiles. However, the genetic diversity of sera5 in Africa and the role of allele/variant-specific immunity remain a major concern. Here, sequence analyses were done on 226 strains collected from the two clinical trial/follow-up studies and 88 strains from two cross-sectional studies in Africa. Compared to other highly polymorphic vaccine candidate antigens, polymorphisms in sera5 were largely confined to the repeat regions of the gene. Results also confirmed a SERA5 consensus sequence with African-specific polymorphisms. Mismatches with the vaccine-type SE36 (BK-SE36) in the octamer repeat, serine repeat, and flanking regions, and single-nucleotide polymorphisms in non-repeat regions could compromise vaccine response and efficacy. However, the haplotype diversity of SERA5 was similar between vaccinated and control participants. There was no marked bias or difference in the patterns of distribution of the SE36 haplotype and no statistically significant genetic differentiation among parasites infecting BK-SE36 vaccinees and controls. Results indicate that BK-SE36 does not elicit an allele-specific immune response.
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Affiliation(s)
- Nobuko Arisue
- Research Center for Infectious Disease Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan,Section of Global Health, Division of Public Health, Department of Hygiene and Public Health, Tokyo Women’s Medical University, Tokyo, Japan,*Correspondence: Nobuko Arisue, ; Nirianne Marie Q. Palacpac,
| | - Nirianne Marie Q. Palacpac
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan,*Correspondence: Nobuko Arisue, ; Nirianne Marie Q. Palacpac,
| | - Edward H. Ntege
- Department of Plastic and Reconstructive Surgery, University of the Ryukyus, Graduate School of Medicine and Hospital, Okinawa, Japan
| | - Adoke Yeka
- Makerere University School of Public Health, Kampala, Uganda
| | - Betty Balikagala
- Department of Tropical Medicine and Parasitology, School of Medicine, Juntendo University, Tokyo, Japan
| | - Bernard N. Kanoi
- Centre for Malaria Elimination (CME) and Centre for Research in Infectious Diseases (CRID), Directorate of Research and Innovation, Mount Kenya University, Thika, Kenya
| | - Edith Christiane Bougouma
- Public Health Department, Institut National de Santé Publique/Centre National de Recherche et de Formation sur le Paludisme (INSP/CNRFP), Ouagadougou, Burkina Faso,Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | - Alfred B. Tiono
- Public Health Department, Institut National de Santé Publique/Centre National de Recherche et de Formation sur le Paludisme (INSP/CNRFP), Ouagadougou, Burkina Faso,Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | - Issa Nebie
- Public Health Department, Institut National de Santé Publique/Centre National de Recherche et de Formation sur le Paludisme (INSP/CNRFP), Ouagadougou, Burkina Faso,Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | - Amidou Diarra
- Public Health Department, Institut National de Santé Publique/Centre National de Recherche et de Formation sur le Paludisme (INSP/CNRFP), Ouagadougou, Burkina Faso,Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | - Sophie Houard
- European Vaccine Initiative (EVI), Universitäts Klinikum Heidelberg, Heidelberg, Germany
| | - Flavia D’Alessio
- European Vaccine Initiative (EVI), Universitäts Klinikum Heidelberg, Heidelberg, Germany
| | - Odile Leroy
- European Vaccine Initiative (EVI), Universitäts Klinikum Heidelberg, Heidelberg, Germany,Sorekara-x consultant, Paris, France
| | - Sodiomon B. Sirima
- Public Health Department, Institut National de Santé Publique/Centre National de Recherche et de Formation sur le Paludisme (INSP/CNRFP), Ouagadougou, Burkina Faso,Groupe de Recherche Action en Santé (GRAS), Ouagadougou, Burkina Faso
| | | | - Toshihiro Horii
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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da Silva KE, Tanmoy AM, Pragasam AK, Iqbal J, Sajib MSI, Mutreja A, Veeraraghavan B, Tamrakar D, Qamar FN, Dougan G, Bogoch I, Seidman JC, Shakya J, Vaidya K, Carey ME, Shrestha R, Irfan S, Baker S, Luby SP, Cao Y, Dyson ZA, Garrett DO, John J, Kang G, Hooda Y, Saha SK, Saha S, Andrews JR. The international and intercontinental spread and expansion of antimicrobial-resistant Salmonella Typhi: a genomic epidemiology study. THE LANCET MICROBE 2022; 3:e567-e577. [PMID: 35750070 PMCID: PMC9329132 DOI: 10.1016/s2666-5247(22)00093-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 03/29/2022] [Accepted: 04/07/2022] [Indexed: 11/25/2022] Open
Abstract
Background The emergence of increasingly antimicrobial-resistant Salmonella enterica serovar Typhi (S Typhi) threatens to undermine effective treatment and control. Understanding where antimicrobial resistance in S Typhi is emerging and spreading is crucial towards formulating effective control strategies. Methods In this genomic epidemiology study, we sequenced the genomes of 3489 S Typhi strains isolated from prospective enteric fever surveillance studies in Nepal, Bangladesh, Pakistan, and India (between 2014 and 2019), and combined these with a global collection of 4169 S Typhi genome sequences isolated between 1905 and 2018 to investigate the temporal and geographical patterns of emergence and spread of antimicrobial-resistant S Typhi. We performed non-parametric phylodynamic analyses to characterise changes in the effective population size of fluoroquinolone-resistant, extensively drug-resistant (XDR), and azithromycin-resistant S Typhi over time. We inferred timed phylogenies for the major S Typhi sublineages and used ancestral state reconstruction methods to estimate the frequency and timing of international and intercontinental transfers. Findings Our analysis revealed a declining trend of multidrug resistant typhoid in south Asia, except for Pakistan, where XDR S Typhi emerged in 2016 and rapidly replaced less-resistant strains. Mutations in the quinolone-resistance determining region (QRDR) of S Typhi have independently arisen and propagated on at least 94 occasions, nearly all occurring in south Asia. Strains with multiple QRDR mutations, including triple mutants with high-level fluoroquinolone resistance, have been increasing in frequency and displacing strains with fewer mutations. Strains containing acrB mutations, conferring azithromycin resistance, emerged in Bangladesh around 2013 and effective population size of these strains has been steadily increasing. We found evidence of frequent international (n=138) and intercontinental transfers (n=59) of antimicrobial-resistant S Typhi, followed by local expansion and replacement of drug-susceptible clades. Interpretation Independent acquisition of plasmids and homoplastic mutations conferring antimicrobial resistance have occurred repeatedly in multiple lineages of S Typhi, predominantly arising in south Asia before spreading to other regions. Funding Bill & Melinda Gates Foundation.
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Escalante AA, Cepeda AS, Pacheco MA. Why Plasmodium vivax and Plasmodium falciparum are so different? A tale of two clades and their species diversities. Malar J 2022; 21:139. [PMID: 35505356 PMCID: PMC9066883 DOI: 10.1186/s12936-022-04130-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/18/2022] [Indexed: 11/29/2022] Open
Abstract
The global malaria burden sometimes obscures that the genus Plasmodium comprises diverse clades with lineages that independently gave origin to the extant human parasites. Indeed, the differences between the human malaria parasites were highlighted in the classical taxonomy by dividing them into two subgenera, the subgenus Plasmodium, which included all the human parasites but Plasmodium falciparum that was placed in its separate subgenus, Laverania. Here, the evolution of Plasmodium in primates will be discussed in terms of their species diversity and some of their distinct phenotypes, putative molecular adaptations, and host–parasite biocenosis. Thus, in addition to a current phylogeny using genome-level data, some specific molecular features will be discussed as examples of how these parasites have diverged. The two subgenera of malaria parasites found in primates, Plasmodium and Laverania, reflect extant monophyletic groups that originated in Africa. However, the subgenus Plasmodium involves species in Southeast Asia that were likely the result of adaptive radiation. Such events led to the Plasmodium vivax lineage. Although the Laverania species, including P. falciparum, has been considered to share “avian characteristics,” molecular traits that were likely in the common ancestor of primate and avian parasites are sometimes kept in the Plasmodium subgenus while being lost in Laverania. Assessing how molecular traits in the primate malaria clades originated is a fundamental science problem that will likely provide new targets for interventions. However, given that the genus Plasmodium is paraphyletic (some descendant groups are in other genera), understanding the evolution of malaria parasites will benefit from studying “non-Plasmodium” Haemosporida.
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Affiliation(s)
- Ananias A Escalante
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA.
| | - Axl S Cepeda
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA
| | - M Andreína Pacheco
- Biology Department/Institute of Genomics and Evolutionary Medicine [iGEM], Temple University, Philadelphia, PA, 19122-1801, USA
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7
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Rougeron V, Daron J, Fontaine MC, Prugnolle F. Evolutionary history of Plasmodium vivax and Plasmodium simium in the Americas. Malar J 2022; 21:141. [PMID: 35505431 PMCID: PMC9066938 DOI: 10.1186/s12936-022-04132-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/18/2022] [Indexed: 11/12/2022] Open
Abstract
Malaria is a vector-borne disease caused by protozoan parasites of the genus Plasmodium. Plasmodium vivax is the most prevalent human-infecting species in the Americas. However, the origins of this parasite in this continent are still debated. Similarly, it is now accepted that the existence of Plasmodium simium is explained by a P. vivax transfer from humans to monkey in America. However, many uncertainties still exist concerning the origin of the transfer and whether several transfers occurred. In this review, the most recent studies that addressed these questions using genetic and genomic approaches are presented.
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Affiliation(s)
- Virginie Rougeron
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa.
| | - Josquin Daron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France
| | - Michael C Fontaine
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900, rue Jean-François Breton, 34900, Montpellier, France.,Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Franck Prugnolle
- International Research Laboratory, REHABS, CNRS-NMU-UCBL, George Campus, Nelson Mandela University, George, South Africa
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Rougeron V, Boundenga L, Arnathau C, Durand P, Renaud F, Prugnolle F. A population genetic perspective on the origin, spread and adaptation of the human malaria agents Plasmodium falciparum and Plasmodium vivax. FEMS Microbiol Rev 2021; 46:6373923. [PMID: 34550355 DOI: 10.1093/femsre/fuab047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 09/06/2021] [Indexed: 01/20/2023] Open
Abstract
Malaria is considered one of the most important scourges that humanity has faced during its history, being responsible every year for numerous deaths worldwide. The disease is caused by protozoan parasites, among which two species are responsible of the majority of the burden, Plasmodium falciparum and Plasmodium vivax. For these two parasite species, the questions of their origin (how and when they appeared in humans), of their spread throughout the world, as well as how they have adapted to humans have long been of interest to the scientific community. Here, we review the current knowledge that has accumulated on these different questions, thanks in particular to the analysis of the genetic and genomic variability of these parasites and comparison with related Plasmodium species infecting other host species (like non-human primates). In this paper we review the existing body of knowledge, including current research dealing with these questions, focusing particularly on genetic analysis and genomic variability of these parasites and comparison with related Plasmodium species infecting other species of host (such as non-human primates).
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Affiliation(s)
- Virginie Rougeron
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Larson Boundenga
- CIRMF, Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Patrick Durand
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - François Renaud
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
| | - Franck Prugnolle
- Laboratory MIVEGEC, University of Montpellier, CNRS, IRD, 900 rue Jean François Breton, 34090 Montpellier, France.,CREES, Centre de Recherches en Écologie et Évolution de la Santé, Montpellier, France
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Rusmini M, Uva P, Amoroso A, Tolomeo M, Cavalli A. How Genetics Might Explain the Unusual Link Between Malaria and COVID-19. Front Med (Lausanne) 2021; 8:650231. [PMID: 33981715 PMCID: PMC8107224 DOI: 10.3389/fmed.2021.650231] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/31/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-associated coronavirus disease 2019 (COVID-19) pandemic has been the subject of a large number of studies in recent times. Here, starting from the evidence that in Italy, the areas with the lowest number of COVID-19 cases were those with the highest incidence of malaria in the early 1900's, we explore possible inverse relationships between malaria and COVID-19. Indeed, some genetic variants, which have been demonstrated to give an advantage against malaria, can also play a role in the incidence and severity of SARS-CoV-2 infections (e.g., the ACE2 receptor). To verify this scientific hypothesis, we here use public data from whole-genome sequencing (WGS) experiments to extrapolate the genetic information of 46 world populations with matched COVID-19 data. In particular, we focus on 47 genes, including ACE2 and genes which have previously been reported to play a role in malaria. Only common variants (>5%) in at least 30% of the selected populations were considered, and, for this subset, we correlate the intra-population allele frequency with the COVID-19 data (cases/million inhabitants), eventually pinpointing meaningful variants in 6 genes. This study allows us to distinguish between positive and negative correlations, i.e., variants whose frequency significantly increases with increasing or decreasing COVID-19 cases. Finally, we discuss the possible molecular mechanisms associated with these variants and advance potential therapeutic options, which may help fight and/or prevent COVID-19.
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Affiliation(s)
- Marta Rusmini
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) G. Gaslini, Genova, Italy
| | - Paolo Uva
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) G. Gaslini, Genova, Italy
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Manlio Tolomeo
- Department of Health Promotion Sciences, Azienda Ospedaliera Universitaria Policlinico Paolo Giaccone, Palermo, Italy
| | - Andrea Cavalli
- Computational and Chemical Biology, Italian Institute of Technology, Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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10
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Arisue N, Chagaluka G, Palacpac NMQ, Johnston WT, Mutalima N, Peprah S, Bhatia K, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Goedert JJ, Molyneux EM, Newton R, Horii T, Mbulaiteye SM. Assessment of Mixed Plasmodium falciparum sera5 Infection in Endemic Burkitt Lymphoma: A Case-Control Study in Malawi. Cancers (Basel) 2021; 13:1692. [PMID: 33918470 PMCID: PMC8038222 DOI: 10.3390/cancers13071692] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/26/2021] [Accepted: 03/29/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Endemic Burkitt lymphoma (eBL) is the most common childhood cancer in Africa and is linked to Plasmodium falciparum (Pf) malaria infection, one of the most common and deadly childhood infections in Africa; however, the role of Pf genetic diversity is unclear. A potential role of Pf genetic diversity in eBL has been suggested by a correlation of age-specific patterns of eBL with the complexity of Pf infection in Ghana, Uganda, and Tanzania, as well as a finding of significantly higher Pf genetic diversity, based on a sensitive molecular barcode assay, in eBL cases than matched controls in Malawi. We examined this hypothesis by measuring diversity in Pf-serine repeat antigen-5 (Pfsera5), an antigenic target of blood-stage immunity to malaria, among 200 eBL cases and 140 controls, all Pf polymerase chain reaction (PCR)-positive, in Malawi. METHODS We performed Pfsera5 PCR and sequencing (~3.3 kb over exons II-IV) to determine single or mixed PfSERA5 infection status. The patterns of Pfsera5 PCR positivity, mixed infection, sequence variants, and haplotypes among eBL cases, controls, and combined/pooled were analyzed using frequency tables. The association of mixed Pfsera5 infection with eBL was evaluated using logistic regression, controlling for age, sex, and previously measured Pf genetic diversity. RESULTS Pfsera5 PCR was positive in 108 eBL cases and 70 controls. Mixed PfSERA5 infection was detected in 41.7% of eBL cases versus 24.3% of controls; the odds ratio (OR) was 2.18, and the 95% confidence interval (CI) was 1.12-4.26, which remained significant in adjusted results (adjusted odds ratio [aOR] of 2.40, 95% CI of 1.11-5.17). A total of 29 nucleotide variations and 96 haplotypes were identified, but these were unrelated to eBL. CONCLUSIONS Our results increase the evidence supporting the hypothesis that infection with mixed Pf infection is increased with eBL and suggest that measuring Pf genetic diversity may provide new insights into the role of Pf infection in eBL.
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Affiliation(s)
- Nobuko Arisue
- Research Center for Infectious Disease Control, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan;
| | - George Chagaluka
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - Nirianne Marie Q. Palacpac
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (N.M.Q.P.); (T.H.)
| | - W. Thomas Johnston
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York YO10 5DD, UK; (W.T.J.); (N.M.); (R.N.)
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York YO10 5DD, UK; (W.T.J.); (N.M.); (R.N.)
- Cancer Epidemiology Unit, University of Oxford, Oxford OX3 7LF, UK
| | - Sally Peprah
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.P.); (K.B.); (J.J.G.)
| | - Kishor Bhatia
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.P.); (K.B.); (J.J.G.)
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - George N. Liomba
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - Collins Mitambo
- National Health Sciences Research Committee, Research Department, Ministry of Health, P.O. Box 30377, Capital City, Lilongwe 3, Malawi;
| | - James J. Goedert
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.P.); (K.B.); (J.J.G.)
| | - Elizabeth M. Molyneux
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Private Bag 360, Chichiri, Blantyre 3, Malawi; (G.C.); (E.B.); (G.N.L.); (S.K.); (N.M.); (E.M.M.)
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York YO10 5DD, UK; (W.T.J.); (N.M.); (R.N.)
| | - Toshihiro Horii
- Department of Malaria Vaccine Development, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan; (N.M.Q.P.); (T.H.)
| | - Sam M. Mbulaiteye
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (S.P.); (K.B.); (J.J.G.)
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Daron J, Boissière A, Boundenga L, Ngoubangoye B, Houze S, Arnathau C, Sidobre C, Trape JF, Durand P, Renaud F, Fontaine MC, Prugnolle F, Rougeron V. Population genomic evidence of Plasmodium vivax Southeast Asian origin. SCIENCE ADVANCES 2021; 7:7/18/eabc3713. [PMID: 33910900 PMCID: PMC8081369 DOI: 10.1126/sciadv.abc3713] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 03/10/2021] [Indexed: 05/15/2023]
Abstract
Plasmodium vivax is the most common and widespread human malaria parasite. It was recently proposed that P. vivax originates from sub-Saharan Africa based on the circulation of its closest genetic relatives (P. vivax-like) among African great apes. However, the limited number of genetic markers and samples investigated questions the robustness of this hypothesis. Here, we extensively characterized the genomic variations of 447 human P. vivax strains and 19 ape P. vivax-like strains collected worldwide. Phylogenetic relationships between human and ape Plasmodium strains revealed that P. vivax is a sister clade of P. vivax-like, not included within the radiation of P. vivax-like By investigating various aspects of P. vivax genetic variation, we identified several notable geographical patterns in summary statistics in function of the increasing geographic distance from Southeast Asia, suggesting that P. vivax may have derived from a single area in Asia through serial founder effects.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
| | - Anne Boissière
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Larson Boundenga
- Centre Interdisciplinaire de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, 46 rue H. Huchard, 75877 Paris Cedex 18, France
| | - Celine Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Christine Sidobre
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Michael C Fontaine
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, PO Box 11103 CC, Groningen, Netherlands
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
| | - Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), 34394 Montpellier, France.
- Centre of Research in Ecology and Evolution of Diseases (CREES), Montpellier, France
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12
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Guery MA, Claessens A. Order within chaos: Harnessing Plasmodium falciparum var gene extreme polymorphism for malaria epidemiology. PLoS Genet 2021; 17:e1009344. [PMID: 33630881 PMCID: PMC7906395 DOI: 10.1371/journal.pgen.1009344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Ribeiro de Castro Duarte AM, Fernandes LN, Silva FS, Sicchi IL, Mucci LF, Curado I, Fernandes A, Medeiros-Sousa AR, Ceretti-Junior W, Marrelli MT, Evangelista E, Teixeira R, Summa JL, Nardi MS, Garnica MR, Loss AC, Buery JC, Cerutti Jr. C, Pacheco MA, Escalante AA, Mureb Sallum MA, Laporta GZ. Complexity of malaria transmission dynamics in the Brazilian Atlantic Forest. CURRENT RESEARCH IN PARASITOLOGY & VECTOR-BORNE DISEASES 2021; 1:100032. [PMID: 35284897 PMCID: PMC8906072 DOI: 10.1016/j.crpvbd.2021.100032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/07/2021] [Accepted: 05/23/2021] [Indexed: 11/26/2022]
Abstract
Plasmodium malariae and Plasmodium vivax are protozoan parasites that can cause malaria in humans. They are genetically indistinguishable from, respectively, Plasmodium brasilianum and Plasmodium simium, i.e. parasites infecting New World non-human primates in South America. In the tropical rainforests of the Brazilian Atlantic coast, it has long been hypothesized that P. brasilianum and P. simium in platyrrhine primates originated from P. malariae and P. vivax in humans. A recent hypothesis proposed the inclusion of Plasmodium falciparum into the transmission dynamics between humans and non-human primates in the Brazilian Atlantic tropical rainforest. Herein, we assess the occurrence of human malaria in simians and sylvatic anophelines using field-collected samples in the Capivari-Monos Environmental Protection Area from 2015 to 2017. We first tested simian blood and anopheline samples. Two simian (Aloutta) blood samples (18%, n = 11) showed Plasmodium cytb DNA sequences, one for P. vivax and another for P. malariae. From a total of 9,416 anopheline females, we found 17 pools positive for Plasmodium species with a 18S qPCR assay. Only three showed P. cytb DNA sequence, one for P. vivax and the others for rodent malaria species (similar to Plasmodium chabaudi and Plasmodium berghei). Based on these results, we tested 25 rodent liver samples for the presence of Plasmodium and obtained P. falciparum cytb DNA sequence in a rodent (Oligoryzomys sp.) liver. The findings of this study indicate complex malaria transmission dynamics composed by parallel spillover-spillback of human malaria parasites, i.e. P. malariae, P. vivax, and P. falciparum, in the Brazilian Atlantic forest. Human malaria parasites circulate in sylvatic cycles in the Brazilian Atlantic forest. Plasmodium vivax and Plasmodium malariae identified in simian blood samples. Plasmodium falciparum detected in a rodent liver sample. Anopheline vectors found to carry human and rodent malaria parasites. Local vector ecology and biology are key to the spillover-spillback of human malaria parasites.
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Rougeron V, Elguero E, Arnathau C, Acuña Hidalgo B, Durand P, Houze S, Berry A, Zakeri S, Haque R, Shafiul Alam M, Nosten F, Severini C, Gebru Woldearegai T, Mordmüller B, Kremsner PG, González-Cerón L, Fontecha G, Gamboa D, Musset L, Legrand E, Noya O, Pumpaibool T, Harnyuttanakorn P, Lekweiry KM, Mohamad Albsheer M, Mahdi Abdel Hamid M, Boukary AOMS, Trape JF, Renaud F, Prugnolle F. Human Plasmodium vivax diversity, population structure and evolutionary origin. PLoS Negl Trop Dis 2020; 14:e0008072. [PMID: 32150544 PMCID: PMC7082039 DOI: 10.1371/journal.pntd.0008072] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 03/19/2020] [Accepted: 01/18/2020] [Indexed: 11/19/2022] Open
Abstract
More than 200 million malaria clinical cases are reported each year due to Plasmodium vivax, the most widespread Plasmodium species in the world. This species has been neglected and understudied for a long time, due to its lower mortality in comparison with Plasmodium falciparum. A renewed interest has emerged in the past decade with the discovery of antimalarial drug resistance and of severe and even fatal human cases. Nonetheless, today there are still significant gaps in our understanding of the population genetics and evolutionary history of P. vivax, particularly because of a lack of genetic data from Africa. To address these gaps, we genotyped 14 microsatellite loci in 834 samples obtained from 28 locations in 20 countries from around the world. We discuss the worldwide population genetic structure and diversity and the evolutionary origin of P. vivax in the world and its introduction into the Americas. This study demonstrates the importance of conducting genome-wide analyses of P. vivax in order to unravel its complex evolutionary history. Among the five Plasmodium species infecting humans, P. vivax is the most prevalent parasite outside Africa. To date, there has been less research on this species than for Plasmodium falciparum, a more lethal species, principally because of the lack of an in vitro culture system and also because P. vivax is considered relatively benign. Nevertheless, P. vivax is responsible for severe and incapacitating clinical symptoms with significant effects on human health. The emergence of new drug resistance and the discovery of severe and even fatal cases due to P. vivax question the benign status of P. vivax malaria. In recent years, there has been increased interest in characterizing the distribution of genetic variation in P. vivax. However, these studies either generated genetic information from a regional geographic scale or combine genetic datasets generated in different molecular platforms, which is known to generate biased results. In this study, we used a single genotyping platform to genotype 14 microsatellite markers in 834 samples of P. vivax obtained from 28 locations in 20 countries from around the world, including several populations from East and West Africa. We discuss the worldwide population genetic structure and the evolutionary origins of P. vivax, as well as its introduction into the Americas.
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Affiliation(s)
- Virginie Rougeron
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
- * E-mail: ,
| | - Eric Elguero
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Céline Arnathau
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Beatriz Acuña Hidalgo
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Patrick Durand
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Sandrine Houze
- Service de Parasitologie-mycologie CNR du Paludisme, AP-HP Hôpital Bichat, Paris, France
| | - Antoine Berry
- Centre de Physiopathologie de Toulouse-Purpan (CPTP), Institut National de la Santé et de la Recherche Médicale (INSERM) UMR1043, CNRS UMR5282, Université de Toulouse Paul Sabatier, F-31300 Toulouse, France
- Service de Parasitologie-Mycologie, Institut Fédératif de Biologie, Centre Hospitalier Universitaire de Toulouse, F-31300 Toulouse, France
| | - Sedigheh Zakeri
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Rashidul Haque
- Emerging Infections & Parasitology Laboratory, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - Mohammad Shafiul Alam
- Emerging Infections & Parasitology Laboratory, icddr,b, Mohakhali, Dhaka, Bangladesh
| | - François Nosten
- Centre for Tropical Medicine and Global Health,Oxford, United Kingdom
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Mae Sot, Thailand
| | - Carlo Severini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Tamirat Gebru Woldearegai
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Medical Laboratory Sciences, College of Medical and Health Sciences, Haramaya University, Harar, Ethiopia
| | - Benjamin Mordmüller
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- German Centre for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | | | - Lilia González-Cerón
- Regional Centre of Research in Public Health, National Institute of Public Health, Tapachula, Chiapas, Mexico
| | - Gustavo Fontecha
- Microbiology Research Institute, Universidad Nacional Autónoma de Honduras, Tegucigalpa, Honduras
| | - Dionicia Gamboa
- Instituto de Medicina Tropical Alexander Von Humboldt, Universidad Peruana Cayetano Heredia, AP, Lima, Peru
| | - Lise Musset
- Unit, Institut Pasteur de Guyane, BP6010, French Guiana
| | - Eric Legrand
- Malaria Genetic and Resistance Group, Biology of Host-Parasite Interactions Unit, Institut Pasteur, Paris, France
| | - Oscar Noya
- Centro para Estudios Sobre Malaria, Instituto de Altos Estudios en Salud “Dr. Arnoldo Gabaldón”, Ministerio del Poder Popular para la Salud and Instituto de Medicina Tropical, Universidad Central de Venezuela, Maracay, Caracas, Venezuela
| | - Tepanata Pumpaibool
- Biomedical Science, Graduate School, Chulalongkorn University, Bangkok, Thailand
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
| | - Pingchai Harnyuttanakorn
- Malaria Research Programme, College of Public Health Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Khadijetou Mint Lekweiry
- UR-Génomes et milieux, Faculté des Sciences et Techniques, Université de Nouakchott Al-Aasriya, Mauritania
| | - Musab Mohamad Albsheer
- Department of Parasitology and Medical Entomology, Medical Campus, University of Khartoum, Sudan
| | | | - Ali Ould Mohamed Salem Boukary
- UR-Génomes et milieux, Faculté des Sciences et Techniques, Université de Nouakchott Al-Aasriya, Mauritania
- Aix Marseille Univ, IRD, AP-HM, SSA, VITROME, Marseille, France
| | - Jean-François Trape
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - François Renaud
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
| | - Franck Prugnolle
- Laboratoire MIVEGEC (Université de Montpellier-CNRS-IRD), CREES, Montpellier, France
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van Dorp L, Gelabert P, Rieux A, de Manuel M, de-Dios T, Gopalakrishnan S, Carøe C, Sandoval-Velasco M, Fregel R, Olalde I, Escosa R, Aranda C, Huijben S, Mueller I, Marquès-Bonet T, Balloux F, Gilbert MTP, Lalueza-Fox C. Plasmodium vivax Malaria Viewed through the Lens of an Eradicated European Strain. Mol Biol Evol 2020; 37:773-785. [PMID: 31697387 PMCID: PMC7038659 DOI: 10.1093/molbev/msz264] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania, and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonization of the Americas. In addition, we found that some known variants for resistance to antimalarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, United Kingdom
| | - Pere Gelabert
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Adrien Rieux
- CIRAD, UMR PVBMT, St. Pierre de la Réunion, France
| | - Marc de Manuel
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Toni de-Dios
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian Carøe
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marcela Sandoval-Velasco
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rosa Fregel
- Department of Genetics, Stanford University, Stanford, CA
- Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Spain
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Raül Escosa
- Consorci de Polítiques Ambientals de les Terres de l'Ebre (COPATE), Deltebre, Spain
| | - Carles Aranda
- Servei de Control de Mosquits, Consell Comarcal del Baix Llobregat, Sant Feliu de Llobregat, Spain
| | - Silvie Huijben
- School of Life Sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
| | - Ivo Mueller
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic-Universitat de Barcelona, Barcelona, Spain
- Population Health and Immunity Division, Walter & Eliza Hall Institute, Parkville, VIC, Australia
- Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Barcelona Institute of Science and Technology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - François Balloux
- UCL Genetics Institute, University College London, London, United Kingdom
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, The GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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Abstract
Malaria is a vector-borne disease that involves multiple parasite species in a variety of ecological settings. However, the parasite species causing the disease, the prevalence of subclinical infections, the emergence of drug resistance, the scale-up of interventions, and the ecological factors affecting malaria transmission, among others, are aspects that vary across areas where malaria is endemic. Such complexities have propelled the study of parasite genetic diversity patterns in the context of epidemiologic investigations. Importantly, molecular studies indicate that the time and spatial distribution of malaria cases reflect epidemiologic processes that cannot be fully understood without characterizing the evolutionary forces shaping parasite population genetic patterns. Although broad in scope, this review in the Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology highlights the need for understanding population genetic concepts when interpreting parasite molecular data. First, we discuss malaria complexity in terms of the parasite species involved. Second, we describe how molecular data are changing our understanding of malaria incidence and infectiousness. Third, we compare different approaches to generate parasite genetic information in the context of epidemiologically relevant questions related to malaria control. Finally, we describe a few Plasmodium genomic studies as evidence of how these approaches will provide new insights into the malaria disease dynamics. *This article is part of a curated collection.
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Malaria. HIGHLY INFECTIOUS DISEASES IN CRITICAL CARE 2020. [PMCID: PMC7120402 DOI: 10.1007/978-3-030-33803-9_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Malaria is a significant cause of morbidity and mortality throughout the world, and environmental changes are likely to increase its importance in the coming years. Diagnosing this disease is difficult and requires a high index of suspicion, especially in non-endemic countries. Critical care providers play a major role in treating severe malaria and its complications, which has management particularities that might not be readily apparent. Fluid resuscitation should be carefully tailored to avoid complications, and dysperfusion seems more related to degree of parasitemia than hypovolemia. Antimalarial agents are effective, but resistance is growing. Complications can be found in nearly every organ, including cerebral malaria, acute respiratory distress syndrome, and acute kidney injury. As such, a critical care unit is frequently required for organ support when they appear. Superimposed infections are not infrequent. Despite all of this, mortality is encouragingly low with a timely diagnosis and access to appropriate treatment.
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The Diversity of the Plasmodium falciparum K13 Propeller Domain Did Not Increase after Implementation of Artemisinin-Based Combination Therapy in Uganda. Antimicrob Agents Chemother 2019; 63:AAC.01234-19. [PMID: 31358588 DOI: 10.1128/aac.01234-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/08/2019] [Indexed: 12/15/2022] Open
Abstract
Artemisinin-based combination therapies (ACTs) are the standard of care to treat uncomplicated falciparum malaria. However, resistance to artemisinins, defined as delayed parasite clearance after therapy, has emerged in Southeast Asia, and the spread of resistance to sub-Saharan Africa could have devastating consequences. Artemisinin resistance has been associated in Southeast Asia with multiple nonsynonymous single nucleotide polymorphisms (NS-SNPs) in the propeller domain of the gene encoding the Plasmodium falciparum K13 protein (K13PD). Some K13PD NS-SNPs have been seen in Africa, but the relevance of these mutations is unclear. To assess whether ACT use has selected for specific K13PD mutations, we compared the K13PD genetic diversity in clinical isolates collected before and after the implementation of ACT use from seven sites across Uganda. We detected K13PD NS-SNPs in 16 of 683 (2.3%) clinical isolates collected between 1999 and 2004 and in 26 of 716 (3.6%) isolates collected between 2012 and 2016 (P = 0.16), representing a total of 29 different polymorphisms at 27 codons. Individual NS-SNPs were usually detected only once, and none were found in more than 0.7% of the isolates. Three SNPs (C469F, P574L, and A675V) associated with delayed clearance in Southeast Asia were seen in samples collected between 2012 and 2016, each in a single isolate. No differences in diversity following implementation of ACT use were found at any of the seven sites, nor was there evidence of selective pressures acting on the locus. Our results suggest that selection by ACTs is not impacting on K13PD diversity in Uganda.
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Evolution and Genetic Diversity of the k13 Gene Associated with Artemisinin Delayed Parasite Clearance in Plasmodium falciparum. Antimicrob Agents Chemother 2019; 63:AAC.02550-18. [PMID: 31085516 DOI: 10.1128/aac.02550-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/28/2019] [Indexed: 01/19/2023] Open
Abstract
Mutations in the Plasmodium falciparum k13 (Pfk13) gene are linked to delayed parasite clearance in response to artemisinin-based combination therapies (ACTs) in Southeast Asia. To explore the evolutionary rate and constraints acting on this gene, k13 orthologs from species sharing a recent common ancestor with P. falciparum and Plasmodium vivax were analyzed. These comparative studies were followed by genetic polymorphism analyses within P. falciparum using 982 complete Pfk13 sequences from public databases and new data obtained by next-generation sequencing from African and Haitian isolates. Although k13 orthologs evolve at heterogeneous rates, the gene was conserved across the genus, with only synonymous substitutions being found at residues where mutations linked to the delayed parasite clearance phenotype have been reported. This suggests that those residues were under constraint from undergoing nonsynonymous changes during evolution of the genus. No fixed nonsynonymous differences were found between Pfk13 and its orthologs in closely related species found in African apes. This indicates that all nonsynonymous substitutions currently found in Pfk13 are younger than the time of divergence between P. falciparum and its closely related species. At the population level, no mutations linked to delayed parasite clearance were found in our samples from Africa and Haiti. However, there is a high number of single Pfk13 mutations segregating in P. falciparum populations, and two predominant alleles are distributed worldwide. This pattern is discussed in terms of how changes in the efficacy of natural selection, affected by population expansion, may have allowed for the emergence of mutations tolerant to ACTs.
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Origin of the New World Plasmodium vivax: Facts and New Approaches. Int Microbiol 2019; 22:337-342. [PMID: 30810995 DOI: 10.1007/s10123-018-00053-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/26/2018] [Accepted: 12/17/2018] [Indexed: 01/05/2023]
Abstract
Malaria is one of the most important human diseases throughout tropical and sub-tropical regions of the world. Global distribution and ample host range have contributed to the genetic diversity of the etiological agent, Plasmodium. Phylogeographical analyses demonstrated that Plasmodium falciparum and Plasmodium vivax follow an Out of Africa (OOA) expansion, having a higher genetic diversity in African populations and a low genetic diversity in South American populations. Modeling the evolutionary rate of conserved genes for both P. falciparum and P. vivax determined the approximate arrival of human malaria in South America. Bayesian computational methods suggest that P. falciparum originated in Africa and arrived in South America through multiple independent introductions by the transatlantic African slave trade; however, in South America, P. vivax could have been introduced through an alternate migratory route. Alignments of P. vivax mitogenomes have revealed low genetic variation between the South American and Southeast Asian populations suggesting introduction through either pre-Columbian human migration or post-colonization events. To confirm the findings of these phylogeographical analyses, molecular methods were used to diagnose malaria infection in archeological remains of pre-Columbian ethnic groups. Immunohistochemistry tests were used and identified P. vivax but not P. falciparum in histologically prepared tissues from pre-Columbian Peruvian mummies, whereas shotgun metagenomics sequencing of DNA isolated from pre-Columbian Caribbean coprolites revealed Plasmodium-homologous reads; current evidence suggests that only P. vivax might have been present in pre-Columbian South America.
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21
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Lo E, Bonizzoni M, Hemming-Schroeder E, Ford A, Janies DA, James AA, Afrane Y, Etemesi H, Zhou G, Githeko A, Yan G. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
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22
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Gilabert A, Otto TD, Rutledge GG, Franzon B, Ollomo B, Arnathau C, Durand P, Moukodoum ND, Okouga AP, Ngoubangoye B, Makanga B, Boundenga L, Paupy C, Renaud F, Prugnolle F, Rougeron V. Plasmodium vivax-like genome sequences shed new insights into Plasmodium vivax biology and evolution. PLoS Biol 2018; 16:e2006035. [PMID: 30142149 PMCID: PMC6130868 DOI: 10.1371/journal.pbio.2006035] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 09/10/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022] Open
Abstract
Although Plasmodium vivax is responsible for the majority of malaria infections outside Africa, little is known about its evolution and pathway to humans. Its closest genetic relative, P. vivax-like, was discovered in African great apes and is hypothesized to have given rise to P. vivax in humans. To unravel the evolutionary history and adaptation of P. vivax to different host environments, we generated using long- and short-read sequence technologies 2 new P. vivax-like reference genomes and 9 additional P. vivax-like genotypes. Analyses show that the genomes of P. vivax and P. vivax-like are highly similar and colinear within the core regions. Phylogenetic analyses clearly show that P. vivax-like parasites form a genetically distinct clade from P. vivax. Concerning the relative divergence dating, we show that the evolution of P. vivax in humans did not occur at the same time as the other agents of human malaria, thus suggesting that the transfer of Plasmodium parasites to humans happened several times independently over the history of the Homo genus. We further identify several key genes that exhibit signatures of positive selection exclusively in the human P. vivax parasites. Two of these genes have been identified to also be under positive selection in the other main human malaria agent, P. falciparum, thus suggesting their key role in the evolution of the ability of these parasites to infect humans or their anthropophilic vectors. Finally, we demonstrate that some gene families important for red blood cell (RBC) invasion (a key step of the life cycle of these parasites) have undergone lineage-specific evolution in the human parasite (e.g., reticulocyte-binding proteins [RBPs]).
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Affiliation(s)
- Aude Gilabert
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Thomas D. Otto
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
- Institute of Infection, Immunity and Inflammation, University of Glasgow, College of Medical, Veterinary and Life Sciences, Glasgow, United Kingdom
| | - Gavin G. Rutledge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, United Kingdom
| | - Blaise Franzon
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Benjamin Ollomo
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Céline Arnathau
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Patrick Durand
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Nancy D. Moukodoum
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Alain-Prince Okouga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | | | - Boris Makanga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Larson Boundenga
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Christophe Paupy
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - François Renaud
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Franck Prugnolle
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
| | - Virginie Rougeron
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
- Centre International de Recherches Médicales de Franceville, Franceville, Gabon
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23
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Daversa DR, Fenton A, Dell AI, Garner TWJ, Manica A. Infections on the move: how transient phases of host movement influence disease spread. Proc Biol Sci 2018; 284:rspb.2017.1807. [PMID: 29263283 PMCID: PMC5745403 DOI: 10.1098/rspb.2017.1807] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 11/20/2017] [Indexed: 11/12/2022] Open
Abstract
Animal movement impacts the spread of human and wildlife diseases, and there is significant interest in understanding the role of migrations, biological invasions and other wildlife movements in spatial infection dynamics. However, the influence of processes acting on infections during transient phases of host movement is poorly understood. We propose a conceptual framework that explicitly considers infection dynamics during transient phases of host movement to better predict infection spread through spatial host networks. Accounting for host transient movement captures key processes that occur while hosts move between locations, which together determine the rate at which hosts spread infections through networks. We review theoretical and empirical studies of host movement and infection spread, highlighting the multiple factors that impact the infection status of hosts. We then outline characteristics of hosts, parasites and the environment that influence these dynamics. Recent technological advances provide disease ecologists unprecedented ability to track the fine-scale movement of organisms. These, in conjunction with experimental testing of the factors driving infection dynamics during host movement, can inform models of infection spread based on constituent biological processes.
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Affiliation(s)
- D R Daversa
- Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK .,Institute of Zoology, Zoological Society of London, Regents Park, London NW1 4RY, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - A Fenton
- Institute of Integrative Biology, Biosciences Building, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - A I Dell
- National Great Rivers Research and Education Centre (NGRREC), East Alton, IL 62024, USA.,Department of Biology, Washington University in St Louis, 1 Brookings Dr, St Louis, MO 63130, USA
| | - T W J Garner
- Institute of Zoology, Zoological Society of London, Regents Park, London NW1 4RY, UK
| | - A Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
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24
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Mita T, Hombhanje F, Takahashi N, Sekihara M, Yamauchi M, Tsukahara T, Kaneko A, Endo H, Ohashi J. Rapid selection of sulphadoxine-resistant Plasmodium falciparum and its effect on within-population genetic diversity in Papua New Guinea. Sci Rep 2018; 8:5565. [PMID: 29615786 PMCID: PMC5882878 DOI: 10.1038/s41598-018-23811-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
The ability of the human malarial parasite Plasmodium falciparum to adapt to environmental changes depends considerably on its ability to maintain within-population genetic variation. Strong selection, consequent to widespread antimalarial drug usage, occasionally elicits a rapid expansion of drug-resistant isolates, which can act as founders. To investigate whether this phenomenon induces a loss of within-population genetic variation, we performed a population genetic analysis on 302 P. falciparum cases detected during two cross-sectional surveys in 2002/2003, just after the official introduction of sulphadoxine/pyrimethamine as a first-line treatment, and again in 2010/2011, in highly endemic areas in Papua New Guinea. We found that a single-origin sulphadoxine-resistant parasite isolate rapidly increased from 0% in 2002/2003 to 54% in 2010 and 84% in 2011. However, a considerable number of pairs exhibited random associations among 10 neutral microsatellite markers located in various chromosomes, suggesting that outcrossing effectively reduced non-random associations, albeit at a low average multiplicity of infection (1.35–1.52). Within-population genetic diversity was maintained throughout the study period. This indicates that the parasites maintained within-population variation, even after a clonal expansion of drug-resistant parasites. Outcrossing played a role in the preservation of within-population genetic diversity despite low levels of multiplicity of infection.
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Affiliation(s)
- Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan.
| | - Francis Hombhanje
- Centre for Health Research & Diagnostics, Divine Word University, Nabasa Road, P.O. Box 483, Madang, Papua New Guinea
| | - Nobuyuki Takahashi
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Makoto Sekihara
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Masato Yamauchi
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo, Tokyo, 113-8421, Japan
| | - Takahiro Tsukahara
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Akira Kaneko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 77, Stockholm, Sweden.,Department of Parasitology, Osaka City University Graduate School of Medicine, Asahi-cho 1-4-3, Abeno-ku, Osaka, 545-8585, Japan
| | - Hiroyoshi Endo
- Department of International Affairs and Tropical Medicine, Tokyo Women's Medical University, 8-1 Kawada-cho, Shinjuku-ku, Tokyo, 162-8666, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
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25
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Population genetic evidence for positive and purifying selection acting at the human IFN-γ locus in Africa. Genes Immun 2018; 20:143-157. [PMID: 29599512 DOI: 10.1038/s41435-018-0016-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/22/2018] [Accepted: 01/26/2018] [Indexed: 01/09/2023]
Abstract
Despite its critical role in the defense against microbial infection and tumor development, little is known about the range of nucleotide and haplotype variation at IFN-γ, or the evolutionary forces that have shaped patterns of diversity at this locus. To address this gap in knowledge, we examined sequence data from the IFN-γ gene in 1461 individuals from 15 worldwide populations. Our analyses uncovered novel patterns of variation in distinct African populations, including an excess of high frequency-derived alleles, unusually long haplotype structure surrounding the IFN-γ gene, and a "star-like" genealogy of African-specific haplotypes carrying variants previously associated with infectious disease. We also inferred a deep time to coalescence of variation at IFN-γ (~ 0.8 million years ago) and ancient ages for common polymorphisms predating the evolution of modern humans. Taken together, these results are congruent with a model of positive selection on standing variation in African populations. Furthermore, we inferred that common variants in intron 3 of IFN-γ are the likely targets of selection. In addition, we observed a paucity of non-synonymous substitutions relative to synonymous changes in the exons of IFN-γ in African and non-African populations, suggestive of strong purifying selection. Therefore, we contend that positive and purifying selection have influenced levels of diversity in different regions of IFN-γ, implying that these distinct genic regions are, or have been, functionally important. Overall, this study provides additional insights into the evolutionary events that have contributed to the frequency and distribution of alleles having a role in human health and disease.
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26
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Kalantari P. The Emerging Role of Pattern Recognition Receptors in the Pathogenesis of Malaria. Vaccines (Basel) 2018; 6:vaccines6010013. [PMID: 29495555 PMCID: PMC5874654 DOI: 10.3390/vaccines6010013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 11/16/2022] Open
Abstract
Despite a global effort to develop an effective vaccine, malaria is still a significant health problem. Much of the pathology of malaria is immune mediated. This suggests that host immune responses have to be finely regulated. The innate immune system initiates and sets the threshold of the acquired immune response and determines the outcome of the disease. Yet, our knowledge of the regulation of innate immune responses during malaria is limited. Theoretically, inadequate activation of the innate immune system could result in unrestrained parasite growth. Conversely, hyperactivation of the innate immune system, is likely to cause excessive production of proinflammatory cytokines and severe pathology. Toll-like receptors (TLRs) have emerged as essential receptors which detect signature molecules and shape the complex host response during malaria infection. This review will highlight the mechanisms by which Plasmodium components are recognized by innate immune receptors with particular emphasis on TLRs. A thorough understanding of the complex roles of TLRs in malaria may allow the delineation of pathological versus protective host responses and enhance the efficacy of anti-malarial treatments and vaccines.
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Affiliation(s)
- Parisa Kalantari
- Department of Immunology, Tufts University School of Medicine, Boston, MA 02111, USA.
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27
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Rodrigues PT, Valdivia HO, de Oliveira TC, Alves JMP, Duarte AMRC, Cerutti-Junior C, Buery JC, Brito CFA, de Souza JC, Hirano ZMB, Bueno MG, Catão-Dias JL, Malafronte RS, Ladeia-Andrade S, Mita T, Santamaria AM, Calzada JE, Tantular IS, Kawamoto F, Raijmakers LRJ, Mueller I, Pacheco MA, Escalante AA, Felger I, Ferreira MU. Human migration and the spread of malaria parasites to the New World. Sci Rep 2018; 8:1993. [PMID: 29386521 PMCID: PMC5792595 DOI: 10.1038/s41598-018-19554-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/03/2018] [Indexed: 01/02/2023] Open
Abstract
We examined the mitogenomes of a large global collection of human malaria parasites to explore how and when Plasmodium falciparum and P. vivax entered the Americas. We found evidence of a significant contribution of African and South Asian lineages to present-day New World malaria parasites with additional P. vivax lineages appearing to originate from Melanesia that were putatively carried by the Australasian peoples who contributed genes to Native Americans. Importantly, mitochondrial lineages of the P. vivax-like species P. simium are shared by platyrrhine monkeys and humans in the Atlantic Forest ecosystem, but not across the Amazon, which most likely resulted from one or a few recent human-to-monkey transfers. While enslaved Africans were likely the main carriers of P. falciparum mitochondrial lineages into the Americas after the conquest, additional parasites carried by Australasian peoples in pre-Columbian times may have contributed to the extensive diversity of extant local populations of P. vivax.
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Affiliation(s)
- Priscila T Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil.
| | - Hugo O Valdivia
- Laboratory of Immunology and Parasite Genomics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- U.S. Naval Medical Research Unit No. 6, Bellavista, Callao, Peru
| | - Thais C de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil
| | - João Marcelo P Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil
| | - Ana Maria R C Duarte
- Laboratory of Biochemistry and Molecular Biology, Superintendency for the Control of Endemics (SUCEN), State Secretary of Health, São Paulo, Brazil
| | | | - Julyana C Buery
- Department of Social Medicine, Federal University of Espírito Santo, Vitória, Brazil
| | - Cristiana F A Brito
- Laboratory of Malaria, René Rachou Research Center, Oswaldo Cruz Foundation, Belo Horizonte, Brazil
| | - Júlio César de Souza
- Regional University of Blumenau, Blumenau, Blumenau, Brazil
- Center of Biological Research of Indaial, Indaial, Brazil
| | - Zelinda M B Hirano
- Regional University of Blumenau, Blumenau, Blumenau, Brazil
- Center of Biological Research of Indaial, Indaial, Brazil
| | - Marina G Bueno
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Luiz Catão-Dias
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Rosely S Malafronte
- Laboratory of Protozoology, Institute of Tropical Medicine of São Paulo, University of São Paulo, São Paulo, Brazil
| | - Simone Ladeia-Andrade
- Laboratory of Parasitic Diseases, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Toshihiro Mita
- Department of Tropical Medicine and Parasitology, Juntendo University School of Medicine, Tokyo, Japan
| | - Ana Maria Santamaria
- Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama
| | - José E Calzada
- Department of Parasitology, Gorgas Memorial Institute of Health, Panama City, Panama
| | - Indah S Tantular
- Department of Parasitology, Faculty of Medicine, and Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Fumihiko Kawamoto
- Department of Social and Environmental Medicine, Institute of Scientific Research, Oita University, Oita, Japan
| | - Leonie R J Raijmakers
- Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Division of Population Health and Immunity, Walter and Eliza Hall Institute, Parkville, Victoria, Australia
- Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
| | - M Andreina Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Ingrid Felger
- Swiss Tropical and Public Health Institute, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, 05508-900, São Paulo, Brazil.
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Range Expansion and the Origin of USA300 North American Epidemic Methicillin-Resistant Staphylococcus aureus. mBio 2018; 9:mBio.02016-17. [PMID: 29295910 PMCID: PMC5750399 DOI: 10.1128/mbio.02016-17] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The USA300 North American epidemic (USA300-NAE) clone of methicillin-resistant Staphylococcus aureus has caused a wave of severe skin and soft tissue infections in the United States since it emerged in the early 2000s, but its geographic origin is obscure. Here we use the population genomic signatures expected from the serial founder effects of a geographic range expansion to infer the origin of USA300-NAE and identify polymorphisms associated with its spread. Genome sequences from 357 isolates from 22 U.S. states and territories and seven other countries are compared. We observe two significant signatures of range expansion, including decreases in genetic diversity and increases in derived allele frequency with geographic distance from the Pennsylvania region. These signatures account for approximately half of the core nucleotide variation of this clone, occur genome wide, and are robust to heterogeneity in temporal sampling of isolates, human population density, and recombination detection methods. The potential for positive selection of a gyrA fluoroquinolone resistance allele and several intergenic regions, along with a 2.4 times higher recombination rate in a resistant subclade, is noted. These results are the first to show a pattern of genetic variation that is consistent with a range expansion of an epidemic bacterial clone, and they highlight a rarely considered but potentially common mechanism by which genetic drift may profoundly influence bacterial genetic variation. The process of geographic spread of an origin population by a series of smaller populations can result in distinctive patterns of genetic variation. We detect these patterns for the first time with an epidemic bacterial clone and use them to uncover the clone’s geographic origin and variants associated with its spread. We study the USA300 clone of methicillin-resistant Staphylococcus aureus, which was first noticed in the early 2000s and subsequently became the leading cause of skin and soft tissue infections in the United States. The eastern United States is the most likely origin of epidemic USA300. Relatively few variants, which include an antibiotic resistance mutation, have persisted during this clone’s spread. Our study suggests that an early chapter in the genetic history of this epidemic bacterial clone was greatly influenced by random subsampling of isolates during the clone’s geographic spread.
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29
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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30
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Abstract
Microbes are found on us, within us and around us. They inhabit virtually every environment on the planet and the bacteria carried by an average human, mostly in their gut, outnumber human cells. The vast majority of microbes are harmless to us, and many play essential roles in plant, animal and human health. Others, however, are either obligate or facultative pathogens exerting a spectrum of deleterious effects on their hosts. Infectious diseases have historically represented the most common cause of death in humans until recently, exceeding by far the toll taken by wars or famines. From the dawn of humanity and throughout history, infectious diseases have shaped human evolution, demography, migrations and history.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute (UGI), Darwin Building, Gower Street, London, WC1E 6BT UK
| | - Lucy van Dorp
- UCL Genetics Institute (UGI), Darwin Building, Gower Street, London, WC1E 6BT UK
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31
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Genetic analysis of ID1-DBL2X predicts its validity as a vaccine candidate in Colombia and supports at least two independently introduced Plasmodium falciparum populations in the region. INFECTION GENETICS AND EVOLUTION 2017; 55:175-185. [PMID: 28893687 DOI: 10.1016/j.meegid.2017.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Revised: 08/29/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
Abstract
Pregnancy-associated malaria (PAM) poses a threat to both the mother and fetus, increasing the risk of severe maternal anemia, fetal growth restriction and low birth weight infants. Two vaccines are currently in development to protect women from Plasmodium falciparum in pregnancy. Both vaccine constructs target the ID1-DBL2X domain of VAR2CSA, a protein expressed on the surface of infected erythrocytes (IEs) that mediates parasite sequestration in the placenta. Although development of an effective vaccine may be hampered by ID1-DBL2X polymorphisms expressed by field isolates, a recent study showed that genetic variation of this domain in South American parasite populations is much lower than in other geographical locations. This suggests that a recombinant vaccine designed to be efficacious in Africa and Asia is likely to be efficacious in South America. However, these studies did not include Colombian parasite populations in their analyses, which are known to be genetically distinct from other South American parasite populations due to their independent introduction from Africa. Therefore, we sought to determine the genetic variation of the ID1-DBL2X domain in Colombian parasites to assess the potential efficacy of the vaccine against PAM in this region. Through sequence analysis and population genetics, we show that there is a low degree of genetic variation amongst Colombian parasite populations and that a vaccine containing conserved antigen variants for worldwide populations is likely to be protective against PAM in Colombia. Our analysis also points towards an African origin for Colombian parasite populations, and suggests that their introduction into Colombia was a recurrent process encompassing multiple introduction events.
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32
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de Oliveira TC, Rodrigues PT, Menezes MJ, Gonçalves-Lopes RM, Bastos MS, Lima NF, Barbosa S, Gerber AL, Loss de Morais G, Berná L, Phelan J, Robello C, de Vasconcelos ATR, Alves JMP, Ferreira MU. Genome-wide diversity and differentiation in New World populations of the human malaria parasite Plasmodium vivax. PLoS Negl Trop Dis 2017; 11:e0005824. [PMID: 28759591 PMCID: PMC5552344 DOI: 10.1371/journal.pntd.0005824] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/10/2017] [Accepted: 07/20/2017] [Indexed: 01/15/2023] Open
Abstract
Background The Americas were the last continent colonized by humans carrying malaria parasites. Plasmodium falciparum from the New World shows very little genetic diversity and greater linkage disequilibrium, compared with its African counterparts, and is clearly subdivided into local, highly divergent populations. However, limited available data have revealed extensive genetic diversity in American populations of another major human malaria parasite, P. vivax. Methods We used an improved sample preparation strategy and next-generation sequencing to characterize 9 high-quality P. vivax genome sequences from northwestern Brazil. These new data were compared with publicly available sequences from recently sampled clinical P. vivax isolates from Brazil (BRA, total n = 11 sequences), Peru (PER, n = 23), Colombia (COL, n = 31), and Mexico (MEX, n = 19). Principal findings/Conclusions We found that New World populations of P. vivax are as diverse (nucleotide diversity π between 5.2 × 10−4 and 6.2 × 10−4) as P. vivax populations from Southeast Asia, where malaria transmission is substantially more intense. They display several non-synonymous nucleotide substitutions (some of them previously undescribed) in genes known or suspected to be involved in antimalarial drug resistance, such as dhfr, dhps, mdr1, mrp1, and mrp-2, but not in the chloroquine resistance transporter ortholog (crt-o) gene. Moreover, P. vivax in the Americas is much less geographically substructured than local P. falciparum populations, with relatively little between-population genome-wide differentiation (pairwise FST values ranging between 0.025 and 0.092). Finally, P. vivax populations show a rapid decline in linkage disequilibrium with increasing distance between pairs of polymorphic sites, consistent with very frequent outcrossing. We hypothesize that the high diversity of present-day P. vivax lineages in the Americas originated from successive migratory waves and subsequent admixture between parasite lineages from geographically diverse sites. Further genome-wide analyses are required to test the demographic scenario suggested by our data. Plasmodium vivax is the most common human malaria parasite in the Americas, but how and when this species arrived in the New World remains unclear. Here we describe high-quality whole-genome sequence data for nine P. vivax isolates from Brazil, a country that accounts for 37% of the malaria burden in this continent, and compare these data with additional publicly available P. vivax genomes from Brazil, Peru, Colombia, and Mexico. P. vivax populations from the New World were found to be as diverse as their counterparts from areas with substantially higher malaria transmission, such as Southeast Asia, and to carry several non-synonymous substitutions in candidate drug-resistance genes. Moreover, genome-wide patterns of linkage disequilibrium between pairs of polymorphic sites are consistent with very frequent outcrossing in these populations. Interestingly, local P. vivax is more polymorphic, with less between-population differentiation, than sympatric populations of P. falciparum, possibly as a result of different demographic histories of these two species in the Americas. We hypothesize that local P. vivax lineages originated from successive migratory waves and subsequent admixture between parasites from geographically diverse sites.
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Affiliation(s)
- Thais C. de Oliveira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Priscila T. Rodrigues
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria José Menezes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Raquel M. Gonçalves-Lopes
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Melissa S. Bastos
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Nathália F. Lima
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Susana Barbosa
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Alexandra L. Gerber
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Guilherme Loss de Morais
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - Luisa Berná
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Carlos Robello
- Unit of Molecular Biology, Pasteur Institute of Montevideo, Montevideo, Uruguay
| | - Ana Tereza R. de Vasconcelos
- Unit of Computational Genomics Darcy Fontoura de Almeida, Laboratory of Bioinformatics, National Laboratory of Scientific Computation, Petrópolis, Brazil
| | - João Marcelo P. Alves
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- * E-mail:
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Geographical distribution of Toxoplasma gondii genotypes in Asia: A link with neighboring continents. INFECTION GENETICS AND EVOLUTION 2017; 53:227-238. [PMID: 28583867 DOI: 10.1016/j.meegid.2017.06.002] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 06/01/2017] [Accepted: 06/02/2017] [Indexed: 11/21/2022]
Abstract
Defining the pattern of genetic diversity of Toxoplasma gondii is important to understand its worldwide distribution. During the last decades, a large number of studies have been published on Toxoplasma genotypes circulating in Europe, in North and South America. Two continents are still largely unexplored, Africa and, to a less extent, Asia. In this last continent, an increasing number of publications reported genotypes circulating in diverse provinces of China, but very few data are available for other Asian countries. After a systematic database search, 47 papers related to T. gondii genotypes in Asia were analyzed. Genetic characterization of DNA was performed by microsatellite markers, or more usually by a multiplex PCR using 11 PCR-RFLP markers, allowing data comparison to draw a first global picture of the population structure of this parasite throughout Asia. Overall, 390 isolates or DNA extracts were completely typed by PCR-RFLP and/or microsatellite marker methods, revealing 36 different PCR-RFLP or equivalent microsatellite genotypes: 15 genotypes identified by a ToxoDB number and 21 atypical or unique genotypes. The most common genotype found in Asia is the genotype ToxoDB#9 (Chinese 1). The clonal types I, II and II variant, and III were also commonly found in Asia. The geographical distribution of these genotypes across Asia may reflect either a continuum with Europe for the western part of Asia (presence of Type II), or the circulation of strains through animal migration or human activities between Africa and the Southwestern part of Asia (Africa 1 genotype in Turkey or ToxoDB#20 both I Sri-Lanka and in Ethiopia or Egypt). Although there are some indications of a genetic population structure in Southeast Asian countries different from the rest of Asia, more studies in this tropical part of Asia will be necessary for a region which represent as well as Africa one of the missing links of the T. gondii genetic diversity.
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Houldcroft CJ, Ramond JB, Rifkin RF, Underdown SJ. Migrating microbes: what pathogens can tell us about population movements and human evolution. Ann Hum Biol 2017; 44:397-407. [PMID: 28511559 DOI: 10.1080/03014460.2017.1325515] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
BACKGROUND The biology of human migration can be observed from the co-evolutionary relationship with infectious diseases. While many pathogens are brief, unpleasant visitors to human bodies, others have the ability to become life-long human passengers. The story of a pathogen's genetic code may, therefore, provide insight into the history of its human host. The evolution and distribution of disease in Africa is of particular interest, because of the deep history of human evolution in Africa, the presence of a variety of non-human primates, and tropical reservoirs of emerging infectious diseases. METHODS This study explores which pathogens leave traces in the archaeological record, and whether there are realistic prospects that these pathogens can be recovered from sub-Saharan African archaeological contexts. RESULTS Three stories are then presented of germs on a journey. The first is the story of HIV's spread on the back of colonialism and the railway networks over the last 150 years. The second involves the spread of Schistosoma mansoni, a parasite which shares its history with the trans-Atlantic slave trade and the origins of fresh-water fishing. Finally, we discuss the tantalising hints of hominin migration and interaction found in the genome of human herpes simplex virus 2. CONCLUSIONS Evidence from modern African pathogen genomes can provide data on human behaviour and migration in deep time and contribute to the improvement of human quality-of-life and longevity.
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Affiliation(s)
- Charlotte J Houldcroft
- a Department of Archaeology and Anthropology, Division of Biological Anthropology , University of Cambridge , Cambridge , UK.,b McDonald Institute of Archaeological Research, University of Cambridge , Cambridge , UK
| | - Jean-Baptiste Ramond
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Riaan F Rifkin
- c Department of Genetics , Centre for Microbial Ecology and Genomics, Genomic Research Institute, University of Pretoria , Hatfield , South Africa
| | - Simon J Underdown
- d Department of Anthropology & Geography, Human Origins and Palaeoenvironmental Research Group (HOPE) , Oxford Brookes University , Oxford , UK.,e Leverhulme Centre for Human Evolutionary Studies , Henry Wellcome Building , Cambridge , UK
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De Nys H, Löhrich T, Wu D, Calvignac-Spencer S, Leendertz F. Wild African great apes as natural hosts of malaria parasites: current knowledge and research perspectives. Primate Biol 2017; 4:47-59. [PMID: 32110692 PMCID: PMC7041518 DOI: 10.5194/pb-4-47-2017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 02/24/2017] [Indexed: 11/24/2022] Open
Abstract
Humans and African great apes (AGAs) are naturally infected with several species of closely related malaria parasites. The need to understand the origins of human malaria as well as the risk of zoonotic transmissions and emergence of new malaria strains in human populations has markedly encouraged research on great ape Plasmodium parasites. Progress in the use of non-invasive methods has rendered investigations into wild ape populations possible. Present knowledge is mainly focused on parasite diversity and phylogeny, with still large gaps to fill on malaria parasite ecology. Understanding what malaria infection means in terms of great ape health is also an important, but challenging avenue of research and has been subject to relatively few research efforts so far. This paper reviews current knowledge on African great ape malaria and identifies gaps and future research perspectives.
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Affiliation(s)
- Hélène Marie De Nys
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- current address: UMI 233, Institut de Recherche pour le Développement (IRD), INSERM U1175, and University of Montpellier, Montpellier, France
| | - Therese Löhrich
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Doris Wu
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | | | - Fabian Hubertus Leendertz
- Project group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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Gitaka JN, Takeda M, Kimura M, Idris ZM, Chan CW, Kongere J, Yahata K, Muregi FW, Ichinose Y, Kaneko A, Kaneko O. Selections, frameshift mutations, and copy number variation detected on the surf 4.1 gene in the western Kenyan Plasmodium falciparum population. Malar J 2017; 16:98. [PMID: 28253868 PMCID: PMC5335827 DOI: 10.1186/s12936-017-1743-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/20/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Plasmodium falciparum SURFIN4.1 is a putative ligand expressed on the merozoite and likely on the infected red blood cell, whose gene was suggested to be under directional selection in the eastern Kenyan population, but under balancing selection in the Thai population. To understand this difference, surf 4.1 sequences of western Kenyan P. falciparum isolates were analysed. Frameshift mutations and copy number variation (CNV) were also examined for the parasites from western Kenya and Thailand. RESULTS Positively significant departures from neutral expectations were detected on the surf 4.1 region encoding C-terminus of the variable region 2 (Var2) by 3 population-based tests in the western Kenyan population as similar in the Thai population, which was not covered by the previous analysis for eastern Kenyan population. Significant excess of non-synonymous substitutions per nonsynonymous site over synonymous substitutions per synonymous site was also detected in the Var2 region. Negatively significant departures from neutral expectations was detected on the region encoding Var1 C-terminus consistent to the previous observation in the eastern Kenyan population. Parasites possessing a frameshift mutation resulting a product without intracellular Trp-rich (WR) domains were 22/23 in western Kenya and 22/36 in Thailand. More than one copy of surf 4.1 gene was detected in western Kenya (4/24), but no CNV was found in Thailand (0/36). CONCLUSIONS The authors infer that the high polymorphism of SURFIN4.1 Var2 C-terminus in both Kenyan and Thai populations were shaped-up by diversifying selection and maintained by balancing selection. These phenomena were most likely driven by immunological pressure. Whereas the SURFIN4.1 Var1 C-terminus is suggested to be under directional selection consistent to the previous report for the eastern Kenyan population. Most western Kenyan isolates possess a frameshift mutation that would limit the expression of SURFIN4.1 on the merozoite, but only 60% of Thai isolates possess this frameshift, which would affect the level and type of the selection pressure against this protein as seen in the two extremities of Tajima's D values for Var1 C-terminus between Kenyan and Thai populations. CNV observed in Kenyan isolates may be a consequence of this frameshift mutation to increase benefits on the merozoite surface.
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Affiliation(s)
- Jesse N. Gitaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
- Department of Clinical Medicine, Mount Kenya University, PO Box 342-01000, Thika, Kenya
| | - Mika Takeda
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
| | - Masatsugu Kimura
- Radioisotope Centre, Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno-ku, Osaka, 545-8585 Japan
| | - Zulkarnain Md Idris
- Island Malaria Group, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Nobels väg 16, SE 171 77 Stockholm, Sweden
- Department of Parasitology and Medical Entomology, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, 56000 Kuala Lumpur, Malaysia
| | - Chim W. Chan
- Island Malaria Group, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Nobels väg 16, SE 171 77 Stockholm, Sweden
| | - James Kongere
- Nairobi Research Station, Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute (NUITM-KEMRI) Project, Institute of Tropical Medicine (NEKKEN), Nagasaki University, P. O. Box 19993-00202, Nairobi, Kenya
| | - Kazuhide Yahata
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
| | - Francis W. Muregi
- Department of Clinical Medicine, Mount Kenya University, PO Box 342-01000, Thika, Kenya
| | - Yoshio Ichinose
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
- Nairobi Research Station, Nagasaki University Institute of Tropical Medicine-Kenya Medical Research Institute (NUITM-KEMRI) Project, Institute of Tropical Medicine (NEKKEN), Nagasaki University, P. O. Box 19993-00202, Nairobi, Kenya
| | - Akira Kaneko
- Island Malaria Group, Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Nobels väg 16, SE 171 77 Stockholm, Sweden
- Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, 1-4-3 Asahimachi, Abeno-ku, Osaka, 545-8585 Japan
- Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
| | - Osamu Kaneko
- Graduate School of Biomedical Sciences, Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
- Department of Protozoology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki, 852-8523 Japan
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Bertranpetit E, Jombart T, Paradis E, Pena H, Dubey J, Su C, Mercier A, Devillard S, Ajzenberg D. Phylogeography of Toxoplasma gondii points to a South American origin. INFECTION GENETICS AND EVOLUTION 2016; 48:150-155. [PMID: 28028000 DOI: 10.1016/j.meegid.2016.12.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]
Abstract
Toxoplasma gondii, a protozoan found ubiquitously in mammals and birds, is the etiologic agent of toxoplasmosis, a disease causing substantial public health burden worldwide, including about 200,000 new cases of congenital toxoplasmosis each year. Clinical severity has been shown to vary across geographical regions, with South America exhibiting the highest burden. Unfortunately, the drivers of these heterogeneities are still poorly understood, and the geographical origin and historical spread of the pathogen worldwide are currently uncertain. A worldwide sample of 168 T. gondii isolates gathered in 13 populations was sequenced for five fragments of genes (140 single nucleotide polymorphisms from 3153bp per isolate). Phylogeny based on Maximum likelihood methods with estimation of the time to the most recent common ancestor (TMRCA) and geostatistical analyses were performed for inferring the putative origin of T. gondii. We show that extant strains of the pathogen likely evolved from a South American ancestor, around 1.5 million years ago, and reconstruct the subsequent spread of the pathogen worldwide. This emergence is much more recent than the appearance of ancestral T. gondii, believed to have taken place about 11 My ago, and follows the arrival of felids in this part of the world. We posit that an ancestral lineage of T. gondii likely arrived in South America with felids and that the evolution of oral infectivity through carnivorism and the radiation of felids in this region enabled a new strain to outcompete the ancestral lineage and undergo a pandemic radiation.
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Affiliation(s)
- Emilie Bertranpetit
- INSERM UMR_S 1094, Neuroépidémiologie Tropicale, Laboratoire de Parasitologie-Mycologie, Faculté de Médecine, Université de Limoges, Limoges 87025, France
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - Emmanuel Paradis
- Institut des Sciences de l'Évolution, Université Montpellier/CNRS/IRD/EPHE, Place Eugène Bataillon, CC 065, 34095 Montpellier cédex 05, France
| | - Hilda Pena
- Departamento de Medicina Veterinária Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, Brazil
| | - Jitender Dubey
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Animal Parasitic Diseases Laboratory, Building 1001, Beltsville, MD 20705-2350, USA
| | - Chunlei Su
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
| | - Aurélien Mercier
- INSERM UMR_S 1094, Neuroépidémiologie Tropicale, Laboratoire de Parasitologie-Mycologie, Faculté de Médecine, Université de Limoges, Limoges 87025, France
| | - Sébastien Devillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive, F-69100 Villeurbanne, France.
| | - Daniel Ajzenberg
- INSERM UMR_S 1094, Neuroépidémiologie Tropicale, Laboratoire de Parasitologie-Mycologie, Faculté de Médecine, Université de Limoges, Limoges 87025, France.
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Ntege EH, Arisue N, Ito D, Hasegawa T, Palacpac NM, Egwang TG, Horii T, Takashima E, Tsuboi T. Identification of Plasmodium falciparum reticulocyte binding protein homologue 5-interacting protein, PfRipr, as a highly conserved blood-stage malaria vaccine candidate. Vaccine 2016; 34:5612-5622. [DOI: 10.1016/j.vaccine.2016.09.028] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 08/10/2016] [Accepted: 09/15/2016] [Indexed: 10/20/2022]
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Carlos BC, Fotoran WL, Menezes MJ, Cabral FJ, Bastos MF, Costa FT, Sousa-Neto JA, Ribolla PE, Wunderlich G, Ferreira MU. Expressed var gene repertoire and variant surface antigen diversity in a shrinking Plasmodium falciparum population. Exp Parasitol 2016; 170:90-99. [DOI: 10.1016/j.exppara.2016.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 09/01/2016] [Accepted: 09/20/2016] [Indexed: 10/21/2022]
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Sugden LA, Ramachandran S. Integrating the signatures of demic expansion and archaic introgression in studies of human population genomics. Curr Opin Genet Dev 2016; 41:140-149. [PMID: 27743539 DOI: 10.1016/j.gde.2016.09.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/19/2016] [Accepted: 09/23/2016] [Indexed: 12/12/2022]
Abstract
Human population genomic studies have repeatedly observed a decrease in heterozygosity and an increase in linkage disequilibrium with geographic distance from Africa. While multiple demographic models can generate these patterns, many studies invoke the serial founder effect model, in which populations expand from a single origin and each new population's founders represent a subset of genetic variation in the previous population. The model assumes no admixture with archaic hominins, however, recent studies have identified loci in Homo sapiens bearing signatures of archaic introgression. These results appear to contradict the validity of analyses invoking the serial founder effect model, but we show these two perspectives are compatible. We also propose using the serial founder effect model as a null model for determining the signature of archaic admixture in modern human genomes at different geographic and genomic scales.
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Affiliation(s)
- Lauren Alpert Sugden
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA
| | - Sohini Ramachandran
- Center for Computational Molecular Biology, Brown University, Providence, RI, USA; Department of Ecology and Evolutionary Biology, Brown University, Providence, RI, USA.
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Molina-Cruz A, Zilversmit MM, Neafsey DE, Hartl DL, Barillas-Mury C. Mosquito Vectors and the Globalization of Plasmodium falciparum Malaria. Annu Rev Genet 2016; 50:447-465. [PMID: 27732796 DOI: 10.1146/annurev-genet-120215-035211] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Plasmodium falciparum malaria remains a devastating public health problem. Recent discoveries have shed light on the origin and evolution of Plasmodium parasites and their interactions with their vertebrate and mosquito hosts. P. falciparum malaria originated in Africa from a single horizontal transfer between an infected gorilla and a human, and became global as the result of human migration. Today, P. falciparum malaria is transmitted worldwide by more than 70 different anopheline mosquito species. Recent studies indicate that the mosquito immune system can be a barrier to malaria transmission and that the P. falciparum Pfs47 gene allows the parasite to evade mosquito immune detection. Here, we review the origin and globalization of P. falciparum and integrate this history with analysis of the biology, evolution, and dispersal of the main mosquito vectors. This new perspective broadens our understanding of P. falciparum population structure and the dispersal of important parasite genetic traits.
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Affiliation(s)
- Alvaro Molina-Cruz
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
| | - Martine M Zilversmit
- Richard Guilder Graduate School and Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY 10024
| | - Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Daniel L Hartl
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852;
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Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China. Sci Rep 2016; 6:34353. [PMID: 27681182 PMCID: PMC5041183 DOI: 10.1038/srep34353] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/09/2016] [Indexed: 11/15/2022] Open
Abstract
Mycobacterium tuberculosis Beijing genotype originated in China and has undergone a dramatic population growth and global spread in the last century. Here, a collection of M. tuberculosis Beijing family isolates from different provinces across all China was genotyped by high-resolution (24-MIRU-VNTR) and low-resolution, high-rank (modern and ancient sublineages) markers. The molecular profiles and global and local phylogenies were compared to the strain phenotype and patient data. The phylogeographic patterns observed in the studied collection demonstrate that large-scale (but not middle/small-scale) distance remains one of the decisive factors of the genetic divergence of M. tuberculosis populations. Analysis of diversity and network topology of the local collections appears to corroborate a recent intriguing hypothesis about Beijing genotype originating in South China. Placing our results within the Eurasian context suggested that important Russian B0/W148 and Asian/Russian A0/94-32 epidemic clones of the Beijing genotype could trace their origins to the northeastern and northwestern regions of China, respectively. The higher clustering of the modern isolates in children and lack of increased MDR rate in any sublineage suggest that not association with drug resistance but other (e.g., speculatively, virulence-related) properties underlie an enhanced dissemination of the evolutionarily recent, modern sublineage of the Beijing genotype in China.
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Mitochondrial DNA from the eradicated European Plasmodium vivax and P. falciparum from 70-year-old slides from the Ebro Delta in Spain. Proc Natl Acad Sci U S A 2016; 113:11495-11500. [PMID: 27671660 DOI: 10.1073/pnas.1611017113] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogenetic analysis of Plasmodium parasites has indicated that their modern-day distribution is a result of a series of human-mediated dispersals involving transport between Africa, Europe, America, and Asia. A major outstanding question is the phylogenetic affinity of the malaria causing parasites Plasmodium vivax and falciparum in historic southern Europe-where it was endemic until the mid-20th century, after which it was eradicated across the region. Resolving the identity of these parasites will be critical for answering several hypotheses on the malaria dispersal. Recently, a set of slides with blood stains of malaria-affected people from the Ebro Delta (Spain), dated between 1942 and 1944, have been found in a local medical collection. We extracted DNA from three slides, two of them stained with Giemsa (on which Plasmodium parasites could still be seen under the microscope) and another one consisting of dried blood spots. We generated the data using Illumina sequencing after using several strategies aimed at increasing the Plasmodium DNA yield: depletion of the human genomic (g)DNA content through hybridization with human gDNA baits, and capture-enrichment using gDNA derived from P. falciparum Plasmodium mitochondrial genome sequences were subsequently reconstructed from the resulting data. Phylogenetic analysis of the eradicated European P. vivax mtDNA genome indicates that the European isolate is closely related to the most common present-day American haplotype and likely entered the American continent post-Columbian contact. Furthermore, the European P. falciparum mtDNA indicates a link with current Indian strains that is in agreement with historical accounts.
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Gallego-Delgado J, Walther T, Rodriguez A. The High Blood Pressure-Malaria Protection Hypothesis. Circ Res 2016; 119:1071-1075. [PMID: 27660286 DOI: 10.1161/circresaha.116.309602] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 08/23/2016] [Indexed: 12/30/2022]
Abstract
RATIONALE A recently proposed hypothesis states that malaria may contribute to hypertension in endemic areas,1 but the role of angiotensin II (Ang II), a major regulator of blood pressure, was not considered. Elevated levels of Ang II may confer protection against malaria morbidity and mortality, providing an alternative explanation for hypertension in malaria endemic areas. OBJECTIVE To discuss a possible alternative cause for hypertension in populations who have been under the selective pressure of malaria. METHODS AND RESULTS We reviewed published scientific literature for studies that could establish a link between Ang II and malaria. Both genetic and functional studies suggested that high levels of Ang II may confer protection against cerebral malaria by strengthening the integrity of the endothelial brain barrier. We also describe strong experimental evidence supporting our hypothesis through genetic, functional, and interventional studies. CONCLUSIONS A causal association between high levels of Ang II and protection from malaria pathogenesis can provide a likely explanation for the increased prevalence in hypertension observed in populations of African and South Asian origin. Furthermore, this potential causative connection might also direct unique approaches for the effective treatment of cerebral malaria.
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Affiliation(s)
- Julio Gallego-Delgado
- From the Department of Microbiology, New York University School of Medicine (J.G.-D., A.R.); and Department of Pharmacology and Therapeutics, School of Medicine and School of Pharmacy, University College Cork (UCC), Ireland (T.W.)
| | - Thomas Walther
- From the Department of Microbiology, New York University School of Medicine (J.G.-D., A.R.); and Department of Pharmacology and Therapeutics, School of Medicine and School of Pharmacy, University College Cork (UCC), Ireland (T.W.).
| | - Ana Rodriguez
- From the Department of Microbiology, New York University School of Medicine (J.G.-D., A.R.); and Department of Pharmacology and Therapeutics, School of Medicine and School of Pharmacy, University College Cork (UCC), Ireland (T.W.)
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Loy DE, Liu W, Li Y, Learn GH, Plenderleith LJ, Sundararaman SA, Sharp PM, Hahn BH. Out of Africa: origins and evolution of the human malaria parasites Plasmodium falciparum and Plasmodium vivax. Int J Parasitol 2016; 47:87-97. [PMID: 27381764 DOI: 10.1016/j.ijpara.2016.05.008] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 05/25/2016] [Accepted: 05/28/2016] [Indexed: 12/22/2022]
Abstract
Plasmodium falciparum and Plasmodium vivax account for more than 95% of all human malaria infections, and thus pose a serious public health challenge. To control and potentially eliminate these pathogens, it is important to understand their origins and evolutionary history. Until recently, it was widely believed that P. falciparum had co-evolved with humans (and our ancestors) over millions of years, whilst P. vivax was assumed to have emerged in southeastern Asia following the cross-species transmission of a parasite from a macaque. However, the discovery of a multitude of Plasmodium spp. in chimpanzees and gorillas has refuted these theories and instead revealed that both P. falciparum and P. vivax evolved from parasites infecting wild-living African apes. It is now clear that P. falciparum resulted from a recent cross-species transmission of a parasite from a gorilla, whilst P. vivax emerged from an ancestral stock of parasites that infected chimpanzees, gorillas and humans in Africa, until the spread of the protective Duffy-negative mutation eliminated P. vivax from human populations there. Although many questions remain concerning the biology and zoonotic potential of the P. falciparum- and P. vivax-like parasites infecting apes, comparative genomics, coupled with functional parasite and vector studies, are likely to yield new insights into ape Plasmodium transmission and pathogenesis that are relevant to the treatment and prevention of human malaria.
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Affiliation(s)
- Dorothy E Loy
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Weimin Liu
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yingying Li
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Gerald H Learn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lindsey J Plenderleith
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Sesh A Sundararaman
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Paul M Sharp
- Institute of Evolutionary Biology, and Centre for Immunity, Infection and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Beatrice H Hahn
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Little Polymorphism at the K13 Propeller Locus in Worldwide Plasmodium falciparum Populations Prior to the Introduction of Artemisinin Combination Therapies. Antimicrob Agents Chemother 2016; 60:3340-7. [PMID: 27001814 DOI: 10.1128/aac.02370-15] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/03/2016] [Indexed: 12/12/2022] Open
Abstract
The emergence and spread of artemisinin-resistant Plasmodium falciparum is of huge concern for the global effort toward malaria control and elimination. Artemisinin resistance, defined as a delayed time to parasite clearance following administration of artemisinin, is associated with mutations in the Pfkelch13 gene of resistant parasites. To date, as many as 60 nonsynonymous mutations have been identified in this gene, but whether these mutations have been selected by artemisinin usage or merely reflect natural polymorphism independent of selection is currently unknown. To clarify this, we sequenced the Pfkelch13 propeller domain in 581 isolates collected before (420 isolates) and after (161 isolates) the implementation of artemisinin combination therapies (ACTs), from various regions of endemicity worldwide. Nonsynonymous mutations were observed in 1% of parasites isolated prior to the introduction of ACTs. Frequencies of mutant isolates, nucleotide diversity, and haplotype diversity were significantly higher in the parasites isolated from populations exposed to artemisinin than in those from populations that had not been exposed to the drug. In the artemisinin-exposed population, a significant excess of dN compared to dS was observed, suggesting the presence of positive selection. In contrast, pairwise comparison of dN and dS and the McDonald and Kreitman test indicate that purifying selection acts on the Pfkelch13 propeller domain in populations not exposed to ACTs. These population genetic analyses reveal a low baseline of Pfkelch13 polymorphism, probably due to purifying selection in the absence of artemisinin selection. In contrast, various Pfkelch13 mutations have been selected under artemisinin pressure.
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Abstract
The current epidemic of artemisinin resistant Plasmodium falciparum in Southeast Asia is the result of a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non-synonymous mutations, many of which cause radical amino-acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of variations that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions. DOI:http://dx.doi.org/10.7554/eLife.08714.001 Malaria is an infectious disease caused by a microscopic parasite called Plasmodium, which is transferred between humans by mosquitos. One species of malaria parasite called Plasmodium falciparum can cause particularly severe and life-threatening forms of the disease. Currently, the most widely used treatment for P. falciparum infections is artemisinin combination therapy, a treatment that combines the drug artemisinin (or a closely related molecule) with another antimalarial drug. However, resistance to artemisinin has started to spread throughout Southeast Asia. Artemisinin resistance is caused by mutations in a parasite gene called kelch13, and researchers have identified over 20 different mutations in P. falciparum that confer artemisinin resistance. The diversity of mutations involved, and the fact that the same mutation can arise independently in different locations, make it difficult to track the spread of resistance using conventional molecular marker approaches. Here, Amato, Miotto et al. sequenced the entire genomes of more than 3,000 clinical samples of P. falciparum from Southeast Asia and Africa, collected as part of a global network of research groups called the MalariaGEN Plasmodium falciparum Community Project. Amato, Miotto et al. found that African parasites had independently acquired many of the same kelch13 mutations that are known to cause resistance to artemisinin in Southeast Asia. However the kelch13 mutations seen in Africa remained at low levels in the parasite population, and appeared to be under much less pressure for evolutionary selection than those found in Southeast Asia. These findings demonstrate that the emergence and spread of resistance to antimalarial drugs does not depend solely on the mutational process, but also on other factors that influence whether the mutations will spread in the population. Understanding how this is affected by different patterns of drug treatments and other environmental conditions will be important in developing more effective strategies for combating malaria. DOI:http://dx.doi.org/10.7554/eLife.08714.002
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Distance from sub-Saharan Africa predicts mutational load in diverse human genomes. Proc Natl Acad Sci U S A 2015; 113:E440-9. [PMID: 26712023 DOI: 10.1073/pnas.1510805112] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Out-of-Africa (OOA) dispersal ∼ 50,000 y ago is characterized by a series of founder events as modern humans expanded into multiple continents. Population genetics theory predicts an increase of mutational load in populations undergoing serial founder effects during range expansions. To test this hypothesis, we have sequenced full genomes and high-coverage exomes from seven geographically divergent human populations from Namibia, Congo, Algeria, Pakistan, Cambodia, Siberia, and Mexico. We find that individual genomes vary modestly in the overall number of predicted deleterious alleles. We show via spatially explicit simulations that the observed distribution of deleterious allele frequencies is consistent with the OOA dispersal, particularly under a model where deleterious mutations are recessive. We conclude that there is a strong signal of purifying selection at conserved genomic positions within Africa, but that many predicted deleterious mutations have evolved as if they were neutral during the expansion out of Africa. Under a model where selection is inversely related to dominance, we show that OOA populations are likely to have a higher mutation load due to increased allele frequencies of nearly neutral variants that are recessive or partially recessive.
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Comas I, Hailu E, Kiros T, Bekele S, Mekonnen W, Gumi B, Tschopp R, Ameni G, Hewinson RG, Robertson BD, Goig GA, Stucki D, Gagneux S, Aseffa A, Young D, Berg S. Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa. Curr Biol 2015; 25:3260-6. [PMID: 26687624 PMCID: PMC4691238 DOI: 10.1016/j.cub.2015.10.061] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 02/06/2023]
Abstract
Colonial medical reports claimed that tuberculosis (TB) was largely unknown in Africa prior to European contact, providing a "virgin soil" for spread of TB in highly susceptible populations previously unexposed to the disease [1, 2]. This is in direct contrast to recent phylogenetic models which support an African origin for TB [3-6]. To address this apparent contradiction, we performed a broad genomic sampling of Mycobacterium tuberculosis in Ethiopia. All members of the M. tuberculosis complex (MTBC) arose from clonal expansion of a single common ancestor [7] with a proposed origin in East Africa [3, 4, 8]. Consistent with this proposal, MTBC lineage 7 is almost exclusively found in that region [9-11]. Although a detailed medical history of Ethiopia supports the view that TB was rare until the 20(th) century [12], over the last century Ethiopia has become a high-burden TB country [13]. Our results provide further support for an African origin for TB, with some genotypes already present on the continent well before European contact. Phylogenetic analyses reveal a pattern of serial introductions of multiple genotypes into Ethiopia in association with human migration and trade. In place of a "virgin soil" fostering the spread of TB in a previously naive population, we propose that increased TB mortality in Africa was driven by the introduction of European strains of M. tuberculosis alongside expansion of selected indigenous strains having biological characteristics that carry a fitness benefit in the urbanized settings of post-colonial Africa.
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Affiliation(s)
- Iñaki Comas
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid 28029, Spain.
| | - Elena Hailu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Teklu Kiros
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Wondale Mekonnen
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Balako Gumi
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Rea Tschopp
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia; Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - R Glyn Hewinson
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK
| | - Brian D Robertson
- Center for Molecular Bacteriology and Infection, Department of Medicine, Flowers Building, South Kensington, Imperial College London, London SW7 2AZ, UK
| | - Galo A Goig
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Douglas Young
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stefan Berg
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK.
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Chavatte JM, Tan SBH, Snounou G, Lin RTPV. Molecular characterization of misidentified Plasmodium ovale imported cases in Singapore. Malar J 2015; 14:454. [PMID: 26577930 PMCID: PMC4650842 DOI: 10.1186/s12936-015-0985-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 11/03/2015] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Plasmodium ovale, considered the rarest of the malaria parasites of humans, consists of two morphologically identical but genetically distinct sympatric species, Plasmodium ovale curtisi and Plasmodium ovale wallikeri. These parasites resemble morphologically to Plasmodium vivax with which they also share a tertian periodicity and the ability to cause relapses, making them easily misidentified as P. vivax. Plasmodium ovale infections are rarely reported, but given the likelihood of misidentification, their prevalence might be underestimated. METHODS Morphological and molecular analysis of confirmed malaria cases admitted in Singapore in 2012-2014 detected nine imported P. ovale cases that had been misidentified as P. vivax. Since P. ovale had not been previously officially reported in Singapore, a retrospective analysis of available, frozen, archival blood samples was performed and returned two additional misidentified P. ovale cases in 2003 and 2006. These eleven P. ovale samples were characterized with respect to seven molecular markers (ssrRNA, Potra, Porbp2, Pog3p, dhfr-ts, cytb, cox1) used in recent studies to distinguish between the two sympatric species, and to a further three genes (tufa, clpC and asl). RESULTS The morphological features of P. ovale and the differential diagnosis with P. vivax were reviewed and illustrated by microphotographs. The genetic dimorphism between P. ovale curtisi and P. ovale wallikeri was assessed by ten molecular markers distributed across the three genomes of the parasite (Genbank KP050361-KP050470). The data obtained for seven of these markers were compared with those published and confirmed that both P. ovale species were present. This dimorphism was also confirmed for the first time on: (1) two genes from the apicoplast genome (tufA and clpC genes); and, (2) the asl gene that was used for phylogenetic analyses of other Plasmodium species, and that was found to harbour the highest number of dimorphic loci between the two P. ovale species. CONCLUSION Misidentified P. ovale infections are reported for the first time among imported malaria cases in Singapore. Genetic dimorphism between P. ovale curtisi and P. ovale wallikeri was confirmed using markers from the parasites' three genomes. The apparent increase of imported P. ovale since 2012 (with yearly detection of cases) is puzzling. Given decrease in the overall number of malaria cases recorded in Singapore since 2010 the 'resurgence' of this neglected species raises public health concerns.
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Affiliation(s)
- Jean-Marc Chavatte
- Malaria Reference Centre - National Public Health Laboratory, Ministry of Health, Singapore, 3 Biopolis Drive, Synapse #05-14/16, 138623, Singapore, Singapore.
| | - Sarah Bee Hui Tan
- Malaria Reference Centre - National Public Health Laboratory, Ministry of Health, Singapore, 3 Biopolis Drive, Synapse #05-14/16, 138623, Singapore, Singapore.
| | - Georges Snounou
- Sorbonne Universités, UPMC Université Paris 06, UPMC UMRS CR7, 75005, Paris, France.
- Centre d'Immunologie et de Maladies Infectieuses (CIMI) Paris, Institut National de la Santé et de la Recherche Médicale (Inserm) U1135, Centre National de la Recherche Scientifique (CNRS) ERL 8255, 75013, Paris, France.
| | - Raymond Tzer Pin Valentine Lin
- Malaria Reference Centre - National Public Health Laboratory, Ministry of Health, Singapore, 3 Biopolis Drive, Synapse #05-14/16, 138623, Singapore, Singapore.
- Department of Laboratory Medicine, National University Hospital, 5 Lower Kent Ridge Road, 119074, Singapore, Singapore.
- Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Block MD4, Level 3, 117545, Singapore, Singapore.
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