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Abagero BR, Rama R, Obeid A, Tolosa T, Lukas B, Teka T, Tesfaye D, Lo E, Yewhalaw D. Detection of Duffy blood group genotypes and submicroscopic Plasmodium infections using molecular diagnostic assays in febrile malaria patients. Malar J 2024; 23:194. [PMID: 38902674 PMCID: PMC11191254 DOI: 10.1186/s12936-024-04875-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/09/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Malaria remains a severe parasitic disease, posing a significant threat to public health and hindering economic development in sub-Saharan Africa. Ethiopia, a malaria endemic country, is facing a resurgence of the disease with a steadily rising incidence. Conventional diagnostic methods, such as microscopy, have become less effective due to low parasite density, particularly among Duffy-negative human populations in Africa. To develop comprehensive control strategies, it is crucial to generate data on the distribution and clinical occurrence of Plasmodium vivax and Plasmodium falciparum infections in regions where the disease is prevalent. This study assessed Plasmodium infections and Duffy antigen genotypes in febrile patients in Ethiopia. METHODS Three hundred febrile patients visiting four health facilities in Jimma town of southwestern Ethiopia were randomly selected during the malaria transmission season (Apr-Oct). Sociodemographic information was collected, and microscopic examination was performed for all study participants. Plasmodium species and parasitaemia as well as the Duffy genotype were assessed by quantitative polymerase chain reaction (qPCR) for all samples. Data were analysed using Fisher's exact test and kappa statistics. RESULTS The Plasmodium infection rate by qPCR was 16% (48/300) among febrile patients, of which 19 (39.6%) were P. vivax, 25 (52.1%) were P. falciparum, and 4 (8.3%) were mixed (P. vivax and P. falciparum) infections. Among the 48 qPCR-positive samples, 39 (13%) were negative by microscopy. The results of bivariate logistic regression analysis showed that agriculture-related occupation, relapse and recurrence were significantly associated with Plasmodium infection (P < 0.001). Of the 300 febrile patients, 85 (28.3%) were Duffy negative, of whom two had P. vivax, six had P. falciparum, and one had mixed infections. Except for one patient with P. falciparum infection, Plasmodium infections in Duffy-negative individuals were all submicroscopic with low parasitaemia. CONCLUSIONS The present study revealed a high prevalence of submicroscopic malaria infections. Plasmodium vivax infections in Duffy-negative individuals were not detected due to low parasitaemia. In this study, an improved molecular diagnostic tool was used to detect and characterize Plasmodium infections, with the goal of quantifying P. vivax infection in Duffy-negative individuals. Advanced molecular diagnostic techniques, such as multiplex real-time PCR, loop-mediated isothermal amplification (LAMP), and CRISPR-based diagnostic methods. These techniques offer increased sensitivity, specificity, and the ability to detect low-parasite-density infections compared to the employed methodologies.
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Affiliation(s)
- Beka R Abagero
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Rei Rama
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Abdulghani Obeid
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Tirusew Tolosa
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Biniyam Lukas
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Taye Teka
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Daniel Tesfaye
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia
| | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA.
| | - Delenasaw Yewhalaw
- School of Medical Laboratory Sciences, Faculty of Health Sciences, Institute of Health, Jimma University, Jimma, Ethiopia.
- Tropical and Infectious Diseases Research Centre, Jimma University, Jimma, Ethiopia.
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Abagero BR, Rama R, Obeid A, Tolossa T, Legese F, Lo E, Yewhalaw D. Detection of Duffy Blood Group Genotypes and Submicroscopic Plasmodium Infections Using Molecular Diagnostic Assays in Febrile Malaria Patients. RESEARCH SQUARE 2023:rs.3.rs-3706814. [PMID: 38105972 PMCID: PMC10723540 DOI: 10.21203/rs.3.rs-3706814/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Background Malaria remains a severe parasitic disease, posing a significant threat to public health and hindering economic development in sub-Saharan Africa. Ethiopia, a malaria endemic country, is facing a resurgence of the disease with a steadily rising incidence. Conventional diagnostic methods, such asmicroscopy, have become less effective due to low parasite density, particularly among Duffy-negative human populations in Africa. To develop comprehensive control strategies, it is crucial to generate data on the distribution and clinical occurrence of Plasmodium vivax and P. falciparum infections in regions where the disease is prevalent. This study assessed Plasmodium infections and Duffy antigen genotypes in febrile patients in Ethiopia. Methods Three hundred febrile patients visiting four health facilities in Jimma town of southwestern Ethiopia were randomly selected during the malaria transmission season (Apr-Oct). Sociodemographic information was collected, and microscopic examination was performed for all study participants. Plasmodiumspecies and parasitemia as well as the Duffy genotype were assessed by quantitative polymerase chain reaction (qPCR) for all samples. Data were analyzed using Fisher's exact test and kappa statistics. Results The Plasmodium infection rate by qPCR was 16% (48/300) among febrile patients, of which 19 (39.6%) were P. vivax, 25 (52.1%) were P. falciparum, and 4 (8.3%) were mixed (P. vivax and P. falciparum) infections. Among the 48 qPCR-positive samples, 39 (13%) were negative by microscopy. The results of bivariate logistic regression analysis showed that agriculture-related occupation, relapse and recurrence were significantly associated withPlasmodium infection (P<0.001). Of the 300 febrile patients, 85 (28.3%) were Duffy negative, of whom two had P. vivax, six had P. falciparum, and one had mixed infections.Except for one patient with P. falciparum infection, Plasmodium infections in Duffy-negative individuals were all submicroscopic with low parasitemia. Conclusions The present study revealed a high prevalence of submicroscopic malaria infections. Plasmodium vivax infections in Duffy-negative individuals were not detected due to low parasitemia. Here, we recommend an improved molecular diagnostic tool to detect and characterize plasmodium infections, with the goal of quantifyingP. vivax infection in Duffy-negative individuals.
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Affiliation(s)
- Beka Raya Abagero
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Rei Rama
- University of North Carolina at Charlotte
| | | | | | | | - Eugenia Lo
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA
| | - Delenasaw Yewhalaw
- Tropical and Infectious Diseases Research Center, Jimma University, Jimma, Ethiopia
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3
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Abate A, Bouyssou I, Mabilotte S, Doderer-Lang C, Dembele L, Menard D, Golassa L. Vivax malaria in Duffy-negative patients shows invariably low asexual parasitaemia: implication towards malaria control in Ethiopia. Malar J 2022; 21:230. [PMID: 35915453 PMCID: PMC9341100 DOI: 10.1186/s12936-022-04250-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/26/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The increase in detections of Plasmodium vivax infection in Duffy-negative individuals in Africa has challenged the dogma establishing the unique P. vivax Duffy Binding Protein-Duffy antigen receptor for chemokines (PvDBP-DARC) pathway used by P. vivax merozoites to invade reticulocytes. Information on the impact of Duffy antigen polymorphisms on the epidemiology of P. vivax malaria remains elusive. The objective of this study was to determine the distribution of asexual parasitaemia of P. vivax according to the Duffy antigen polymorphisms in Ethiopia. METHODS DNA was extracted from dried blood spots (DBS) collected from prospectively recruited 138 P. vivax-infected patients from health centres. The identification and estimation of P. vivax asexual parasitaemia were performed by microscopic examination and quantitative real-time polymerase chain reaction (PCR). Duffy genotyping was conducted by DNA sequencing in a total of 138 P.vivax infected samples. RESULTS The proportion of Duffy-negatives (FY*BES/FY*BES) in P. vivax infected patients was 2.9% (4/138). Duffy genotype FY*B/FY*BES (48.6%) was the most common, followed by FY*A/FY*BES genotype (25.4%). In one patient, the FY*02 W.01/FY*02 N.01 genotype conferring a weak expression of the Fyb antigen was observed. All P.vivax infected Duffy-negative patients showed low asexual parasitaemia (≤ 110 parasites/µL). The median P. vivax parasitaemia in Duffy-negative patients (53 parasites/µL) was significantly lower than those found in homozygous and heterozygous individuals (P < 0.0001). CONCLUSION Plasmodium vivax in Duffy-negative patients shows invariably low asexual parasitaemia. This finding suggests that the pathway used by P. vivax to invade Duffy-negative reticulocytes is much less efficient than that used in Duffy-positives. Moreover, the low asexual parasitaemia observed in Duffy-negative individuals could constitute an 'undetected silent reservoir', thus likely delaying the elimination of vivax malaria in Ethiopia.
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Affiliation(s)
- Andargie Abate
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia.
- College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia.
| | - Isabelle Bouyssou
- Malaria Genetics and Resistance Unit, Institut Pasteur, INSERM U1201, Paris, France
- ED515 Complexité du Vivant, Sorbonne Université, Paris, France
| | - Solenne Mabilotte
- Institute of Parasitology and Tropical Diseases, UR7292 Dynamics of Host-Pathogen Interactions, Federation of Translational Medicine, University of Strasbourg, Strasbourg, France
| | - Cecile Doderer-Lang
- Institute of Parasitology and Tropical Diseases, UR7292 Dynamics of Host-Pathogen Interactions, Federation of Translational Medicine, University of Strasbourg, Strasbourg, France
| | - Laurent Dembele
- Malaria Research and Training Centre (MRTC), Université des Sciences, des Techniques et des Technologies de Bamako (USTTB), Bamako, Mali
| | - Didier Menard
- Malaria Genetics and Resistance Unit, Institut Pasteur, INSERM U1201, Paris, France
- Institute of Parasitology and Tropical Diseases, UR7292 Dynamics of Host-Pathogen Interactions, Federation of Translational Medicine, University of Strasbourg, Strasbourg, France
- Laboratory of Parasitology and Medical Mycology, Strasbourg University Hospital, Strasbourg, France
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
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Tennessen JA, Duraisingh MT. Three Signatures of Adaptive Polymorphism Exemplified by Malaria-Associated Genes. Mol Biol Evol 2021; 38:1356-1371. [PMID: 33185667 PMCID: PMC8042748 DOI: 10.1093/molbev/msaa294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Malaria has been one of the strongest selective pressures on our species. Many of the best-characterized cases of adaptive evolution in humans are in genes tied to malaria resistance. However, the complex evolutionary patterns at these genes are poorly captured by standard scans for nonneutral evolution. Here, we present three new statistical tests for selection based on population genetic patterns that are observed more than once among key malaria resistance loci. We assess these tests using forward-time evolutionary simulations and apply them to global whole-genome sequencing data from humans, and thus we show that they are effective at distinguishing selection from neutrality. Each test captures a distinct evolutionary pattern, here called Divergent Haplotypes, Repeated Shifts, and Arrested Sweeps, associated with a particular period of human prehistory. We clarify the selective signatures at known malaria-relevant genes and identify additional genes showing similar adaptive evolutionary patterns. Among our top outliers, we see a particular enrichment for genes involved in erythropoiesis and for genes previously associated with malaria resistance, consistent with a major role for malaria in shaping these patterns of genetic diversity. Polymorphisms at these genes are likely to impact resistance to malaria infection and contribute to ongoing host-parasite coevolutionary dynamics.
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Oboh MA, Singh US, Ndiaye D, Badiane AS, Ali NA, Bharti PK, Das A. Presence of additional Plasmodium vivax malaria in Duffy negative individuals from Southwestern Nigeria. Malar J 2020; 19:229. [PMID: 32590997 PMCID: PMC7318376 DOI: 10.1186/s12936-020-03301-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Abstract
Background Malaria in sub-Saharan Africa (sSA) is thought to be mostly caused by Plasmodium falciparum. Recently, growing reports of cases due to Plasmodium ovale, Plasmodium malariae, and Plasmodium vivax have been increasingly observed to play a role in malaria epidemiology in sSA. This in fact is due to the usage of very sensitive diagnostic tools (e.g. PCR), which have highlighted the underestimation of non-falciparum malaria in this sub-region. Plasmodium vivax was historically thought to be absent in sSA due to the high prevalence of the Duffy negativity in individuals residing in this sub-continent. Recent studies reporting detection of vivax malaria in Duffy-negative individuals from Mali, Mauritania, Cameroon challenge this notion. Methods Following previous report of P. vivax in Duffy-negative individuals in Nigeria, samples were further collected and assessed RDT and/or microscopy. Thereafter, malaria positive samples were subjected to conventional PCR method and DNA sequencing to confirm both single/mixed infections as well as the Duffy status of the individuals. Results Amplification of Plasmodium gDNA was successful in 59.9% (145/242) of the evaluated isolates and as expected P. falciparum was the most predominant (91.7%) species identified. Interestingly, four P. vivax isolates were identified either as single (3) or mixed (one P. falciparum/P. vivax) infection. Sequencing results confirmed all vivax isolates as truly vivax malaria and the patient were of Duffy-negative genotype. Conclusion Identification of additional vivax isolates among Duffy-negative individuals from Nigeria, substantiate the expanding body of evidence on the ability of P. vivax to infect RBCs that do not express the DARC gene. Hence, such genetic-epidemiological study should be conducted at the country level in order to evaluate the true burden of P. vivax in Nigeria.
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Affiliation(s)
- Mary Aigbiremo Oboh
- Medical Research Council Unit The Gambia at LSHTM, Fajara, P.O. Box 273, Banjul, Gambia.
| | - Upasana Shyamsunder Singh
- School of Earth and Environmental Sciences, University of Manchester, Manchester, UK.,Genomic Epidemiology Laboratory, Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Daouda Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Aida Sadikh Badiane
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Nazia Anwar Ali
- National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, 482003, India
| | - Praveen Kumar Bharti
- National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, 482003, India
| | - Aparup Das
- Genomic Epidemiology Laboratory, Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India.
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6
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Gai PP, van Loon W, Siegert K, Wedam J, Kulkarni SS, Rasalkar R, Boloor A, Kumar A, Jain A, Mahabala C, Baliga S, Devi R, Shenoy D, Gai P, Mockenhaupt FP. Duffy antigen receptor for chemokines gene polymorphisms and malaria in Mangaluru, India. Malar J 2019; 18:328. [PMID: 31551092 PMCID: PMC6760058 DOI: 10.1186/s12936-019-2966-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022] Open
Abstract
Background Duffy blood group antigens serve as receptors for Plasmodium vivax invasion into erythrocytes, and they are determined by polymorphisms of the Duffy antigen receptor for chemokines (DARC), also known as Fy glycoprotein (FY). Duffy negativity, i.e., absence of the antigens, protects against P. vivax infection and is rare among non-African populations. However, data on DARC polymorphisms and their impact on Plasmodium infection in India are scarce. Methods In a case–control study among 909 malaria patients and 909 healthy community controls in Mangaluru, southwestern India, DARC polymorphisms T-33C (rs2814778), G125A (rs12075), C265T (rs34599082), and G298A (rs13962) were genotyped. Associations of the polymorphisms with the odds of malaria, parasite species and manifestation were assessed. Results Among patients, vivax malaria (70%) predominated over falciparum malaria (9%) and mixed species infections (21%). DARC T-33C was absent and C265T was rare (1%). FYB carriage (deduced from DARC G125A) was not associated with the risk of malaria per se but it protected against severe falciparum malaria (P = 0.03), and hospitalization (P = 0.006) due to falciparum malaria. Vice versa, carriage of DARC 298A was associated with increased odds of malaria (aOR, 1.46 (1.07–1.99), P = 0.015) and vivax malaria (aOR, 1.60 (1.14–2.22), P = 0.006) and with several reported symptoms and findings of the patients. Conclusion This report from southern India is the first to show an independent effect of the DARC 298A polymorphism on the risk of malaria. Functional studies are required to understand the underlying mechanism. Moreover, FYB carriage appears to protect against severe falciparum malaria in southern India.
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Affiliation(s)
- Prabhanjan P Gai
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Institute of Tropical Medicine and International Health, Berlin, Germany.
| | - Welmoed van Loon
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Konrad Siegert
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Institute of Tropical Medicine and International Health, Berlin, Germany
| | - Jakob Wedam
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Institute of Tropical Medicine and International Health, Berlin, Germany
| | | | - Rashmi Rasalkar
- Karnataka Institute for DNA Research, Dharwad, Karnataka, India
| | - Archith Boloor
- Kasturba Medical College, Mangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Arun Kumar
- District Vector Borne Disease Control Programme Office, Dakshina Kannada, Mangaluru, Karnataka, India
| | - Animesh Jain
- Kasturba Medical College, Mangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Chakrapani Mahabala
- Kasturba Medical College, Mangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Shantaram Baliga
- Kasturba Medical College, Mangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | | | - Damodara Shenoy
- Kasturba Medical College, Mangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Pramod Gai
- Karnataka Institute for DNA Research, Dharwad, Karnataka, India
| | - Frank P Mockenhaupt
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health; Institute of Tropical Medicine and International Health, Berlin, Germany
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Lo E, Hostetler JB, Yewhalaw D, Pearson RD, Hamid MMA, Gunalan K, Kepple D, Ford A, Janies DA, Rayner JC, Miller LH, Yan G. Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance. PLoS Negl Trop Dis 2019; 13:e0007222. [PMID: 31509523 PMCID: PMC6756552 DOI: 10.1371/journal.pntd.0007222] [Citation(s) in RCA: 21] [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: 02/05/2019] [Revised: 09/23/2019] [Accepted: 07/23/2019] [Indexed: 01/20/2023] Open
Abstract
Plasmodium vivax invasion of human erythrocytes depends on the Duffy Binding Protein (PvDBP) which interacts with the Duffy antigen. PvDBP copy number has been recently shown to vary between P. vivax isolates in Sub-Saharan Africa. However, the extent of PvDBP copy number variation, the type of PvDBP multiplications, as well as its significance across broad samples are still unclear. We determined the prevalence and type of PvDBP duplications, as well as PvDBP copy number variation among 178 Ethiopian P. vivax isolates using a PCR-based diagnostic method, a novel quantitative real-time PCR assay and whole genome sequencing. For the 145 symptomatic samples, PvDBP duplications were detected in 95 isolates, of which 81 had the Cambodian and 14 Malagasy-type PvDBP duplications. PvDBP varied from 1 to >4 copies. Isolates with multiple PvDBP copies were found to be higher in symptomatic than asymptomatic infections. For the 33 asymptomatic samples, PvDBP was detected with two copies in two of the isolates, and both were the Cambodian-type PvDBP duplication. PvDBP copy number in Duffy-negative heterozygotes was not significantly different from that in Duffy-positives, providing no support for the hypothesis that increased copy number is a specific association with Duffy-negativity, although the number of Duffy-negatives was small and further sampling is required to test this association thoroughly. Plasmodium vivax invasion of human erythrocytes relies on interaction between the Duffy antigen and P. vivax Duffy Binding Protein (PvDBP). Whole genome sequences from P. vivax field isolates in Madagascar identified a duplication of the PvDBP gene and PvDBP duplication has also been detected in non-African P. vivax-endemic countries. Two types of PvDBP duplications have been reported, termed Cambodian and Malagasy-type duplications. Our study used a combination of PCR-based diagnostic method, a novel quantitative real-time PCR assay, and whole genome sequencing to determine the prevalence and type of PvDBP duplications, as well as PvDBP copy number on a broad number of P. vivax samples in Ethiopia. We found that over 65% of P. vivax isolated from the symptomatic infections were detected with PvDBP duplications and PvDBP varied from 1 to >4 copies. The majority of PvDBP duplications belongs to the Cambodian-type while the Malagasy-type duplications was also detected. For the asymptomatic infections, despite a small sample size, the majority of P. vivax were detected with a single-copy based on both PCR and qPCR assays. There was no significant difference in PvDBP copy number between Duffy-null heterozygote and Duffy-positive homozygote/heterozygote. Further investigation is needed with expanded Duffy-null homozygotes to examine the functional significance of PvDBP expansion.
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Affiliation(s)
- Eugenia Lo
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
- * E-mail: (EL); (LHM); (GY)
| | - Jessica B. Hostetler
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Richard D. Pearson
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Muzamil M. A. Hamid
- Department of Parasitology and Medical Entomology, University of Khartoum, Khartoum, Sudan
| | - Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Daniel Kepple
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Anthony Ford
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Daniel A. Janies
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC, United States of America
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Wellcome Genome Campus, Cambridge, United Kingdom
| | - Louis H. Miller
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail: (EL); (LHM); (GY)
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, United States of America
- * E-mail: (EL); (LHM); (GY)
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8
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Kaur H, Sehgal R, Rani S. Duffy antigen receptor for chemokines (DARC) and susceptibility to Plasmodium vivax malaria. Parasitol Int 2019; 71:73-75. [PMID: 30928426 DOI: 10.1016/j.parint.2019.03.013] [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: 12/17/2018] [Revised: 03/04/2019] [Accepted: 03/25/2019] [Indexed: 12/25/2022]
Abstract
DARC is thought to act as a key invasion receptor in P. vivax malaria. It is known that the expression of DARC and susceptibility to P. vivax malaria is influenced by the presence of specific DARC genotypes. Studies have reported the low probability of P. vivax malaria in individuals carrying FyA allele due to the significantly reduced binding of the P. vivax duffy binding protein. No association of the allele frequency and severe vivax malaria epidemiology has been yet established in our country. In the present study, a high level of heterozygotes was observed with a statistically significant deviation from the H-W equilibrium in the group with complicated malaria; which is indicative of demographic disequilibrium. Significantly upregulated expression of the DARC receptor in FyA/FyB heterozygote patients is suggestive of a greater receptor repertoire responsible for the possible variation in the parasite ligand binding with the host receptor and thus might have a role to play in severe malaria.
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Affiliation(s)
- Hargobinder Kaur
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Rakesh Sehgal
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India.
| | - Sofia Rani
- Department of Medical Parasitology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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9
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Red cell groups and Basque population(s): From anthropology to public health. Transfus Clin Biol 2019; 26:69-75. [DOI: 10.1016/j.tracli.2018.11.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/14/2018] [Indexed: 11/19/2022]
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10
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Palmblad J, Höglund P. Ethnic benign neutropenia: A phenomenon finds an explanation. Pediatr Blood Cancer 2018; 65:e27361. [PMID: 30117263 DOI: 10.1002/pbc.27361] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/21/2018] [Accepted: 06/25/2018] [Indexed: 01/29/2023]
Abstract
Ethnic benign neutropenia (ENP) is the most common form of neutropenia (NP) worldwide, if an absolute blood neutrophil count (ANC) of < 1.5 G/L is used as definition. In 2009, ENP was associated with a gene variation in the ACKR1/DARC gene, the same variation that also confers the Duffy-null trait. In 2017, a novel mechanism for ENP was introduced, questioning if ENP is a true neutropenic state, when the body's total neutrophil count (TBNC) is concerned. Here, we summarize the current knowledge of ENP, asking (1) How well does the peripheral blood ANC predict the TBNC? (2) Can we improve methods for assessing TBNC? (3) Will estimates of TBNC predict infection propensity and reduce the need for further, costly workup?
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Affiliation(s)
- Jan Palmblad
- Department of Medicine Karolinska Institutet, The Hematology Center, Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Petter Höglund
- Department of Medicine Karolinska Institutet, Department of Clinical Immunology and Transfusion Medicine, Karolinska University Hospital Huddinge, and Center for Hematology and Regenerative Medicine (HERM), Stockholm, Sweden
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11
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Oboh MA, Badiane AS, Ntadom G, Ndiaye YD, Diongue K, Diallo MA, Ndiaye D. Molecular identification of Plasmodium species responsible for malaria reveals Plasmodium vivax isolates in Duffy negative individuals from southwestern Nigeria. Malar J 2018; 17:439. [PMID: 30486887 PMCID: PMC6263541 DOI: 10.1186/s12936-018-2588-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/22/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Malaria in Nigeria is principally due to Plasmodium falciparum and, to a lesser extent to Plasmodium malariae and Plasmodium ovale. Plasmodium vivax is thought to be absent in Nigeria in particular and sub-Saharan Africa in general, due to the near fixation of the Duffy negative gene in this population. Nevertheless, there are frequent reports of P. vivax infection in Duffy negative individuals in the sub-region, including reports from two countries sharing border with Nigeria to the west (Republic of Benin) and east (Cameroon). Additionally, there were two cases of microscopic vivax-like malaria from Nigerian indigenous population. Hence molecular surveillance of the circulating Plasmodium species in two states (Lagos and Edo) of southwestern Nigeria was carried out. METHODS A cross-sectional survey between September 2016 and March 2017 was conducted. 436 febrile patients were included for the present work. Venous blood of these patients was subjected to RDT as well as microscopy. Further, parasite DNA was isolated from positive samples and PCR diagnostic was employed followed by direct sequencing of the 18S rRNA of Plasmodium species as well as sequencing of a portion of the promoter region of the Duffy antigen receptor for chemokines. Samples positive for P. vivax were re-amplified several times and finally using the High Fidelity Taq to rule out any bias introduced. RESULTS Of the 256 (58.7%) amplifiable malaria parasite DNA, P. falciparum was, as expected, the major cause of infection, either alone 85.5% (219/256; 97 from Edo and 122 from Lagos), or mixed with P. malariae 6.3% (16/256) or with P. vivax 1.6% (4/256). Only one of the five P. vivax isolates was found to be a single infection. DNA sequencing and subsequent alignment of the 18S rRNA of P. vivax with the reference strains displayed very high similarities (100%). Remarkably, the T-33C was identified in all P. vivax samples, thus confirming that all vivax-infected patients in the current study are Duffy negative. CONCLUSION The present study gave the first molecular evidence of P. vivax in Nigeria in Duffy negative individuals. Though restricted to two states; Edo in South-South and Lagos in South-west Nigeria, the real burden of this species in Nigeria and sub-Saharan Africa might have been underestimated, hence there is need to put in place a country-wide, as well as a sub-Saharan Africa-wide surveillance and appropriate control measures.
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MESH Headings
- Child, Preschool
- Cross-Sectional Studies
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Duffy Blood-Group System/genetics
- Female
- Humans
- Infant
- Infant, Newborn
- Malaria, Vivax/epidemiology
- Malaria, Vivax/parasitology
- Male
- Nigeria/epidemiology
- Plasmodium vivax/classification
- Plasmodium vivax/genetics
- Plasmodium vivax/isolation & purification
- RNA, Ribosomal, 18S/genetics
- Receptors, Cell Surface/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- Mary Aigbiremo Oboh
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal.
| | - Aida Sadikh Badiane
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Godwin Ntadom
- National Malaria Elimination Programme/Epidemiology Division, Department of Public Health, Federal Ministry of Health, Abuja, Nigeria
| | - Yaye Die Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Khadim Diongue
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Mamadou Alpha Diallo
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Daouda Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
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12
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Oboh MA, Singh US, Antony HA, Ndiaye D, Badiane AS, Ali NA, Bharti PK, Das A. Molecular epidemiology and evolution of drug-resistant genes in the malaria parasite Plasmodium falciparum in southwestern Nigeria. INFECTION GENETICS AND EVOLUTION 2018; 66:222-228. [PMID: 30316883 DOI: 10.1016/j.meegid.2018.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 10/02/2018] [Accepted: 10/11/2018] [Indexed: 11/27/2022]
Abstract
Malaria is an age-old disease of human kind living in the tropical and sub-tropical regions of the globe, with Africa contributing the highest incidence of morbidity and mortality. Among many hurdles, evolution and spread of drug-resistant Plasmodium falciparum parasites constitute major challenges to malaria control and elimination. Information on molecular epidemiology and pattern of evolution of genes conferring resistance to different antimalarials are needed to track the route of the spread of resistant parasites and also to inform if the drug-resistant genes are adapted in the population following the Darwinian model of evolution. In the present study, we have followed molecular methods to detect both the known and emerging mutations in three genes (Pfcrt, Pfdhfr and Pfdhps) of P. falciparum conferring resistance to chloroquine and sulfadoxine-pyrimethamine from two different states (Edo: meso-endemic and Lagos: hypo-endemic) in southwestern Nigeria. High diversities in haplotypes and nucleotides in genes responsible for chloroquine (Pfcrt) and sulfadoxine (Pfdhps) resistance are recorded. About 96% of Pfdhfr and Pfdhps gene in both the meso- and hypo- endemic areas were mutant type, followed by 61% in Pfcrt gene. Many unique haplotypes of Pfdhps and Pfcrt were found to be segregated in these two populations. One particular mutant haplotype of Pfdhfr (AIRNI) was found to be in very high frequency in both Lagos and Edo. While the net haplotype diversity was highest in Pfdhps (0.81 in Lagos, 0.87 in Edo), followed by Pfcrt (0.69 in Lagos, 0.65 in Edo); highest number of haplotype was found in Pfdhps with 13 distinct haplotypes, followed by seven in Pfcrt and four in Pfdhfr gene. Moreover, detection of strong linkage among mutations of Pfcrt and Pfdhfr and feeble evidence for balancing selection in Pfdhps are indicative of evolutionary potential of mutation in genes responsible for drug resistance in Nigerian populations of P. falciparum.
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Affiliation(s)
- Mary Aigbiremo Oboh
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Upasana Shyamsunder Singh
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Hiasindh Ashmi Antony
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Daouda Ndiaye
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Aida Sadikh Badiane
- Parasitology and Mycology Laboratory, Université Cheikh Anta Diop, Dakar, Senegal
| | - Nazia Anwar Ali
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Praveen Kumar Bharti
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India
| | - Aparup Das
- Division of Vector Borne Diseases, ICMR-National Institute of Research in Tribal Health, Jabalpur, India.
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13
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Benson TW, Weintraub DS, Crowe M, Yiew NKH, Popoola O, Pillai A, Joseph J, Archer K, Greenway C, Chatterjee TK, Mintz J, Stepp DW, Stansfield BK, Chen W, Brittain J, Bogdanov VY, Gao Y, Wilson JG, Tang Y, Kim HW, Weintraub NL. Deletion of the Duffy antigen receptor for chemokines (DARC) promotes insulin resistance and adipose tissue inflammation during high fat feeding. Mol Cell Endocrinol 2018; 473:79-88. [PMID: 29341885 PMCID: PMC6045443 DOI: 10.1016/j.mce.2018.01.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Inflammation in adipose tissues in obesity promotes insulin resistance and metabolic disease. The Duffy antigen receptor for chemokines (DARC) is a promiscuous non-signaling receptor expressed on erythrocytes and other cell types that modulates tissue inflammation by binding chemokines such as monocyte chemoattractant protein-1 (MCP-1) and by acting as a chemokine reservoir. DARC allelic variants are common in humans, but the role of DARC in modulating obesity-related metabolic disease is unknown. METHODS We examined body weight gain, tissue adiposity, metabolic parameters and inflammatory marker expression in wild-type and DARC knockout mice fed a chow diet (CD) and high fat diet (HFD). RESULTS Compared to wild-type mice, HFD-fed DARC knockout mice developed glucose intolerance and insulin resistance independent of increases in body weight or adiposity. Interestingly, insulin sensitivity was also diminished in lean male DARC knockout mice fed a chow diet. Insulin production was not reduced by DARC gene deletion, and plasma leptin levels were similar in HFD fed wild-type and DARC knockout mice. MCP-1 levels in plasma rose significantly in the HFD fed wild-type mice, but not in the DARC knockout mice. Conversely, adipose tissue MCP-1 levels were higher, and more macrophage crown-like structures were detected, in the HFD fed DARC knockout mice as compared with the wild-type mice, consistent with augmented adipose tissue inflammation that is not accurately reflected by plasma levels of DARC-bound MCP-1 in these mice. CONCLUSIONS These findings suggest that DARC regulates metabolic function and adipose tissue inflammation, which may impact obesity-related disease in ethnic populations with high frequencies of DARC allelic variants.
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Affiliation(s)
- Tyler W Benson
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Daniel S Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Matthew Crowe
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Nicole K H Yiew
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Departments of Pharmacology and Toxicology, Medical College of Georgia at Augusta University, United States
| | - Orishebawo Popoola
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Ajay Pillai
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Joel Joseph
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Krystal Archer
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Charlotte Greenway
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - Tapan K Chatterjee
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - James Mintz
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States
| | - David W Stepp
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Physiology, Medical College of Georgia at Augusta University, United States
| | - Brian K Stansfield
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Pediatrics, Medical College of Georgia at Augusta University, United States
| | - Weiqin Chen
- Physiology, Medical College of Georgia at Augusta University, United States
| | - Julia Brittain
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Cellular Biology and Anatomy, Medical College of Georgia at Augusta University, United States
| | - Vladimir Y Bogdanov
- Department of Medicine, University of Cincinnati College of Medicine, United States
| | - Yan Gao
- Department of Physiology and Biophysics, University of Mississippi Medical Center, United States
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, United States
| | - Yaoliang Tang
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Medicine, Medical College of Georgia at Augusta University, United States
| | - Ha Won Kim
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Medicine, Medical College of Georgia at Augusta University, United States.
| | - Neal L Weintraub
- Vascular Biology Center, Medical College of Georgia at Augusta University, United States; Medicine, Medical College of Georgia at Augusta University, United States.
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14
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McManus KF, Taravella AM, Henn BM, Bustamante CD, Sikora M, Cornejo OE. Population genetic analysis of the DARC locus (Duffy) reveals adaptation from standing variation associated with malaria resistance in humans. PLoS Genet 2017; 13:e1006560. [PMID: 28282382 PMCID: PMC5365118 DOI: 10.1371/journal.pgen.1006560] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 03/24/2017] [Accepted: 12/30/2016] [Indexed: 12/22/2022] Open
Abstract
The human DARC (Duffy antigen receptor for chemokines) gene encodes a membrane-bound chemokine receptor crucial for the infection of red blood cells by Plasmodium vivax, a major causative agent of malaria. Of the three major allelic classes segregating in human populations, the FY*O allele has been shown to protect against P. vivax infection and is at near fixation in sub-Saharan Africa, while FY*B and FY*A are common in Europe and Asia, respectively. Due to the combination of strong geographic differentiation and association with malaria resistance, DARC is considered a canonical example of positive selection in humans. Despite this, details of the timing and mode of selection at DARC remain poorly understood. Here, we use sequencing data from over 1,000 individuals in twenty-one human populations, as well as ancient human genomes, to perform a fine-scale investigation of the evolutionary history of DARC. We estimate the time to most recent common ancestor (TMRCA) of the most common FY*O haplotype to be 42 kya (95% CI: 34-49 kya). We infer the FY*O null mutation swept to fixation in Africa from standing variation with very low initial frequency (0.1%) and a selection coefficient of 0.043 (95% CI:0.011-0.18), which is among the strongest estimated in the human genome. We estimate the TMRCA of the FY*A mutation in non-Africans to be 57 kya (95% CI: 48-65 kya) and infer that, prior to the sweep of FY*O, all three alleles were segregating in Africa, as highly diverged populations from Asia and ≠Khomani San hunter-gatherers share the same FY*A haplotypes. We test multiple models of admixture that may account for this observation and reject recent Asian or European admixture as the cause.
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Affiliation(s)
- Kimberly F. McManus
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Angela M. Taravella
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Brenna M. Henn
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States of America
| | - Carlos D. Bustamante
- Department of Biology, Stanford University, Stanford, California, United States of America
- Department of Genetics, Stanford University, Stanford, California, United States of America
| | - Martin Sikora
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Centre for Geogenetics, Natural History Museum Denmark, Copenhagen, Denmark
| | - Omar E. Cornejo
- Department of Genetics, Stanford University, Stanford, California, United States of America
- Department of Biological Sciences, Washington State University, Pullman, washington, United States of America
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15
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The hide and seek of Plasmodium vivax in West Africa: report from a large-scale study in Beninese asymptomatic subjects. Malar J 2016; 15:570. [PMID: 27887647 PMCID: PMC5123334 DOI: 10.1186/s12936-016-1620-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 11/15/2016] [Indexed: 11/30/2022] Open
Abstract
Background Plasmodium vivax is considered to be absent from western Africa, where the prevalence of Duffy-negative red blood cell phenotype proves to be high. Several studies have, however, detected P. vivax infection cases in this part of Africa, raising the question of what is the actual prevalence of P. vivax in local populations.
Methods The presence of P. vivax was investigated in a large population of healthy blood donors in Benin using microscopy, serology and molecular detection. The seroprevalence was measured with species-specific ELISA using two recombinant P. vivax proteins, namely rPvMSP1 and rPvCSP1. Specific molecular diagnosis of P. vivax infection was carried out using nested-PCR. The performances and cut-off values of both rPvCSP1 and rPvMSP1 ELISA were first assessed using sera from P. vivax-infected patients and from non-exposed subjects. Results Among 1234 Beninese blood donors, no parasites were detected when using microscopy, whereas 28.7% (354/1234) of patients exhibited had antibodies against rPvMSP1, 21.6% (266/1234) against rPvCSP1, and 15.2% (187/1234) against both. Eighty-four samples were selected for nested-PCR analyses, of which 13 were positive for P. vivax nested-PCR and all Duffy negative.
Conclusion The results of the present study highlight an unexpectedly high exposure of Beninese subjects to P. vivax, resulting in sub-microscopic infections. This suggests a probably underestimated and insidious parasite presence in western Africa. While the vaccination campaigns and therapeutic efforts are all focused on Plasmodium falciparum, it is also essential to consider the epidemiological impact of P. vivax. Electronic supplementary material The online version of this article (doi:10.1186/s12936-016-1620-z) contains supplementary material, which is available to authorized users.
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16
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Hostetler JB, Lo E, Kanjee U, Amaratunga C, Suon S, Sreng S, Mao S, Yewhalaw D, Mascarenhas A, Kwiatkowski DP, Ferreira MU, Rathod PK, Yan G, Fairhurst RM, Duraisingh MT, Rayner JC. Independent Origin and Global Distribution of Distinct Plasmodium vivax Duffy Binding Protein Gene Duplications. PLoS Negl Trop Dis 2016; 10:e0005091. [PMID: 27798646 PMCID: PMC5087946 DOI: 10.1371/journal.pntd.0005091] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/03/2016] [Indexed: 11/23/2022] Open
Abstract
Background Plasmodium vivax causes the majority of malaria episodes outside Africa, but remains a relatively understudied pathogen. The pathology of P. vivax infection depends critically on the parasite’s ability to recognize and invade human erythrocytes. This invasion process involves an interaction between P. vivax Duffy Binding Protein (PvDBP) in merozoites and the Duffy antigen receptor for chemokines (DARC) on the erythrocyte surface. Whole-genome sequencing of clinical isolates recently established that some P. vivax genomes contain two copies of the PvDBP gene. The frequency of this duplication is particularly high in Madagascar, where there is also evidence for P. vivax infection in DARC-negative individuals. The functional significance and global prevalence of this duplication, and whether there are other copy number variations at the PvDBP locus, is unknown. Methodology/Principal Findings Using whole-genome sequencing and PCR to study the PvDBP locus in P. vivax clinical isolates, we found that PvDBP duplication is widespread in Cambodia. The boundaries of the Cambodian PvDBP duplication differ from those previously identified in Madagascar, meaning that current molecular assays were unable to detect it. The Cambodian PvDBP duplication did not associate with parasite density or DARC genotype, and ranged in prevalence from 20% to 38% over four annual transmission seasons in Cambodia. This duplication was also present in P. vivax isolates from Brazil and Ethiopia, but not India. Conclusions/Significance PvDBP duplications are much more widespread and complex than previously thought, and at least two distinct duplications are circulating globally. The same duplication boundaries were identified in parasites from three continents, and were found at high prevalence in human populations where DARC-negativity is essentially absent. It is therefore unlikely that PvDBP duplication is associated with infection of DARC-negative individuals, but functional tests will be required to confirm this hypothesis. Malaria parasites must be adaptable to evade the human immune system and successfully transmit themselves to different individuals. Key to this adaptability is the fact that malaria parasite genomes are highly variable, containing mutations ranging from simple small changes in DNA sequence to complex large-scale changes in the number of copies of individual genes. Some samples of Plasmodium vivax, the parasite that causes most malaria episodes outside Africa, have recently been found to have duplicated the gene encoding Duffy Binding Protein, which enables P. vivax parasites to recognize and invade human red blood cells. By studying parasites from Cambodian patients with P. vivax malaria, we have discovered that there are actually two different types of gene duplication, with the new duplication type identified in this study present in 20% to 38% of Cambodian P. vivax isolates tested. The same gene duplication was also found in parasites from Brazilian and Ethiopian patients with P. vivax malaria, suggesting that variation in this gene is more complex and common than previously thought. The functional significance and origin of these two gene duplications requires further study.
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Affiliation(s)
- Jessica B. Hostetler
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Eugenia Lo
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Usheer Kanjee
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Chanaki Amaratunga
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Seila Suon
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sokunthea Sreng
- National Center for Parasitology, Entomology, and Malaria Control, Phnom Penh, Cambodia
| | - Sivanna Mao
- Sampov Meas Referral Hospital, Pursat, Cambodia
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia
| | - Anjali Mascarenhas
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- MESA-ICEMR, Goa Medical College and Hospital, Bambolim, Goa, India
| | | | - Marcelo U. Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Brazil
| | - Pradipsinh K. Rathod
- Department of Chemistry, University of Washington, Seattle, Washington, United States of America
- MESA-ICEMR, Goa Medical College and Hospital, Bambolim, Goa, India
| | - Guiyun Yan
- Program in Public Health, University of California, Irvine, California, United States of America
| | - Rick M. Fairhurst
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland, United States of America
| | - Manoj T. Duraisingh
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Julian C. Rayner
- Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
- * E-mail:
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17
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Gunalan K, Lo E, Hostetler JB, Yewhalaw D, Mu J, Neafsey DE, Yan G, Miller LH. Role of Plasmodium vivax Duffy-binding protein 1 in invasion of Duffy-null Africans. Proc Natl Acad Sci U S A 2016; 113:6271-6. [PMID: 27190089 PMCID: PMC4896682 DOI: 10.1073/pnas.1606113113] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of the malaria parasite Plasmodium vivax to invade erythrocytes is dependent on the expression of the Duffy blood group antigen on erythrocytes. Consequently, Africans who are null for the Duffy antigen are not susceptible to P. vivax infections. Recently, P. vivax infections in Duffy-null Africans have been documented, raising the possibility that P. vivax, a virulent pathogen in other parts of the world, may expand malarial disease in Africa. P. vivax binds the Duffy blood group antigen through its Duffy-binding protein 1 (DBP1). To determine if mutations in DBP1 resulted in the ability of P. vivax to bind Duffy-null erythrocytes, we analyzed P. vivax parasites obtained from two Duffy-null individuals living in Ethiopia where Duffy-null and -positive Africans live side-by-side. We determined that, although the DBP1s from these parasites contained unique sequences, they failed to bind Duffy-null erythrocytes, indicating that mutations in DBP1 did not account for the ability of P. vivax to infect Duffy-null Africans. However, an unusual DNA expansion of DBP1 (three and eight copies) in the two Duffy-null P. vivax infections suggests that an expansion of DBP1 may have been selected to allow low-affinity binding to another receptor on Duffy-null erythrocytes. Indeed, we show that Salvador (Sal) I P. vivax infects Squirrel monkeys independently of DBP1 binding to Squirrel monkey erythrocytes. We conclude that P. vivax Sal I and perhaps P. vivax in Duffy-null patients may have adapted to use new ligand-receptor pairs for invasion.
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Affiliation(s)
- Karthigayan Gunalan
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | - Eugenia Lo
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA 92697
| | - Jessica B Hostetler
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852; Malaria Programme, Wellcome Trust, Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1RQ, United Kingdom
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Health Sciences, Jimma University, Jimma 5195, Ethiopia; Tropical and Infectious Diseases Research Center, Jimma University, Jimma 5195, Ethiopia
| | - Jianbing Mu
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852
| | | | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California, Irvine, CA 92697
| | - Louis H Miller
- Laboratory of Malaria and Vector Research, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852;
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18
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Denic S, Narchi H, Al Mekaini LA, Al-Hammadi S, Al Jabri ON, Souid AK. Prevalence of neutropenia in children by nationality. BMC HEMATOLOGY 2016; 16:15. [PMID: 27213048 PMCID: PMC4875641 DOI: 10.1186/s12878-016-0054-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/14/2016] [Indexed: 01/15/2023]
Abstract
Background A high prevalence of neutropenia has been reported in several ethnic groups amongst whom many healthy individuals with low neutrophil counts undergo unnecessary investigations. This study aims to ascertain the prevalence of neutropenia (NP) in a large cohort of children from North African, Middle Eastern, and Asian countries residing in the United Arab Emirates. Methods Neutrophil counts of 26,542 children (one day to six years of age) from 86 countries were analyzed. The subjects were enrolled in the Well-Child-Care program of Ambulatory Health Services of Emirate of Abu Dhabi, United Arab Emirates. NP was defined as a neutrophil count <1.5 × 109/L and severe NP <0.5 × 109/L. Results The neutrophil counts reached a nadir in the fourth week of life and changed slightly from the age of six-months to six-years. The frequency of NP was (from West-to-East): North African Arabs 15.4 %, Green Crescent Arabs 9.8 %, Peninsular Arabs 10.9 %, Iranians 3.1 %, Afghanis 2.5 %, Pakistanis 5.6 %, Indians 10.2 %, and Filipinos 7.3 %. The frequency of severe NP in North African Arabs (Sudanese) was 2.8 %, Green Crescent and Peninsular Arabs ≤1 %, Indians 1.5 %, and Filipinos 1.8 %. In 12,703 Emirati children, the frequency of NP was 10.6 % similar to their adult counterparts. Conclusion The prevalence of childhood NP varied considerably by geoethnicity. Measures to prevent the inappropriate investigations of healthy children with benign neutropenia are proposed. Electronic supplementary material The online version of this article (doi:10.1186/s12878-016-0054-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Srdjan Denic
- Department of Medicine, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 17666, Al-Ain, United Arab of Emirates
| | - Hassib Narchi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab of Emirates
| | - Lolowa A Al Mekaini
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab of Emirates
| | - Suleiman Al-Hammadi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab of Emirates
| | - Omar N Al Jabri
- Ambulatory Healthcare Services, Abu Dhabi, United Arab of Emirates
| | - Abdul-Kader Souid
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al-Ain, United Arab of Emirates
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19
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Das A. The distinctive features of Indian malaria parasites. Trends Parasitol 2015; 31:83-6. [PMID: 25748059 DOI: 10.1016/j.pt.2015.01.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/18/2015] [Accepted: 01/20/2015] [Indexed: 11/30/2022]
Abstract
Malaria and factors driving malaria are heterogeneous in India, unlike in other countries, and the epidemiology of malaria therefore is considered 'highly complex'. This complexity is primarily attributed to several unique features of the malaria parasites, mosquito vectors, malaria-susceptible populations, and ecoclimatic variables in India. Recent research on the genetic epidemiology of Indian malaria parasites has been successful in partly unraveling the mysteries underlying these complexities.
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Affiliation(s)
- Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India.
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20
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Mbenda HGN, Awasthi G, Singh PK, Gouado I, Das A. Does malaria epidemiology project Cameroon as 'Africa in miniature'? J Biosci 2015; 39:727-38. [PMID: 25116627 DOI: 10.1007/s12038-014-9451-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cameroon, a west-central African country with a ~ 20 million population, is commonly regarded as 'Africa in miniature' due to the extensive biological and cultural diversities of whole Africa being present in a single-country setting. This country is inhabited by ancestral human lineages in unique eco-climatic conditions and diverse topography. Over 90 percent Cameroonians are at risk of malaria infection, and ~ 41 percent have at least one episode of malaria each year. Historically, the rate of malaria infection in Cameroon has fluctuated over the years; the number of cases was about 2 million in 2010 and 2011. The Cameroonian malaria control programme faces an uphill task due to high prevalence of multidrug-resistant parasites and insecticide-resistant malaria vectors. Above all, continued human migration from the rural to urban areas as well as population exchange with adjoining countries, high rate of ecological instabilities caused by deforestation, poor housing, lack of proper sanitation and drainage system might have resulted in the recent increase in incidences of malaria and other vector-borne diseases in Cameroon. The available data on eco-environmental variability and intricate malaria epidemiology in Cameroon reflect the situation in the whole of Africa, and warrant the need for in-depth study by using modern surveillance tools for meaningful basic understanding of the malaria triangle (host-parasite-vector-environment).
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Affiliation(s)
- Huguette Gaelle Ngassa Mbenda
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, New Delhi 110 077, India
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21
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Lo E, Yewhalaw D, Zhong D, Zemene E, Degefa T, Tushune K, Ha M, Lee MC, James AA, Yan G. Molecular epidemiology of Plasmodium vivax and Plasmodium falciparum malaria among Duffy-positive and Duffy-negative populations in Ethiopia. Malar J 2015; 14:84. [PMID: 25884875 PMCID: PMC4340780 DOI: 10.1186/s12936-015-0596-4] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/30/2015] [Indexed: 11/28/2022] Open
Abstract
Background Malaria is the most prevalent communicable disease in Ethiopia, with 75% of the country’s landmass classified as endemic for malaria. Accurate information on the distribution and clinical prevalence of Plasmodium vivax and Plasmodium falciparum malaria in endemic areas, as well as in Duffy-negative populations, is essential to develop integrated control strategies. Methods A total of 390 and 416 community and clinical samples, respectively, representing different localities and age groups across Ethiopia were examined. Malaria prevalence was estimated using nested PCR of the 18S rRNA region. Parasite gene copy number was measured by quantitative real-time PCR and compared between symptomatic and asymptomatic samples, as well as between children/adolescents and adults from the local community. An approximately 500-bp segment of the human DARC gene was amplified and sequenced to identify Duffy genotype at the -33rd nucleotide position for all the clinical and community samples. Results Plasmodium vivax prevalence was higher in the south while P. falciparum was higher in the north. The prevalence of P. vivax and P. falciparum malaria is the highest in children compared to adolescents and adults. Four P. vivax infections were detected among the Duffy-negative samples. Samples from asymptomatic individuals show a significantly lower parasite gene copy number than those from symptomatic infections for P. vivax and P. falciparum. Conclusions Geographical and age differences influence the distribution of P. vivax and P. falciparum malaria in Ethiopia. These findings offer evidence-based guidelines in targeting malaria control efforts in the country. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0596-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eugenia Lo
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Delenasaw Yewhalaw
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Endalew Zemene
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Teshome Degefa
- Department of Medical Laboratory Sciences and Pathology, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Kora Tushune
- Department of Health Services Management, College of Public Health and Medical Sciences, Jimma University, Jimma, Ethiopia.
| | - Margaret Ha
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Ming-Chieh Lee
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Anthony A James
- Departments of Microbiology & Molecular Genetics and Molecular Biology & Biochemistry, University of California at Irvine, Irvine, CA, 92697, USA.
| | - Guiyun Yan
- Program in Public Health, College of Health Sciences, University of California at Irvine, Irvine, CA, 92697, USA.
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Dixit J, Arunyawat U, Huong NT, Das A. Multilocus nuclear DNA markers reveal population structure and demography of Anopheles minimus. Mol Ecol 2014; 23:5599-618. [PMID: 25266341 DOI: 10.1111/mec.12943] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 09/21/2014] [Accepted: 09/22/2014] [Indexed: 01/11/2023]
Abstract
Utilization of multiple putatively neutral DNA markers for inferring evolutionary history of species population is considered to be the most robust approach. Molecular population genetic studies have been conducted in many species of Anopheles genus, but studies based on single nucleotide polymorphism (SNP) data are still very scarce. Anopheles minimus is one of the principal malaria vectors of Southeast (SE) Asia including the Northeastern (NE) India. Although population genetic studies with mitochondrial genetic variation data have been utilized to infer phylogeography of the SE Asian populations of this species, limited information on the population structure and demography of Indian An. minimus is available. We herewith have developed multilocus nuclear genetic approach with SNP markers located in X chromosome of An. minimus in eight Indian and two SE Asian population samples (121 individual mosquitoes in total) to infer population history and test several hypotheses on the phylogeography of this species. While the Thai population sample of An. minimus presented the highest nucleotide diversity, majority of the Indian samples were also fairly diverse. In general, An. minimus populations were moderately substructured in the distribution range covering SE Asia and NE India, largely falling under three distinct genetic clusters. Moreover, demographic expansion events could be detected in the majority of the presently studied populations of An. minimus. Additional DNA sequencing of the mitochondrial COII region in a subset of the samples (40 individual mosquitoes) corroborated the existing hypothesis of Indian An. minimus falling under the earlier reported mitochondrial lineage B.
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Affiliation(s)
- Jyotsana Dixit
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector-8, Dwarka, New Delhi, 110077, India
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23
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Ngassa Mbenda HG, Das A. Molecular evidence of Plasmodium vivax mono and mixed malaria parasite infections in Duffy-negative native Cameroonians. PLoS One 2014; 9:e103262. [PMID: 25084090 PMCID: PMC4118857 DOI: 10.1371/journal.pone.0103262] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 06/30/2014] [Indexed: 11/18/2022] Open
Abstract
The malaria parasite Plasmodium vivax is known to be majorly endemic to Asian and Latin American countries with no or very few reports of Africans infected with this parasite. Since the human Duffy antigens act as receptors for P. vivax to invade human RBCs and Africans are generally Duffy-negative, non-endemicity of P. vivax in Africa has been attributed to this fact. However, recent reports describing P. vivax infections in Duffy-negative Africans from West and Central parts of Africa have been surfaced including a recent report on P. vivax infection in native Cameroonians. In order to know if Cameroonians living in the southern regions are also susceptible to P. vivax infection, we collected finger-prick blood samples from 485 malarial symptomatic patients in five locations and followed PCR diagnostic assays with DNA sequencing of the 18S ribosomal RNA gene. Out of the 201 malaria positive cases detected, 193 were pure P. falciparum, six pure P. vivax and two mixed parasite infections (P. falciparum + P. vivax). The eight P. vivax infected samples (six single + two mixed) were further subjected to DNA sequencing of the P. vivax multidrug resistance 1 (pvmdr1) and the P.vivax circumsporozoite (pvcsp) genes. Alignment of the eight Cameroonian pvmdr1 sequences with the reference sequence showed high sequence similarities, reconfirming P. vivax infection in all the eight patients. DNA sequencing of the pvcsp gene indicated all the eight P. vivax to be of VK247 type. Interestingly, DNA sequencing of a part of the human Duffy gene covering the promoter region in the eight P. vivax-infected Cameroonians to identify the T-33C mutation revealed all these patients as Duffy-negative. The results provide evidence of single P. vivax as well as mixed malaria parasite infection in native Cameroonians and add knowledge to the growing evidences of P. vivax infection in Duffy-negative Africans.
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Affiliation(s)
- Huguette Gaelle Ngassa Mbenda
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India
| | - Aparup Das
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi, India
- * E-mail:
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24
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Menard D, Chan ER, Benedet C, Ratsimbasoa A, Kim S, Chim P, Do C, Witkowski B, Durand R, Thellier M, Severini C, Legrand E, Musset L, Nour BYM, Mercereau-Puijalon O, Serre D, Zimmerman PA. Whole genome sequencing of field isolates reveals a common duplication of the Duffy binding protein gene in Malagasy Plasmodium vivax strains. PLoS Negl Trop Dis 2013; 7:e2489. [PMID: 24278487 PMCID: PMC3836732 DOI: 10.1371/journal.pntd.0002489] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 09/07/2013] [Indexed: 12/02/2022] Open
Abstract
Background Plasmodium vivax is the most prevalent human malaria parasite, causing serious public health problems in malaria-endemic countries. Until recently the Duffy-negative blood group phenotype was considered to confer resistance to vivax malaria for most African ethnicities. We and others have reported that P. vivax strains in African countries from Madagascar to Mauritania display capacity to cause clinical vivax malaria in Duffy-negative people. New insights must now explain Duffy-independent P. vivax invasion of human erythrocytes. Methods/Principal Findings Through recent whole genome sequencing we obtained ≥70× coverage of the P. vivax genome from five field-isolates, resulting in ≥93% of the Sal I reference sequenced at coverage greater than 20×. Combined with sequences from one additional Malagasy field isolate and from five monkey-adapted strains, we describe here identification of DNA sequence rearrangements in the P. vivax genome, including discovery of a duplication of the P. vivax Duffy binding protein (PvDBP) gene. A survey of Malagasy patients infected with P. vivax showed that the PvDBP duplication was present in numerous locations in Madagascar and found in over 50% of infected patients evaluated. Extended geographic surveys showed that the PvDBP duplication was detected frequently in vivax patients living in East Africa and in some residents of non-African P. vivax-endemic countries. Additionally, the PvDBP duplication was observed in travelers seeking treatment of vivax malaria upon returning home. PvDBP duplication prevalence was highest in west-central Madagascar sites where the highest frequencies of P. vivax-infected, Duffy-negative people were reported. Conclusions/Significance The highly conserved nature of the sequence involved in the PvDBP duplication suggests that it has occurred in a recent evolutionary time frame. These data suggest that PvDBP, a merozoite surface protein involved in red cell adhesion is rapidly evolving, possibly in response to constraints imposed by erythrocyte Duffy negativity in some human populations. Malaria results from infection of human red blood cells (RBC) by Plasmodium parasite's merozoite. For Plasmodium vivax the process of RBC invasion has been hypothesized to depend on interactions between the parasite's Duffy binding protein (PvDBP) and human Duffy blood group antigen because Duffy-negative people (most often people of African descent) were shown to be highly resistant to RBC infection and disease. Over the past five years, researchers are reporting with increasing frequency that Duffy-negative individuals are infected with P. vivax. This raises new questions as to how P. vivax infects the RBC when the Duffy blood group antigen is not available. Here we show that the parasite's Duffy binding protein gene has been duplicated in multiple P. vivax strains, especially at high prevalence in Madagascar. The specificity and prevalence of this polymorphism suggest that the parasite genome has responded to the barrier of Duffy negativity through the duplication of the PvDBP gene. Our results indicate that the PvDBP duplication is a recent event and provide novel research avenues to understand alternative pathways for P. vivax RBC invasion.
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Affiliation(s)
- Didier Menard
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
- * E-mail: (DM); (OMP); (DS); (PAZ)
| | - Ernest R. Chan
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
| | - Christophe Benedet
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Arsène Ratsimbasoa
- Direction de la lutte contre les maladies infectieuses, Ministère de la santé, du planning familial et de la protection sociale du Madagascar, Antananarivo, Madagascar
| | - Saorin Kim
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Pheaktra Chim
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Catherine Do
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Benoit Witkowski
- Unité d'Epidémiologie Moléculaire du Paludisme, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Remy Durand
- Laboratoire de Parasitologie-Mycologie, Hôpital Avicenne, AP-HP, Bobigny, France
| | - Marc Thellier
- National Center for Malaria Research, AP-HP, CHU Pitie Salpêtrière, Paris, France
| | - Carlo Severini
- Department of Infectious, Parasitic and Immunomediated Diseases, Istituto Superiore di Sanità (ISS), Rome, Italy
| | - Eric Legrand
- Laboratoire de parasitologie, National Reference Centre of Malaria Resistance in French Guiana and West Indies, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Lise Musset
- Laboratoire de parasitologie, National Reference Centre of Malaria Resistance in French Guiana and West Indies, Institut Pasteur de la Guyane, Cayenne, French Guiana
| | - Bakri Y. M. Nour
- Blue Nile National Institute for Communicable Diseases, University of Gezira, Wad Medani, Sudan
| | - Odile Mercereau-Puijalon
- Unité d'lmmunologie Moléculaire des Parasites, Institut Pasteur, Paris, France
- * E-mail: (DM); (OMP); (DS); (PAZ)
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, Ohio, United States of America
- * E-mail: (DM); (OMP); (DS); (PAZ)
| | - Peter A. Zimmerman
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, Ohio, United States of America
- * E-mail: (DM); (OMP); (DS); (PAZ)
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Chauhan K, Pande V, Das A. Analyses of genetic variations at microsatellite loci present in-and-around the Pfcrt gene in Indian Plasmodium falciparum. INFECTION GENETICS AND EVOLUTION 2013; 20:476-87. [PMID: 24157593 DOI: 10.1016/j.meegid.2013.10.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 10/10/2013] [Accepted: 10/10/2013] [Indexed: 10/26/2022]
Abstract
Evolution and spread of chloroquine resistant (CQR) malaria parasite Plasmodium falciparum have posed great threat in malaria intervention across the globe. The occurrence of K76T mutation in the P. falciparum chloroquine resistance transporter (pfcrt) gene has been widely attributed to CQR with four neighboring mutations providing compensatory fitness benefit to the parasite survival. Understanding evolutionary patterns of the pfcrt gene is of great relevance not only for devising new malaria control measures but also could serve as a model to understand evolution and spread of other human drug-resistant pathogens. Several studies, mainly based on differential patterns of diversities of the microsatellite loci placed in-and-around the pfcrt gene have indicated the role of positive natural selection under the 'hitchhiking' model of molecular evolution. However, the studies were restricted to limited number of microsatellite loci present inside the pfcrt gene. Moreover, comparatively higher level of diversities in microsatellite loci present inside the pfcrt gene than the loci flanking the pfcrt gene are hallmarks of Indian P. falciparum, presenting contrasting evolutionary models to global isolates. With a view to infer evolutionary patterns of the pfcrt gene in Indian P. falciparum, we have adopted a unique sampling scheme of two types of populations (cultured and field collected) and utilized 20 polymorphic microsatellite loci (16 located inside the pfcrt gene and four in the two flanking regions) to disentangle between genetic drift (inbred cultured isolates) and natural selection (field isolates). Data analyses employing different population genetic tests could not straightforwardly explain either the model invoking 'genetic hitchhiking' or 'genetic drift'. However, complex evolutionary models influenced by both demography and natural selection or an alternative model of natural selection (e.g. diversifying/balancing selection) might better explain the observed microsatellite variation in-and-around the pfcrt gene in Indian P. falciparum.
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Affiliation(s)
- Kshipra Chauhan
- Evolutionary Genomics and Bioinformatics Laboratory, Division of Genomics and Bioinformatics, National Institute of Malaria Research, Sector 8, Dwarka, New Delhi 110077, India
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Prajapati SK, Joshi H, Carlton JM, Rizvi MA. Neutral polymorphisms in putative housekeeping genes and tandem repeats unravels the population genetics and evolutionary history of Plasmodium vivax in India. PLoS Negl Trop Dis 2013; 7:e2425. [PMID: 24069480 PMCID: PMC3777877 DOI: 10.1371/journal.pntd.0002425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 08/01/2013] [Indexed: 11/18/2022] Open
Abstract
The evolutionary history and age of Plasmodium vivax has been inferred as both recent and ancient by several studies, mainly using mitochondrial genome diversity. Here we address the age of P. vivax on the Indian subcontinent using selectively neutral housekeeping genes and tandem repeat loci. Analysis of ten housekeeping genes revealed a substantial number of SNPs (n = 75) from 100 P. vivax isolates collected from five geographical regions of India. Neutrality tests showed a majority of the housekeeping genes were selectively neutral, confirming the suitability of housekeeping genes for inferring the evolutionary history of P. vivax. In addition, a genetic differentiation test using housekeeping gene polymorphism data showed a lack of geographical structuring between the five regions of India. The coalescence analysis of the time to the most recent common ancestor estimate yielded an ancient TMRCA (232,228 to 303,030 years) and long-term population history (79,235 to 104,008) of extant P. vivax on the Indian subcontinent. Analysis of 18 tandem repeat loci polymorphisms showed substantial allelic diversity and heterozygosity per locus, and analysis of potential bottlenecks revealed the signature of a stable P. vivax population, further corroborating our ancient age estimates. For the first time we report a comparable evolutionary history of P. vivax inferred by nuclear genetic markers (putative housekeeping genes) to that inferred from mitochondrial genome diversity.
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Affiliation(s)
- Surendra K Prajapati
- Molecular Biology Division, National Institute of Malaria Research, New Delhi, India
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27
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Carlton JM, Das A, Escalante AA. Genomics, population genetics and evolutionary history of Plasmodium vivax. ADVANCES IN PARASITOLOGY 2013; 81:203-22. [PMID: 23384624 DOI: 10.1016/b978-0-12-407826-0.00005-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Plasmodium vivax is part of a highly diverse clade that includes several Plasmodium species found in nonhuman primates from Southeast Asia. The diversity of primate malarias in Asia is staggering; nevertheless, their origin was relatively recent in the evolution of Plasmodium. We discuss how humans acquired the lineage leading to P. vivax from a nonhuman primate determined by the complex geological processes that took place in Southeast Asia during the last few million years. We conclude that widespread population genomic investigations are needed in order to understand the demographic processes involved in the expansion of P. vivax in the human populations. India represents one of the few countries with widespread vivax malaria. Earlier studies have indicated high genetic polymorphism at antigenic loci and no evidence for geographic structuring. However, new studies using genetic markers in selectively neutral genetic regions indicate that Indian P. vivax presents complex evolutionary history but possesses features consistent with being part of the ancestral distribution range of this species. Such studies are possible due to the availability of the first P. vivax genome sequences. Next generation sequencing technologies are now paving the way for the sequencing of more P. vivax genomes that will dramatically increase our understanding of the unique biology of this species.
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Affiliation(s)
- Jane M Carlton
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
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