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Abebe A, Dieng CC, Dugassa S, Abera D, Shenkutie TT, Assefa A, Menard D, Lo E, Golassa L. Genetic differentiation of Plasmodium vivax duffy binding protein in Ethiopia and comparison with other geographical isolates. Malar J 2024; 23:55. [PMID: 38395885 PMCID: PMC10885561 DOI: 10.1186/s12936-024-04887-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/21/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Plasmodium vivax Duffy binding protein (PvDBP) is a merozoite surface protein located in the micronemes of P. vivax. The invasion of human reticulocytes by P. vivax merozoites depends on the parasite DBP binding domain engaging Duffy Antigen Receptor for Chemokine (DARC) on these red blood cells (RBCs). PvDBPII shows high genetic diversity which is a major challenge to its use in the development of a vaccine against vivax malaria. METHODS A cross-sectional study was conducted from February 2021 to September 2022 in five study sites across Ethiopia. A total of 58 blood samples confirmed positive for P. vivax by polymerase chain reaction (PCR) were included in the study to determine PvDBPII genetic diversity. PvDBPII were amplified using primers designed from reference sequence of P. vivax Sal I strain. Assembling of sequences was done using Geneious Prime version 2023.2.1. Alignment and phylogenetic tree constructions using MEGA version 10.1.1. Nucleotide diversity and haplotype diversity were analysed using DnaSP version 6.12.03, and haplotype network was generated with PopART version 1.7. RESULTS The mean age of the participants was 25 years, 5 (8.6%) participants were Duffy negatives. From the 58 PvDBPII sequences, seven haplotypes based on nucleotide differences at 8 positions were identified. Nucleotide diversity and haplotype diversity were 0.00267 ± 0.00023 and 0.731 ± 0.036, respectively. Among the five study sites, the highest numbers of haplotypes were identified in Arbaminch with six different haplotypes while only two haplotypes were identified in Gambella. The phylogenetic tree based on PvDBPII revealed that parasites of different study sites shared similar genetic clusters with few exceptions. Globally, a total of 39 haplotypes were identified from 223 PvDBPII sequences representing different geographical isolates obtained from NCBI archive. The nucleotide and haplotype diversity were 0.00373 and 0.845 ± 0.015, respectively. The haplotype prevalence ranged from 0.45% to 27.3%. Two haplotypes were shared among isolates from all geographical areas of the globe. CONCLUSIONS PvDBPII of the Ethiopian P. vivax isolates showed low nucleotide but high haplotype diversity, this pattern of genetic variability suggests that the population may have undergone a recent expansion. Among the Ethiopian P. vivax isolates, almost half of the sequences were identical to the Sal-I reference sequence. However, there were unique haplotypes observed in the Ethiopian isolates, which does not share with isolates from other geographical areas. There were two haplotypes that were common among populations across the globe. Categorizing population haplotype frequency can help to determine common haplotypes for designing an effective blood-stage vaccine which will have a significant role for the control and elimination of P. vivax.
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Affiliation(s)
- Abnet Abebe
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 24756, Addis Ababa, Ethiopia.
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia.
| | - Cheikh Cambel Dieng
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, USA
| | - Sisay Dugassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 24756, Addis Ababa, Ethiopia
| | - Deriba Abera
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 24756, Addis Ababa, Ethiopia
| | - Tassew T Shenkutie
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, USA
| | - Ashenafi Assefa
- Institute of Infectious Disease and Global Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Didier Menard
- Malaria Genetics and Resistance Unit, INSERM U1201, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- Dynamics of Host-Pathogen Interactions, Université de Strasbourg, Institute of Parasitology and Tropical Diseases, 67000, Strasbourg, France
| | - Eugenia Lo
- Department of Microbiology and Immunology, College of Medicine, Drexel University, Philadelphia, USA
| | - Lemu Golassa
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, P.O. Box 24756, Addis Ababa, Ethiopia.
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Tapaopong P, da Silva G, Chainarin S, Suansomjit C, Manopwisedjaroen K, Cui L, Koepfli C, Sattabongkot J, Nguitragool W. Genetic diversity and molecular evolution of Plasmodium vivax Duffy Binding Protein and Merozoite Surface Protein-1 in northwestern Thailand. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 113:105467. [PMID: 37330027 PMCID: PMC10548344 DOI: 10.1016/j.meegid.2023.105467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/22/2023] [Accepted: 06/14/2023] [Indexed: 06/19/2023]
Abstract
The local diversity and population structure of malaria parasites vary across different regions of the world, reflecting variations in transmission intensity, host immunity, and vector species. This study aimed to use amplicon sequencing to investigate the genotypic patterns and population structure of P. vivax isolates from a highly endemic province of Thailand in recent years. Amplicon deep sequencing was performed on 70 samples for the 42-kDa region of pvmsp1 and domain II of pvdbp. Unique haplotypes were identified and a network constructed to illustrate genetic relatedness in northwestern Thailand. Based on this dataset of 70 samples collected between 2015 and 2021, 16 and 40 unique haplotypes were identified in pvdbpII and pvmsp142kDa, respectively. Nucleotide diversity was higher in pvmsp142kDa than in pvdbpII (π = 0.027 and 0.012), as was haplotype diversity (Hd = 0.962 and 0.849). pvmsp142kDa also showed a higher recombination rate and higher levels of genetic differentiation (Fst) in northwestern Thailand versus other regions (0.2761-0.4881). These data together suggested that the genetic diversity of P. vivax in northwestern Thailand at these two studied loci evolved under a balancing selection, most likely host immunity. The lower genetic diversity of pvdbpII may reflect its stronger functional constrain. In addition, despite the balancing selection, a decrease in genetic diversity was observed. Hd of pvdbpII decreased from 0.874 in 2015-2016 to 0.778 in 2018-2021; π of pvmsp142kDa decreased from 0.030 to 0.022 over the same period. Thus, the control activities must have had a strong impact on the parasite population size. The findings from this study provide an understanding of P. vivax population structure and the evolutionary force on vaccine candidates. They also established a new baseline for tracking future changes in P. vivax diversity in the most malarious area of Thailand.
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Affiliation(s)
- Parsakorn Tapaopong
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Gustavo da Silva
- Department of Biological Sciences, Eck Institute for Global Health, Galvin Life Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Sittinont Chainarin
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Chayanut Suansomjit
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | | | - Liwang Cui
- Division of Infectious Diseases and International Medicine, Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Cristian Koepfli
- Department of Biological Sciences, Eck Institute for Global Health, Galvin Life Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jetsumon Sattabongkot
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Wang Nguitragool
- Mahidol Vivax Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
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Núñez A, Ntumngia FB, Guerra Y, Adams JH, Sáenz FE. Genetic diversity and natural selection of Plasmodium vivax reticulocyte invasion genes in Ecuador. Malar J 2023; 22:225. [PMID: 37537581 PMCID: PMC10398936 DOI: 10.1186/s12936-023-04640-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 07/04/2023] [Indexed: 08/05/2023] Open
Abstract
BACKGROUND Knowledge of the diversity of invasion ligands in malaria parasites in endemic regions is essential to understand how natural selection influences genetic diversity of these ligands and their feasibility as possible targets for future vaccine development. In this study the diversity of four genes for merozoite invasion ligands was studied in Ecuadorian isolates of Plasmodium vivax. METHODS Eighty-eight samples from P. vivax infected individuals from the Coast and Amazon region of Ecuador were obtained between 2012 and 2015. The merozoite invasion genes pvmsp-1-19, pvdbpII, pvrbp1a-2 and pvama1 were amplified, sequenced, and compared to the Sal-1 strain. Polymorphisms were mapped and genetic relationships between haplotypes were determined. RESULTS Only one nonsynonymous polymorphism was detected in pvmsp-1-19, while 44 nonsynonymous polymorphisms were detected in pvdbpII, 56 in pvrbp1a-2 and 33 in pvama1. While haplotypes appeared to be more related within each area of study and there was less relationship between parasites of the coastal and Amazon regions of the country, diversification processes were observed in the two Amazon regions. The highest haplotypic diversity for most genes occurred in the East Amazon of the country. The high diversity observed in Ecuadorian samples is closer to Brazilian and Venezuelan isolates, but lower than reported in other endemic regions. In addition, departure from neutrality was observed in Ecuadorian pvama1. Polymorphisms for pvdbpII and pvama1 were associated to B-cell epitopes. CONCLUSIONS pvdbpII and pvama1 genetic diversity found in Ecuadorian P. vivax was very similar to that encountered in other malaria endemic countries with varying transmission levels and segregated by geographic region. The highest diversity of P. vivax invasion genes in Ecuador was found in the Amazonian region. Although selection appeared to have small effect on pvdbpII and pvrbp1a-2, pvama1 was influenced by significant balancing selection.
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Affiliation(s)
- Andrés Núñez
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Francis B Ntumngia
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, FL, Tampa, USA
| | - Yasel Guerra
- Grupo de Bio-Quimioinformática, Universidad de Las Américas, Quito, Ecuador
| | - John H Adams
- Center for Global Health and Interdisciplinary Research, College of Public Health, University of South Florida, FL, Tampa, USA
| | - Fabián E Sáenz
- Centro de Investigación para la Salud en América Latina, Facultad de Ciencias Exactas y Naturales, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.
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Spatiotemporal Changes in Plasmodium vivax msp142 Haplotypes in Southern Mexico: From the Control to the Pre-Elimination Phase. Microorganisms 2022; 10:microorganisms10010186. [PMID: 35056635 PMCID: PMC8779127 DOI: 10.3390/microorganisms10010186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 01/27/2023] Open
Abstract
For 20 years, Plasmodium vivax has been the only prevalent malaria species in Mexico, and cases have declined significantly and continuously. Spatiotemporal genetic studies can be helpful for understanding parasite dynamics and developing strategies to weaken malaria transmission, thus facilitating the elimination of the parasite. The aim of the current contribution was to analyze P. vivax-infected blood samples from patients in southern Mexico during the control (1993–2007) and pre-elimination phases (2008–2011). Nucleotide and haplotype changes in the pvmsp142 fragment were evaluated over time. The majority of multiple genotype infections occurred in the 1990s, when the 198 single nucleotide sequences exhibited 57 segregating sites, 64 mutations, and 17 haplotypes. Nucleotide and genetic diversity parameters showed subtle fluctuations from across time, in contrast to the reduced haplotype diversity and the increase in the R2 index and Tajima’s D value from 2008 to 2011. The haplotype network consisted of four haplogroups, the geographical distribution of which varied slightly over time. Haplogroup-specific B-cell epitopes were predicted. Since only high-frequency and divergent haplotypes persisted, there was a contraction of the parasite population. Given that 84% of haplotypes were exclusive to Mesoamerica, P. vivax flow is likely circumscribed to this region, representing important information for parasite surveillance.
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González-Cerón L, Cebrián-Carmona J, Mesa-Valle CM, García-Maroto F, Santillán-Valenzuela F, Garrido-Cardenas JA. Plasmodium vivax Cysteine-Rich Protective Antigen Polymorphism at Exon-1 Shows Recombination and Signatures of Balancing Selection. Genes (Basel) 2020; 12:genes12010029. [PMID: 33379267 PMCID: PMC7823296 DOI: 10.3390/genes12010029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 12/18/2020] [Accepted: 12/23/2020] [Indexed: 11/16/2022] Open
Abstract
Plasmodium vivax Cysteine-Rich Protective Antigen (CyRPA) is a merozoite protein participating in the parasite invasion of human reticulocytes. During natural P. vivax infection, antibody responses against PvCyRPA have been detected. In children, low anti-CyRPA antibody titers correlated with clinical protection, which suggests this protein as a potential vaccine candidate. This work analyzed the genetic and amino acid diversity of pvcyrpa in Mexican and global parasites. Consensus coding sequences of pvcyrpa were obtained from seven isolates. Other sequences were extracted from a repository. Maximum likelihood phylogenetic trees, genetic diversity parameters, linkage disequilibrium (LD), and neutrality tests were analyzed, and the potential amino acid polymorphism participation in B-cell epitopes was investigated. In 22 sequences from Southern Mexico, two synonymous and 21 nonsynonymous mutations defined nine private haplotypes. These parasites had the highest LD-R2 index and the lowest nucleotide diversity compared to isolates from South America or Asia. The nucleotide diversity and Tajima's D values varied across the coding gene. The exon-1 sequence had greater diversity and Rm values than those of exon-2. Exon-1 had significant positive values for Tajima's D, β-α values, and for the Z (HA: dN > dS) and MK tests. These patterns were similar for parasites of different origin. The polymorphic amino acid residues at PvCyRPA resembled the conformational B-cell peptides reported in PfCyRPA. Diversity at pvcyrpa exon-1 is caused by mutation and recombination. This seems to be maintained by balancing selection, likely due to selective immune pressure, all of which merit further study.
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MESH Headings
- Antigens, Protozoan/genetics
- Antigens, Protozoan/immunology
- Cysteine/genetics
- Epitopes, B-Lymphocyte/genetics
- Epitopes, B-Lymphocyte/immunology
- Exons/genetics
- Host-Parasite Interactions/genetics
- Host-Parasite Interactions/immunology
- Humans
- Malaria, Vivax/immunology
- Malaria, Vivax/parasitology
- Mutation
- Plasmodium vivax/genetics
- Plasmodium vivax/immunology
- Plasmodium vivax/pathogenicity
- Polymorphism, Genetic/immunology
- Protozoan Proteins/genetics
- Protozoan Proteins/immunology
- Recombination, Genetic/immunology
- Selection, Genetic/immunology
- Sequence Analysis, DNA
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Affiliation(s)
- Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula 30700, Chiapas, Mexico;
- Correspondence: (L.G.-C.); (J.A.G.-C.); Tel.: +52-962-6262219 (L.G.-C.); +34-950-215894 (J.A.G.-C.)
| | - José Cebrián-Carmona
- Departamento de Biología y Geología, Universidad de Almería, 04120 Almería, Spain; (J.C.-C.); (C.M.M.-V.)
| | - Concepción M. Mesa-Valle
- Departamento de Biología y Geología, Universidad de Almería, 04120 Almería, Spain; (J.C.-C.); (C.M.M.-V.)
| | | | - Frida Santillán-Valenzuela
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula 30700, Chiapas, Mexico;
| | - Jose Antonio Garrido-Cardenas
- Departamento de Biología y Geología, Universidad de Almería, 04120 Almería, Spain; (J.C.-C.); (C.M.M.-V.)
- Correspondence: (L.G.-C.); (J.A.G.-C.); Tel.: +52-962-6262219 (L.G.-C.); +34-950-215894 (J.A.G.-C.)
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Almeida-de-Oliveira NK, Abreu-Fernandes R, Lavigne AR, Pina-Costa A, Perce-da-Silva DDS, Catanho M, Rossi ÁD, Brasil P, Daniel-Ribeiro CT, Ferreira-da-Cruz MDF. Exploration of Plasmodium vivax merozoite surface proteins 1 and 7 genetic diversity in Brazilian Amazon and Rio de Janeiro Atlantic Forest. INFECTION GENETICS AND EVOLUTION 2020; 86:104592. [PMID: 33059085 DOI: 10.1016/j.meegid.2020.104592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 09/22/2020] [Accepted: 10/07/2020] [Indexed: 11/29/2022]
Abstract
Plasmodium vivax merozoite surface proteins (PvMSP) 1 and 7 are considered vaccine targets. Genetic diversity knowledge is crucial to assess their potential as immunogens and to provide insights about population structure in different epidemiological contexts. Here, we investigate the variability of pvmsp-142, pvmsp-7E, and pvmsp-7F genes in 227 samples from the Brazilian Amazon (BA) and Rio de Janeiro Atlantic Forest (AF). pvmsp-142 has 63 polymorphisms - 57 nonsynonymous - generating a nucleotide diversity of π = 0.009 in AF, and π = 0.018 in BA. In pvmsp-7E, 134 polymorphisms - 103 nonsynonymous - generate the nucleotide diversity of π = 0.027 in AF, and π = 0.042 in BA. The pvmsp-7F has only two SNPs - A610G and A1054T -, with nucleotide diversity of π = 0.0004 in AF, and π = 0.0007 in BA. The haplotype diversity of pvmsp-142, pvmsp-7E, and pvmsp-7F genes is 0.997, 1.00, and 0.649, respectively. None of the pvmsp-142 or pvmsp-7E sequences are identical to the Salvador 1 strain's sequence. Conversely, most of pvmsp-7F sequences (94/48%) are identical to Sal-1. We evaluated eight B-cell epitopes in pvmsp-7E, four of them showed higher nucleotide diversity compared to pvmsp-7E's epitopes. Positive selection was detected in pvmsp-142, pvmsp-7E central region, and pvmsp-7F with Tajima's D. In pvmsp-7E, the significant nucleotide and haplotype diversities with low genetic differentiation, could be indicative of balancing selection. The genetic differentiation of pvmsp-142 (0.315) and pvmsp-7F (0.354) genes between AF and BA regions is significant, which is not the case for pvmsp-7E (0.193). We conclude that pvmsp-142 and pvmsp-7E have great genetic diversity even in AF region, an enclosure area with deficient transmission levels of P. vivax zoonotic malaria. In both Brazilian regions, pvmsp-119, pvmsp-7E, and pvmsp-7F are conserved, most likely due to their roles in parasite survival, and could be considered potential targets for a "blood-stage vaccine".
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Affiliation(s)
- Natália Ketrin Almeida-de-Oliveira
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Rebecca Abreu-Fernandes
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Aline Rosa Lavigne
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Anielle Pina-Costa
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil; Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, RJ, Brazil; Centro Universitário Serra dos Órgãos (UNIFESO), Teresópolis, RJ, Brazil
| | - Daiana de Souza Perce-da-Silva
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil; Laboratório de Imunologia Básica e Aplicada, Faculdade de Medicina de Petrópolis - FMP/FASE, Petrópolis, RJ, Brazil
| | - Marcos Catanho
- Laboratório de Genética Molecular de Microrganismos, IOC, Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Átila Duque Rossi
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, RJ, Brazil
| | - Patrícia Brasil
- Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil; Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Instituto Nacional de Infectologia Evandro Chagas, Fiocruz, Rio de Janeiro, RJ, Brazil.
| | - Cláudio Tadeu Daniel-Ribeiro
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil
| | - Maria de Fátima Ferreira-da-Cruz
- Laboratório de Pesquisa em Malária, Instituto Oswaldo Cruz (IOC), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, RJ, Brazil; Centro de Pesquisa, Diagnóstico e Treinamento em Malária (CPD-Mal), Reference Laboratory for Malaria in the Extra-Amazonian Region for the Brazilian Ministry of Health, SVS & Fiocruz, Rio de Janeiro, RJ, Brazil.
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Mittal P, Mishra S, Kar S, Pande V, Sinha A, Sharma A. Global distribution of single amino acid polymorphisms in Plasmodium vivax Duffy-binding-like domain and implications for vaccine development efforts. Open Biol 2020; 10:200180. [PMID: 32993415 PMCID: PMC7536081 DOI: 10.1098/rsob.200180] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Plasmodium vivax (Pv) malaria continues to be geographically widespread with approximately 15 million worldwide cases annually. Along with other proteins, Duffy-binding proteins (DBPs) are used by plasmodium for RBC invasion and the parasite-encoded receptor binding regions lie in their Duffy-binding-like (DBL) domains-thus making it a prime vaccine candidate. This study explores the sequence diversity in PvDBL globally, with an emphasis on India as it remains a major contributor to the global Pv malaria burden. Based on 1358 PvDBL protein sequences available in NCBI, we identified 140 polymorphic sites within 315 residues of PvDBL. Alarmingly, country-wise mapping of SAAPs from field isolates revealed varied and distinct polymorphic profiles for different nations. We report here 31 polymorphic residue positions in the global SAAP profile, most of which map to the PvDBL subdomain 2 (α1-α6). A distinct clustering of SAAPs distal to the DARC-binding sites is indicative of immune evasive strategies by the parasite. Analyses of PvDBL-neutralizing antibody complexes revealed that between 24% and 54% of interface residues are polymorphic. This work provides a framework to recce and expand the polymorphic space coverage in PvDBLs as this has direct implications for vaccine development studies. It also emphasizes the significance of surveying global SAAP distributions before or alongside the identification of vaccine candidates.
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Affiliation(s)
- Payal Mittal
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.,ICMR-National Institute of Malaria Research, New Delhi, 110077, India
| | - Siddhartha Mishra
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.,ICMR-National Institute of Malaria Research, New Delhi, 110077, India
| | - Sonalika Kar
- ICMR-National Institute of Malaria Research, New Delhi, 110077, India.,Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Veena Pande
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, 263001 India
| | - Abhinav Sinha
- ICMR-National Institute of Malaria Research, New Delhi, 110077, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India.,ICMR-National Institute of Malaria Research, New Delhi, 110077, India
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8
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Bittencourt NC, Leite JA, Silva ABIE, Pimenta TS, Silva-Filho JL, Cassiano GC, Lopes SCP, Dos-Santos JCK, Bourgard C, Nakaya HI, da Silva Ventura AMR, Lacerda MVG, Ferreira MU, Machado RLD, Albrecht L, Costa FTM. Genetic sequence characterization and naturally acquired immune response to Plasmodium vivax Rhoptry Neck Protein 2 (PvRON2). Malar J 2018; 17:401. [PMID: 30382855 PMCID: PMC6208078 DOI: 10.1186/s12936-018-2543-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 10/22/2018] [Indexed: 12/28/2022] Open
Abstract
Background The genetic diversity of malaria antigens often results in allele variant-specific immunity, imposing a great challenge to vaccine development. Rhoptry Neck Protein 2 (PvRON2) is a blood-stage antigen that plays a key role during the erythrocyte invasion of Plasmodium vivax. This study investigates the genetic diversity of PvRON2 and the naturally acquired immune response to P. vivax isolates. Results Here, the genetic diversity of PvRON21828–2080 and the naturally acquired humoral immune response against PvRON21828–2080 in infected and non-infected individuals from a vivax malaria endemic area in Brazil was reported. The diversity analysis of PvRON21828–2080 revealed that the protein is conserved in isolates in Brazil and worldwide. A total of 18 (19%) patients had IgG antibodies to PvRON21828–2080. Additionally, the analysis of the antibody response in individuals who were not acutely infected with malaria, but had been infected with malaria in the past indicated that 32 patients (33%) exhibited an IgG immune response against PvRON2. Conclusions PvRON2 was conserved among the studied isolates. The presence of naturally acquired antibodies to this protein in the absence of the disease suggests that PvRON2 induces a long-term antibody response. These results indicate that PvRON2 is a potential malaria vaccine candidate. Electronic supplementary material The online version of this article (10.1186/s12936-018-2543-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Najara C Bittencourt
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Juliana A Leite
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | | | - Tamirys S Pimenta
- Laboratório de Ensaios Clínicos e Imunogenética em Malária, Instituto Evandro Chagas/SVS/MS, Ananindeua, PA, Brazil
| | - João Luiz Silva-Filho
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Gustavo C Cassiano
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Stefanie C P Lopes
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz - FIOCRUZ, Manaus, AM, Brazil.,Fundação de Medicina Tropical-Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Joao C K Dos-Santos
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Catarina Bourgard
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil
| | - Helder I Nakaya
- School of Pharmaceutical Sciences, University of São Paulo, São Paulo, Brazil
| | | | - Marcus V G Lacerda
- Instituto Leônidas & Maria Deane, Fundação Oswaldo Cruz - FIOCRUZ, Manaus, AM, Brazil.,Fundação de Medicina Tropical-Dr. Heitor Vieira Dourado, Manaus, AM, Brazil
| | - Marcelo U Ferreira
- Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo-USP, São Paulo, Brazil
| | - Ricardo L D Machado
- Laboratório de Ensaios Clínicos e Imunogenética em Malária, Instituto Evandro Chagas/SVS/MS, Ananindeua, PA, Brazil
| | - Letusa Albrecht
- Instituto Carlos Chagas, Fundação Oswaldo Cruz - FIOCRUZ, Curitiba, PR, Brazil.
| | - Fabio T M Costa
- Laboratory of Tropical Diseases-Prof. Dr. Luiz Jacintho da Silva, Department of Genetics, Evolution, Microbiology and Immunology, University of Campinas-UNICAMP, Campinas, SP, Brazil.
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9
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Goryacheva II, Baranova AM, Lukashev AN, Gordeev MI, Usenbaev NT, Shaikevich EV. Genetic characterization of Plasmodium vivax in the Kyrgyz Republic. INFECTION GENETICS AND EVOLUTION 2018; 66:262-268. [PMID: 30339983 DOI: 10.1016/j.meegid.2018.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/14/2018] [Accepted: 10/15/2018] [Indexed: 10/28/2022]
Abstract
At the end of 2016, Kyrgyz Republic was certified by the World Health Organization as a malaria-free country, while only a decade ago this disease posed a serious health threat. The progress achieved by Kyrgyz Republic provides a unique example of tertian (Plasmodium vivax) malaria elimination. This success was based on an integrated approach, including measures for the treatment of infected people and disease prevention, vector control and the development of an effective national epidemiological surveillance system. Lower P. vivax msp-1, msp-3α, csp and dbpII genes polymorphism was revealed in Kyrgyz Republic in compare with that in Tajikistan. Molecular characterization of the causative agent found that P. vivax populations in Kyrgyz Republic was comprised by several lineages, highly divergent in the south-western and genetically homogeneous in the northern regions of Kyrgyz Republic, d. Such profile in the northern regions was compatible with several recent introductions rather than a long-term endemic circulation of the parasite. A low level of genetic variability suggested that the parasitic systems of tertian malaria, were not adapted, which, along with other factors, largely determined the possibility of malaria elimination in northern Kyrgyz Republic. Other determinants included environmental, social, and epidemiological factors that limited the spread of malaria. South-western Kyrgyz Republic, a region with a high level of interstate migration, requires considerable attention to prevent the spread of malaria.
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Affiliation(s)
- I I Goryacheva
- Vavilov Institute of General Genetics, Moscow 119991, Russia
| | | | | | - M I Gordeev
- Moscow Region State University, Moscow 105005, Russia
| | - N T Usenbaev
- Sanitary-Epidemiological Department of Kyrgyz Republic MOH, Bishkek, Kyrgyzstan
| | - E V Shaikevich
- Vavilov Institute of General Genetics, Moscow 119991, Russia.
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10
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Hoque MR, Elfaki MMA, Ahmed MA, Lee SK, Muh F, Ali Albsheer MM, Hamid MMA, Han ET. Diversity pattern of Duffy binding protein sequence among Duffy-negatives and Duffy-positives in Sudan. Malar J 2018; 17:297. [PMID: 30119671 PMCID: PMC6098642 DOI: 10.1186/s12936-018-2425-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 07/21/2018] [Indexed: 02/08/2023] Open
Abstract
Background Vivax malaria is a leading public health concern worldwide. Due to the high prevalence of Duffy-negative blood group population, Plasmodium vivax in Africa historically is less attributable and remains a neglected disease. The interaction between Duffy binding protein and its cognate receptor, Duffy antigen receptor for chemokine plays a key role in the invasion of red blood cells and serves as a novel vaccine candidate against P. vivax. However, the polymorphic nature of P. vivax Duffy binding protein (DBP), particularly N-terminal cysteine-rich region (PvDBPII), represents a major obstacle for the successful design of a DBP-based vaccine to enable global protection. In this study, the level of pvdbpII sequence variations, Duffy blood group genotypes, number of haplotypes circulating, and the natural selection at pvdbpII in Sudan isolates were analysed and the implication in terms of DBP-based vaccine design was discussed. Methods Forty-two P. vivax-infected blood samples were collected from patients from different areas of Sudan during 2014–2016. For Duffy blood group genotyping, the fragment that indicates GATA-1 transcription factor binding site of the FY gene (− 33T > C) was amplified by PCR and sequenced by direct sequencing. The region II flanking pvdbpII was PCR amplified and sequenced by direct sequencing. The genetic diversity and natural selection of pvdbpII were done using DnaSP ver 5.0 and MEGA ver 5.0 programs. Based on predominant, non-synonymous, single nucleotide polymorphisms (SNPs), prevalence of Sudanese haplotypes was assessed in global isolates. Results Twenty SNPs (14 non-synonymous and 6 synonymous) were identified in pvdbpII among the 42 Sudan P. vivax isolates. Sequence analysis revealed that 11 different PvDBP haplotypes exist in Sudan P. vivax isolates and the region has evolved under positive selection. Among the identified PvDBP haplotypes five PvDBP haplotypes were shared among Duffy-negative as well as Duffy-positive individuals. The high selective pressure was mainly found on the known B cell epitopes (H3) of pvdbpII. Comparison of Sudanese haplotypes, based on 10 predominant non-synonymous SNPs with 10 malaria-endemic countries, demonstrated that Sudanese haplotypes were prevalent in most endemic countries. Conclusion This is the first pvdbp genetic diversity study from an African country. Sudanese isolates display high haplotype diversity and the gene is under selective pressure. Haplotype analysis indicated that Sudanese haplotypes are a representative sample of the global population. However, studies with a large number of samples are needed. These findings would be valuable for the development of PvDBP-based malaria vaccine. Electronic supplementary material The online version of this article (10.1186/s12936-018-2425-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mohammad Rafiul Hoque
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Mohammed Mohieldien Abbas Elfaki
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Qassr Street, Khartoum, Sudan.,Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Jizan, Saudi Arabia
| | - Md Atique Ahmed
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Seong-Kyun Lee
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Fauzi Muh
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea
| | - Musab M Ali Albsheer
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Qassr Street, Khartoum, Sudan
| | - Muzamil Mahdi Abdel Hamid
- Department of Parasitology and Medical Entomology, Institute of Endemic Diseases, University of Khartoum, Qassr Street, Khartoum, Sudan.
| | - Eun-Taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, Republic of Korea.
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11
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Flores-Alanis A, González-Cerón L, Santillán F, Ximenez C, Sandoval MA, Cerritos R. Temporal genetic changes in Plasmodium vivax apical membrane antigen 1 over 19 years of transmission in southern Mexico. Parasit Vectors 2017; 10:217. [PMID: 28464959 PMCID: PMC5414334 DOI: 10.1186/s13071-017-2156-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2016] [Accepted: 04/25/2017] [Indexed: 01/21/2023] Open
Abstract
Background Mexico advanced to the pre-elimination phase in 2009 due to a significant reduction in malaria cases, and since 2000, Plasmodium vivax is the only species transmitted. During the last two decades, malaria transmission has been mostly local and isolated to a few regions. It is important to gain further insights into the impact of control measures on the parasite population structure. Hence, the aim of the current study was to determine detailed changes in P. vivax genetic diversity and population structure based on analysing the gene that encodes the apical membrane antigen 1 (pvama1). This analysis covered from control to pre-elimination (1993–2011) in a hypo-endemic region in southern Mexico. Results The 213 pvama1I-II sequences presently analysed were grouped into six periods of three years each. They showed low genetic diversity, with 15 haplotypes resolved. Among the DNA sequences, there was a gradual decrease in genetic diversity, the number of mixed genotype infections and the intensity of positive selection, in agreement with the parallel decline in malaria cases. At the same time, linkage disequilibrium (R2) increased. The three-dimensional haplotype network revealed that pvama1I-II haplotypes were separated by 1–11 mutational steps, and between one another by 0–3 unsampled haplotypes. In the temporal network, seven haplotypes were detected in at least two of the six-time layers, and only four distinct haplotypes were evidenced in the pre-elimination phase. Structure analysis indicated that three subpopulations fluctuated over time. Only 8.5% of the samples had mixed ancestry. In the pre-elimination phase, subpopulation P1 was drastically reduced, and the admixture was absent. Conclusions The results suggest that P. vivax in southern Mexico evolved based on local adaptation into three “pseudoclonal” subpopulations that diversified at the regional level and persisted over time, although with varying frequency. Control measures and climate events influenced the number of malaria cases and the genetic structure. The sharp decrease in parasite diversity and other related genetic parameters during the pre-elimination phase suggests that malaria elimination is possible in the near future. These results are useful for epidemiological surveillance. Electronic supplementary material The online version of this article (doi:10.1186/s13071-017-2156-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alejandro Flores-Alanis
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico
| | - Lilia González-Cerón
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico.
| | - Frida Santillán
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico
| | - Cecilia Ximenez
- Departamento de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 06729, Mexico
| | - Marco A Sandoval
- Centro Regional de Investigación en Salud Pública, Instituto Nacional de Salud Pública, Tapachula, Chiapas, 30700, Mexico
| | - René Cerritos
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, 04510, Mexico.
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