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Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Shabani ZI, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. Malar J 2024; 23:139. [PMID: 38720288 PMCID: PMC11080125 DOI: 10.1186/s12936-024-04974-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/03/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND In 2021 and 2023, the World Health Organization approved RTS,S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made of Plasmodium falciparum circumsporozoite protein (PfCSP), but polymorphisms in the gene raise concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed the Pfcsp genetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission intensities in Mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country. METHODS The analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of Mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright's inbreeding coefficient (Fws), Wright's fixation index (FST), principal component analysis, nucleotide diversity, and Tajima's D were used to assess within-host parasite diversity, population structure and natural selection. RESULTS Based on Fws (< 0.95), there was high polyclonality (ranging from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in the Pfcsp gene in the five regions (mean FST = 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region of Pfcsp showed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima's D were observed in the Th2R and Th3R regions consistent with balancing selection. The Pfcsp C-terminal sequences revealed 50 different haplotypes (H_1 to H_50), with only 2% of sequences matching the 3D7 strain haplotype (H_50). Conversely, with the NF54 strain, the Pfcsp C-terminal sequences revealed 49 different haplotypes (H_1 to H_49), with only 0.4% of the sequences matching the NF54 strain (Hap_49). CONCLUSIONS The findings demonstrate high diversity of the Pfcsp gene with limited population differentiation. The Pfcsp gene showed positive Tajima's D values, consistent with balancing selection for variants within Th2R and Th3R regions. The study observed differences between the intended haplotypes incorporated into the design of RTS,S and R21 vaccines and those present in natural parasite populations. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines.
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Affiliation(s)
- Beatus M Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania.
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania.
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Misago D Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Zulfa I Shabani
- Dar Es Salaam University College of Education, University of Dar es Salaam, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth Boniface
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Celine I Mandara
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Rashid Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Deus S Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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Friedman-Klabanoff DJ, Adu-Gyasi D, Asante KP. Malaria prevention in children: an update. Curr Opin Pediatr 2024; 36:164-170. [PMID: 38299986 PMCID: PMC10932812 DOI: 10.1097/mop.0000000000001332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
PURPOSE OF REVIEW Malaria cases and deaths decreased from 2000 to 2015 but remain increased since 2019. Several new developments and strategies could help reverse this trend. The purpose of this review is to discuss new World Health Organization (WHO) guidelines and recent research on malaria prevention in children. RECENT FINDINGS Fifteen countries have now rolled out seasonal malaria chemoprophylaxis (SMC) in children at highest risk for severe malaria, and new WHO recommendations provide more flexibility for SMC implementation in terms of target age groups, geographic region, and number of cycles. Recent studies confirm that malaria burden in school aged children, and their contribution to transmission, is high. New guidelines permit expanded chemoprevention options for these children. Two vaccines have been approved for use in malaria endemic countries, RTS,S/AS01 E and R21/Matrix-M. Additionally, pyrethroid-chlorfenapyr bed nets are being deployed to combat resistant mosquitoes. SUMMARY While challenges remain in malaria control towards elimination, new guidelines and recently approved vaccines offer hope. Monitoring for continued vaccine and chemoprevention effectiveness, and for possible epidemiologic shifts in severe malaria presentation and deaths as additional prevention efforts roll out will be paramount.
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Affiliation(s)
- DeAnna J Friedman-Klabanoff
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Dennis Adu-Gyasi
- Kintampo Health Research Centre, Research and Development Division, Ghana Health Service, Kintampo North Municipality, Bono East Region, Ghana
- Centre for Research in Applied Biology, School of Sciences, University of Energy and Natural Resources, Sunyani, Bono Region, Ghana, West Africa
| | - Kwaku Poku Asante
- Kintampo Health Research Centre, Research and Development Division, Ghana Health Service, Kintampo North Municipality, Bono East Region, Ghana
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Lyimo BM, Bakari C, Popkin-Hall ZR, Giesbrecht DJ, Seth MD, Pereus D, Moshi R, Boniface R, Mandara CI, Madebe R, Juliano JJ, Bailey JA, Ishengoma DS. Genetic polymorphism and evidence of signatures of selection in the Plasmodium falciparum circumsporozoite protein gene in Tanzanian regions with different malaria endemicity. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.23.24301587. [PMID: 38343796 PMCID: PMC10854334 DOI: 10.1101/2024.01.23.24301587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Background In 2021 and 2023, the World Health Organization approved RTS, S/AS01 and R21/Matrix M malaria vaccines, respectively, for routine immunization of children in African countries with moderate to high transmission. These vaccines are made of Plasmodium falciparum circumsporozoite protein (Pfcsp) but polymorphisms in this gene raises concerns regarding strain-specific responses and the long-term efficacy of these vaccines. This study assessed the Pfcsp genetic diversity, population structure and signatures of selection among parasites from areas of different malaria transmission in mainland Tanzania, to generate baseline data before the introduction of the malaria vaccines in the country. Methods The analysis involved 589 whole genome sequences generated by and as part of the MalariaGEN Community Project. The samples were collected between 2013 and January 2015 from five regions of mainland Tanzania: Morogoro and Tanga (Muheza) (moderate transmission areas), and Kagera (Muleba), Lindi (Nachingwea), and Kigoma (Ujiji) (high transmission areas). Wright's inbreeding coefficient (Fws), Wright's fixation index (FST), principal component analysis, nucleotide diversity, and Tajima's D were used to assess within-host parasite diversity, population structure and natural selection. Results Based on Fws (< 0.95), there was high polyclonality (ranged from 69.23% in Nachingwea to 56.9% in Muheza). No population structure was detected in the Pfcsp gene in the five regions (mean FST= 0.0068). The average nucleotide diversity (π), nucleotide differentiation (K) and haplotype diversity (Hd) in the five regions were 4.19, 0.973 and 0.0035, respectively. The C-terminal region of Pfcsp showed high nucleotide diversity at Th2R and Th3R regions. Positive values for the Tajima's D were observed in the Th2R and Th3R regions consistent with balancing selection. The Pfcsp C-terminal sequences had 50 different haplotypes (H_1 to H_50) and only 2% of sequences matched the 3D7 strain haplotype (H_50). Conclusions The findings demonstrate high diversity of the Pfcsp gene with limited population differentiation. The Pfcsp gene showed positive Tajima's D values for parasite populations, consistent with balancing selection for variants within Th2R and Th3R regions. This data is consistent with other studies conducted across Africa and worldwide, which demonstrate low 3D7 haplotypes and little population structure. Therefore, additional research is warranted, incorporating other regions and more recent data to comprehensively assess trends in genetic diversity within this important gene. Such insights will inform the choice of alleles to be included in the future vaccines.
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Affiliation(s)
- Beatus M. Lyimo
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Catherine Bakari
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Misago D. Seth
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Dativa Pereus
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Ramadhan Moshi
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | - Ruth Boniface
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | | | - Rashid Madebe
- National Institute for Medical Research, Dar es Salaam, Tanzania
| | | | | | - Deus S. Ishengoma
- National Institute for Medical Research, Dar es Salaam, Tanzania
- Harvard T.H Chan School of Public Health, Boston, MA, USA
- Faculty of Pharmaceutical Sciences, Monash University, Melbourne, Australia
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Ludwig J, Scally SW, Costa G, Hoffmann S, Murugan R, Lossin J, Prieto K, Obraztcova A, Lobeto N, Franke-Fayard B, Janse CJ, Lebas C, Collin N, Binter S, Kellam P, Levashina EA, Wardemann H, Julien JP. Glycosylated nanoparticle-based PfCSP vaccine confers long-lasting antibody responses and sterile protection in mouse malaria model. NPJ Vaccines 2023; 8:52. [PMID: 37029167 PMCID: PMC10080175 DOI: 10.1038/s41541-023-00653-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 03/23/2023] [Indexed: 04/09/2023] Open
Abstract
The development of an effective and durable vaccine remains a central goal in the fight against malaria. Circumsporozoite protein (CSP) is the major surface protein of sporozoites and the target of the only licensed Plasmodium falciparum (Pf) malaria vaccine, RTS,S/AS01. However, vaccine efficacy is low and short-lived, highlighting the need for a second-generation vaccine with superior efficacy and durability. Here, we report a Helicobacter pylori apoferritin-based nanoparticle immunogen that elicits strong B cell responses against PfCSP epitopes that are targeted by the most potent human monoclonal antibodies. Glycan engineering of the scaffold and fusion of an exogenous T cell epitope enhanced the anti-PfCSP B cell response eliciting strong, long-lived and protective humoral immunity in mice. Our study highlights the power of rational vaccine design to generate a highly efficacious second-generation anti-infective malaria vaccine candidate and provides the basis for its further development.
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Affiliation(s)
- Julia Ludwig
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stephen W Scally
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Giulia Costa
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany
| | - Sandro Hoffmann
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rajagopal Murugan
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jana Lossin
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Katherine Prieto
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Department of Immunology, University of Toronto, Toronto, ON, Canada
| | - Anna Obraztcova
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Nina Lobeto
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Blandine Franke-Fayard
- Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Chris J Janse
- Malaria Research Group, Department of Parasitology, Leiden University Medical Center, Leiden, The Netherlands
| | - Celia Lebas
- Vaccine Formulation Institute, Plan-les-Ouates, Switzerland
| | - Nicolas Collin
- Vaccine Formulation Institute, Plan-les-Ouates, Switzerland
| | - Spela Binter
- Kymab a Sanofi Company, Babraham Research Campus, Cambridge, UK
| | - Paul Kellam
- Kymab a Sanofi Company, Babraham Research Campus, Cambridge, UK
- Department of Infectious Diseases, Faculty of Medicine, Imperial College London, London, UK
| | - Elena A Levashina
- Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany.
| | - Hedda Wardemann
- B Cell Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.
- Department of Immunology, University of Toronto, Toronto, ON, Canada.
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
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An In Silico Analysis of Malaria Pre-Erythrocytic-Stage Antigens Interpreting Worldwide Genetic Data to Suggest Vaccine Candidate Variants and Epitopes. Microorganisms 2022; 10:microorganisms10061090. [PMID: 35744609 PMCID: PMC9231253 DOI: 10.3390/microorganisms10061090] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/12/2022] [Accepted: 05/19/2022] [Indexed: 02/05/2023] Open
Abstract
Failure to account for genetic diversity of antigens during vaccine design may lead to vaccine escape. To evaluate the vaccine escape potential of antigens used in vaccines currently in development or clinical testing, we surveyed the genetic diversity, measured population differentiation, and performed in silico prediction and analysis of T-cell epitopes of ten such Plasmodium falciparum pre-erythrocytic-stage antigens using whole-genome sequence data from 1010 field isolates. Of these, 699 were collected in Africa (Burkina Faso, Cameroon, Guinea, Kenya, Malawi, Mali, and Tanzania), 69 in South America (Brazil, Colombia, French Guiana, and Peru), 59 in Oceania (Papua New Guinea), and 183 in Asia (Cambodia, Myanmar, and Thailand). Antigens surveyed include cell-traversal protein for ookinetes and sporozoites, circumsporozoite protein, liver-stage antigens 1 and 3, sporozoite surface proteins P36 and P52, sporozoite asparagine-rich protein-1, sporozoite microneme protein essential for cell traversal-2, and upregulated-in-infectious-sporozoite 3 and 4 proteins. The analyses showed that a limited number of these protein variants, when combined, would be representative of worldwide parasite populations. Moreover, predicted T-cell epitopes were identified that could be further explored for immunogenicity and protective efficacy. Findings can inform the rational design of a multivalent malaria vaccine.
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Nadeem AY, Shehzad A, Islam SU, Al-Suhaimi EA, Lee YS. Mosquirix™ RTS, S/AS01 Vaccine Development, Immunogenicity, and Efficacy. Vaccines (Basel) 2022; 10:vaccines10050713. [PMID: 35632469 PMCID: PMC9143879 DOI: 10.3390/vaccines10050713] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/11/2022] [Accepted: 04/17/2022] [Indexed: 12/10/2022] Open
Abstract
Malaria is a parasitic infection caused by bites from Plasmodium falciparum (P. falciparum)-infected mosquitoes with a present scale of symptoms ranging from moderate fever to neurological disorders. P. falciparum is the most lethal of the five strains of malaria, and is a major case of morbidity and mortality in endemic regions. Recent advancements in malaria diagnostic tools and prevention strategies have improved conjugation antimalarial therapies using fumigation and long-lasting insecticidal sprays, thus lowering malarial infections. Declines in the total number of infected individuals have been correlated with antimalarial drugs. Despite this, malaria remains a major health threat, affecting more than 30 million men, women, and children around the globe, and 20 percent of all children around the globe have malaria parasites in their blood. To overcome this life-threatening condition, novel therapeutic strategies, including immunization, are urgently needed to tackle this infection around the world. In line with this, the development of the RTS, S vaccine was a significant step forward in the fight against malaria. RTS, S is a vaccine for P. falciparum in which R specifies central repeat units, T the T-cell epitopes, and S indicates surface antigen. The RTS, S/AS01 malarial vaccine was synthesized and screened in several clinical trials between 2009 and 2014, involving thousands of young children in seven African countries, showing that children who received the vaccine did not suffer from severe malaria. Mosquirix™ was approved by the World Health Organization in 2021, indicating it to be safe and advocating its integration into routine immunization programs and existing malaria control measures. This paper examines the various stages of the vaccine’s development, including the evaluation of its immunogenicity and efficacy on the basis of a total of 2.3 million administered doses through a routine immunization program. The protection and effectiveness provided by the vaccine are strong, and evidence shows that it can be effectively delivered through the routine child immunization platform. The economic cost of the vaccine remains to be considered.
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Affiliation(s)
- Aroosa Younis Nadeem
- Department of Biomedical Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan; (A.Y.N.); (A.S.)
| | - Adeeb Shehzad
- Department of Biomedical Sciences, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad 44000, Pakistan; (A.Y.N.); (A.S.)
| | - Salman Ul Islam
- Department of Pharmacy, CECOS University, Peshawar 25000, Pakistan;
| | - Ebtesam A. Al-Suhaimi
- Biology Department, College of Science and Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia;
| | - Young Sup Lee
- BK21 FOUR KNU Creative BioResearch Group, School of Life Sciences, College of Natural Sciences, Kyungpook National University, Daegu 41566, Korea
- Correspondence: ; Tel.: +82-53-950-6353; Fax: +82-53-943-2762
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Genetic Diversity, Repeat Motifs, and Natural Selection at the C-Terminal Knob-Associated Histidine Rich Protein (KAHRP) of Plasmodium falciparum Clinical Samples from Saudi Arabia. J Trop Med 2022; 2022:3740889. [PMID: 35387278 PMCID: PMC8979686 DOI: 10.1155/2022/3740889] [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: 10/10/2021] [Accepted: 03/03/2022] [Indexed: 11/24/2022] Open
Abstract
Background Malaria is still a public health problem in Saudi Arabia specifically in the Jazan region. Plasmodium falciparum knob-associated histidine-rich proteins (PfKAHRPs) play an important role in cerebral malaria pathophysiology as well as pathogenesis of P. falciparum infections. The repeat region of PfKAHRP C-terminal interaction domain has been found to bind to the infected red blood cells and the vascular endothelium. Thus, this study aimed to assess the allelic variations, genetic diversity, and natural selection acting at the C-terminal PfKAHRP between parasite isolates from Saudi Arabia. Materials and Methods The PfKHARP C-terminal interaction domain was successfully PCR-amplified and sequence data from 441 clinical isolates from Saudi Arabia were obtained. The DnaSP v5.10 software was used to determine the genetic diversity, polymorphism, haplotype, and natural selection. Haplotype network analysis was constructed by using the median-joining method in the NETWORK version 5.0.0.1 software. Results Alignment and analysis of 441 C-terminal PfKAHRP-deduced amino acid sequences identified 5 genotypes (I–V) based on the decapeptide repeat arrangements (TKEASTSKEA, TKEASTSKGA, TKEASTTEGA, and TKEASTSKRA). Among the repeat types, Type I (49.43%, 218/441) was the most abundant in Saudi Arabia, followed by Type II (48.29%, 213/441). Overall, the nucleotide diversity in the PfKHARP C-terminal region was found to be low in Saudi Arabia (π = 0.00142); however, natural selection tests indicated positive selection (dN-dS = 1.64, P < 0.05) which was due to the variations within the repeat motifs. Genealogical relationship haplotype network of PfKAHRP from 4 different countries (i.e., Saudi Arabia, Iran, Burundi, and India) revealed 1 major shared haplotype cluster (H_1) with samples representative from all 4 countries (Saudi Arabia; n = 441, Burundi; n = 4, Iran; n = 13, and India; n = 1). Conclusion Since this is the first study to report on genetic diversity of C-terminal PfKAHRP interaction domain and the repeat motifs from clinical samples in Saudi Arabia, it will contribute towards the rational design of antiadhesion drug therapies for P. falciparum malaria.
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Langowski MD, Khan FA, Savransky S, Brown DR, Balasubramaniyam A, Harrison WB, Zou X, Beck Z, Matyas GR, Regules JA, Miller R, Soisson LA, Batchelor AH, Dutta S. Restricted valency (NPNA) n repeats and junctional epitope-based circumsporozoite protein vaccines against Plasmodium falciparum. NPJ Vaccines 2022; 7:13. [PMID: 35087099 PMCID: PMC8795123 DOI: 10.1038/s41541-022-00430-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
The Circumsporozoite Protein (CSP) of Plasmodium falciparum contains an N-terminal region, a conserved Region I (RI), a junctional region, 25-42 copies of major (NPNA) and minor repeats followed by a C-terminal domain. The recently approved malaria vaccine, RTS,S/AS01 contains NPNAx19 and the C-terminal region of CSP. The efficacy of RTS,S against natural infection is low and short-lived, and mapping epitopes of inhibitory monoclonal antibodies may allow for rational improvement of CSP vaccines. Tobacco Mosaic Virus (TMV) was used here to display the junctional epitope (mAb CIS43), Region I (mAb 5D5), NPNAx5, and NPNAx20 epitope of CSP (mAbs 317 and 580). Protection studies in mice revealed that Region I did not elicit protective antibodies, and polyclonal antibodies against the junctional epitope showed equivalent protection to NPNAx5. Combining the junctional and NPNAx5 epitopes reduced immunogenicity and efficacy, and increasing the repeat valency to NPNAx20 did not improve upon NPNAx5. TMV was confirmed as a versatile vaccine platform for displaying small epitopes defined by neutralizing mAbs. We show that polyclonal antibodies against engineered VLPs can recapitulate the binding specificity of the mAbs and immune-focusing by reducing the structural complexity of an epitope may be superior to immune-broadening as a vaccine design approach. Most importantly the junctional and restricted valency NPNA epitopes can be the basis for developing highly effective second-generation malaria vaccine candidates.
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Affiliation(s)
- Mark D Langowski
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Farhat A Khan
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sofya Savransky
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Dallas R Brown
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Arasu Balasubramaniyam
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - William B Harrison
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Xiaoyan Zou
- Malaria Department, Naval Medical Research Center, Silver Spring, MD, USA
| | - Zoltan Beck
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
- Pfizer, 401N Middletown Rd, Pearl River, NY, 10965, USA
| | - Gary R Matyas
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Jason A Regules
- Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Robin Miller
- United States Agency for International Development, Washington, DC, USA
| | | | - Adrian H Batchelor
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Sheetij Dutta
- Structural Vaccinology Lab, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA.
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Abstract
Almost 20 years have passed since the first reference genome assemblies were published for Plasmodium falciparum, the deadliest malaria parasite, and Anopheles gambiae, the most important mosquito vector of malaria in sub-Saharan Africa. Reference genomes now exist for all human malaria parasites and nearly half of the ~40 important vectors around the world. As a foundation for genetic diversity studies, these reference genomes have helped advance our understanding of basic disease biology and drug and insecticide resistance, and have informed vaccine development efforts. Population genomic data are increasingly being used to guide our understanding of malaria epidemiology, for example by assessing connectivity between populations and the efficacy of parasite and vector interventions. The potential value of these applications to malaria control strategies, together with the increasing diversity of genomic data types and contexts in which data are being generated, raise both opportunities and challenges in the field. This Review discusses advances in malaria genomics and explores how population genomic data could be harnessed to further support global disease control efforts.
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Affiliation(s)
- Daniel E Neafsey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
| | - Aimee R Taylor
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Bronwyn L MacInnis
- Infectious Disease and Microbiome Program, Broad Institute, Cambridge, MA, USA.
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10
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Amegashie EA, Amenga-Etego L, Adobor C, Ogoti P, Mbogo K, Amambua-Ngwa A, Ghansah A. Population genetic analysis of the Plasmodium falciparum circumsporozoite protein in two distinct ecological regions in Ghana. Malar J 2020; 19:437. [PMID: 33246470 PMCID: PMC7694917 DOI: 10.1186/s12936-020-03510-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/19/2020] [Indexed: 01/02/2023] Open
Abstract
Background Extensive genetic diversity in the Plasmodium falciparum circumsporozoite protein (PfCSP) is a major contributing factor to the moderate efficacy of the RTS,S/AS01 vaccine. The transmission intensity and rates of recombination within and between populations influence the extent of its genetic diversity. Understanding the extent and dynamics of PfCSP genetic diversity in different transmission settings will help to interpret the results of current RTS,S efficacy and Phase IV implementation trials conducted within and between populations in malaria-endemic areas such as Ghana. Methods Pfcsp sequences were retrieved from the Illumina-generated paired-end short-read sequences of 101 and 131 malaria samples from children aged 6–59 months presenting with clinical malaria at health facilities in Cape Coast (in the coastal belt) and Navrongo (Guinea savannah region), respectively, in Ghana. The sequences were mapped onto the 3D7 reference strain genome to yield high-quality genome-wide coding sequence data. Following data filtering and quality checks to remove missing data, 220 sequences were retained and analysed for the allele frequency spectrum, genetic diversity both within the host and between populations and signatures of selection. Population genetics tools were used to determine the extent and dynamics of Pfcsp diversity in P. falciparum from the two geographically distinct locations in Ghana. Results Pfcsp showed extensive diversity at the two sites, with the higher transmission site, Navrongo, exhibiting higher within-host and population-level diversity. The vaccine strain C-terminal epitope of Pfcsp was found in only 5.9% and 45.7% of the Navrongo and Cape Coast sequences, respectively. Between 1 and 6 amino acid variations were observed in the TH2R and TH3R epitope regions of PfCSP. Tajima’s D was negatively skewed, especially for the population from Cape Coast, given the expected historical population expansion. In contrast, a positive Tajima’s D was observed for the Navrongo P. falciparum population, consistent with balancing selection acting on the immuno-dominant TH2R and TH3R vaccine epitopes. Conclusion The low frequencies of the Pfcsp vaccine haplotype in the analysed populations indicate a need for additional molecular and immuno-epidemiological studies with broader temporal and geographic sampling in endemic populations targeted for RTS,S application. These results have implications for the efficacy of the vaccine in Ghana and will inform the choice of alleles to be included in future multivalent or chimeric vaccines.
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Affiliation(s)
- Elikplim A Amegashie
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Lucas Amenga-Etego
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Legon, Ghana
| | - Courage Adobor
- Parasitology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, , Legon, Ghana
| | - Peter Ogoti
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Kevin Mbogo
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya
| | - Alfred Amambua-Ngwa
- Disease Control and Elimination, Medical Research Council Unit, The Gambia Unit, Bakau, The Gambia
| | - Anita Ghansah
- Parasitology Department, Noguchi Memorial Institute of Medical Research, University of Ghana, , Legon, Ghana.
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11
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Molina-Franky J, Cuy-Chaparro L, Camargo A, Reyes C, Gómez M, Salamanca DR, Patarroyo MA, Patarroyo ME. Plasmodium falciparum pre-erythrocytic stage vaccine development. Malar J 2020; 19:56. [PMID: 32013956 PMCID: PMC6998842 DOI: 10.1186/s12936-020-3141-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 01/25/2020] [Indexed: 12/13/2022] Open
Abstract
Worldwide strategies between 2010 and 2017 aimed at controlling malarial parasites (mainly Plasmodium falciparum) led to a reduction of just 18% regarding disease incidence rates. Many biologically-derived anti-malarial vaccine candidates have been developed to date; this has involved using many experimental animals, an immense amount of work and the investment of millions of dollars. This review provides an overview of the current state and the main results of clinical trials for sporozoite-targeting vaccines (i.e. the parasite stage infecting the liver) carried out by research groups in areas having variable malaria transmission rates. However, none has led to promising results regarding the effective control of the disease, thereby making it necessary to complement such efforts at finding/introducing new vaccine candidates by adopting a multi-epitope, multi-stage approach, based on minimal subunits of the main sporozoite proteins involved in the invasion of the liver.
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Affiliation(s)
- Jessica Molina-Franky
- Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Laura Cuy-Chaparro
- Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Anny Camargo
- Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - César Reyes
- PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia.,Animal Science Faculty, Universidad de Ciencias Aplicadas y Ambientales (U.D.C.A), Bogotá, Colombia.,3D Structures Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
| | - Marcela Gómez
- Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - David Ricardo Salamanca
- Health Sciences Faculty, Universidad de Boyacá, Tunja, Colombia.,Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,PhD Program in Biomedical and Biological Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia. .,Basic Sciences Department, School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia.
| | - Manuel Elkin Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia. .,Medical School, Universidad Nacional de Colombia, Bogotá, Colombia.
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12
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Ouattara A, Tran TM, Doumbo S, Adams M, Agrawal S, Niangaly A, Nelson-Owens S, Doumtabé D, Tolo Y, Ongoiba A, Takala-Harrison S, Traoré B, Silva JC, Crompton PD, Doumbo OK, Plowe CV. Extent and Dynamics of Polymorphism in the Malaria Vaccine Candidate Plasmodium falciparum Reticulocyte-Binding Protein Homologue-5 in Kalifabougou, Mali. Am J Trop Med Hyg 2018; 99:43-50. [PMID: 29848401 PMCID: PMC6085788 DOI: 10.4269/ajtmh.17-0737] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Reticulocyte-binding homologues (RH) are a ligand family that mediates merozoite invasion of erythrocytes in Plasmodium falciparum. Among the five members of this family identified so far, only P. falciparum reticulocyte–binding homologue-5 (PfRH5) has been found to be essential for parasite survival across strains that differ in virulence and route of host-cell invasion. Based on its essential role in invasion and early evidence of sequence conservation, PfRH5 has been prioritized for development as a vaccine candidate. However, little is known about the extent of genetic variability of RH5 in the field and the potential impact of such diversity on clinical outcomes or on vaccine evasion. Samples collected during a prospective cohort study of malaria incidence conducted in Kalifabougou, in southwestern Mali, were used to estimate genetic diversity, measure haplotype prevalence, and assess the within-host dynamics of PfRH5 variants over time and in relation to clinical malaria. A total of 10 nonsynonymous polymorphic sites were identified in the Pfrh5 gene, resulting in 13 haplotypes encoding unique protein variants. Four of these variants have not been previously observed. Plasmodium falciparum reticulocyte–binding homologue-5 had low amino acid haplotype (h = 0.58) and nucleotide (π = 0.00061) diversity. By contrast to other leading blood-stage malaria vaccine candidate antigens, amino acid differences were not associated with changes in the risk of febrile malaria in consecutive infections. Conserved B- and T-cell epitopes were identified. These results support the prioritization of PfRH5 for possible inclusion in a broadly cross-protective vaccine.
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Affiliation(s)
- Amed Ouattara
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali.,Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Tuan M Tran
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland.,Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Safiatou Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Matthew Adams
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Sonia Agrawal
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Amadou Niangaly
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | | | - Didier Doumtabé
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Youssouf Tolo
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Aissata Ongoiba
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Shannon Takala-Harrison
- Division of Malaria Research, Institute for Global Health, University of Maryland School of Medicine, Baltimore, Maryland
| | - Boubacar Traoré
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
| | - Joana C Silva
- Institute for Genome Sciences, University of Maryland Baltimore, Baltimore, Maryland
| | - Peter D Crompton
- Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - Ogobara K Doumbo
- Malaria Research and Training Center, University of Sciences, Techniques and Technology, Bamako, Mali
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13
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Wardemann H, Murugan R. From human antibody structure and function towards the design of a novel Plasmodium falciparum circumsporozoite protein malaria vaccine. Curr Opin Immunol 2018; 53:119-123. [PMID: 29751213 DOI: 10.1016/j.coi.2018.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/18/2018] [Accepted: 04/24/2018] [Indexed: 11/19/2022]
Abstract
Malaria is a life-threatening vector-borne disease caused by Plasmodium parasites that infect millions of people in endemic areas every year. The most advanced malaria vaccine candidate RTS,S targets the immune response against circumsporozoite protein of Plasmodium falciparum (PfCSP), the most deadly Plasmodium species in humans. PfCSP plays a fundamental role in parasite development as well as the establishment of the infection and is a molecular target of protective antibodies. However, RTS,S shows overall low efficacy and insufficient long-term protection. Therefore, a major goal in the development of an improved PfCSP-based vaccine remains the reliable and stable induction of protective and ideally sterilizing antibody titers. The molecular and functional characterization of human anti-PfCSP antibody responses paves the way for the rational design of novel immunogens for the development of an improved next-generation PfCSP malaria vaccine.
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Affiliation(s)
- Hedda Wardemann
- German Cancer Research Center, Im Neuenheimer Feld 280, 69121 Heidelberg, Germany.
| | - Rajagopal Murugan
- German Cancer Research Center, Im Neuenheimer Feld 280, 69121 Heidelberg, Germany
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14
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Nguetse CN, Ojo JA, Nchotebah C, Ikegbunam MN, Meyer CG, Thomas BN, Velavan TP, Ojurongbe O. Genetic Diversity of the Plasmodium falciparum Glutamate-Rich Protein R2 Region Before and Twelve Years after Introduction of Artemisinin Combination Therapies among Febrile Children in Nigeria. Am J Trop Med Hyg 2018; 98:667-676. [PMID: 29363449 PMCID: PMC5930894 DOI: 10.4269/ajtmh.17-0621] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 11/14/2017] [Indexed: 11/07/2022] Open
Abstract
The genetic diversity of glutamate-rich protein (GLURP) R2 region in Plasmodium falciparum isolates collected before and 12 years after the introduction of artemisinin combination treatment of malaria in Osogbo, Osun State, Nigeria, was compared in this study. Blood samples were collected on filter paper in 2004 and 2015 from febrile children from ages 1-12 years. The R2 region of the GLURP gene was genotyped using nested polymerase chain reaction and by nucleotide sequencing. In all, 12 GLURP alleles were observed in a total of 199 samples collected in the two study years. The multiplicity of infection (MOI) marginally increased over the two study years; however, the differences were statistically insignificant (2004 samples MOI = 1.23 versus 2015 samples MOI = 1.47). Some alleles were stable in their prevalence, whereas two GLURP alleles, VIII and XI, showed considerable variability between both years. This variability was replicated when GLURP sequences from other regions were compared with ours. The expected heterozygosity (He) values (He = 0.87) were identical for the two groups. High variability in the rearrangement of the amino acid repeat units in the R2 region were observed, with the amino acid repeat sequence DKNEKGQHEIVEVEEILPE more prevalent in both years, compared with the two other repeat sequences observed in the study. The parasite population characterized in this study displayed extensive genetic diversity. The detailed genetic profile of the GLURP R2 region has the potential to help guide further epidemiological studies aimed toward the rational design of novel chemotherapies that are antagonistic toward malaria.
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Affiliation(s)
- Christian N. Nguetse
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California
| | - Johnson Adeyemi Ojo
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo, Nigeria
| | - Charles Nchotebah
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Moses Nkechukwu Ikegbunam
- Department of Pharmaceutical Microbiology and Biotechnology, Nnamdi Azikwe University, Akwa, Nigeria
| | - Christian G. Meyer
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Duy Tan University, Da Nang, Vietnam
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, Rochester Institute of Technology, Rochester, New York
| | - Thirumalaisamy P. Velavan
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Duy Tan University, Da Nang, Vietnam
- Fondation Congolaise pour la Recherche Médicale, Brazzaville, Republic of Congo
| | - Olusola Ojurongbe
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Osogbo, Nigeria
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15
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Neafsey DE, Volkman SK. Malaria Genomics in the Era of Eradication. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a025544. [PMID: 28389516 DOI: 10.1101/cshperspect.a025544] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The first reference genome assembly for the Plasmodium falciparum malaria parasite was completed over a decade ago, and the impact of this and other genomic resources on malaria research has been significant. Genomic resources for other malaria parasites are being established, even as P. falciparum continues to be the focus of development of new genomic methods and applications. Here we review the impact and applications of genomic data on malaria research, and discuss future needs and directions as genomic data generation becomes less expensive and more decentralized. Specifically, we focus on how population genomic strategies can be utilized to advance the malaria eradication agenda.
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Affiliation(s)
- Daniel E Neafsey
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Sarah K Volkman
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115.,Infectious Disease Initiative, Broad Institute of MIT and Harvard, Cambridge Massachusetts 02142.,School of Nursing and Health Sciences, Simmons College, Boston, MA 02115
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16
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Wamae KK, Ochola-Oyier LI. Implications from predicted B-cell and T-cell epitopes of Plasmodium falciparum merozoite proteins EBA175-RII and Rh5. Bioinformation 2016; 12:82-91. [PMID: 28149040 PMCID: PMC5267949 DOI: 10.6026/97320630012082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/21/2016] [Accepted: 03/25/2016] [Indexed: 11/23/2022] Open
Abstract
The leading circumsporozoite protein (CSP) based malaria vaccine, RTS,S, though promising, has shown limited efficacy in field studies. There is therefore, still a need to identify other malaria vaccine targets. Merozoite antigens are potential vaccine candidates, since naturally acquired antibodies generated against them inhibit erythrocyte invasion and in some cases result in the clinical protection from disease. We thus used in silico tools (BCPreds, NetMHCcons and NetMHCIIpan 3.0) to predict B-cell epitopes (BCEs) and T-cell epitopes (TCEs) in two merozoite invasion proteins, EBA175-RII and Rh5. Initially, we validated these tools using CSP to determine whether the algorithms could predict the epitopes in the RTS,S vaccine. In EBA175-RII, we prioritised three BCEs 15REKRKGMKWDCKKKNDRSNY34, 420SNRKLVGKINTNSNYVHRNKQ440 and 528WISKKKEEYNKQAKQYQEYQ547, a CD8+ epitope 553KMYSEFKSI561 and a CD4+ epitope 440QNDKLFRDEWWK VIKKD456. Three Rh5 epitopes were prioritised, a BCE 344SCYNNNFCNTNGIRYHYDEY363, a CD8+ epitope 198STYGKCIAV206 and a Rh5 CD4+ epitope 180TFLDYYKHLSYNSIYHKSSTY200. All these epitopes are in the region involved in the proteins' interaction with their erythrocyte receptors, thus enabling erythrocyte invasion. Therefore, upon validation of their immunogenicity, by ELISA using serum from a malaria endemic population, antibodies to these epitopes may inhibit erythrocyte invasion. All the epitopes we predicted in EBA175-RII and Rh5 are novel. We also identified polymorphic epitopes that may escape host immunity, as some variants were not predicted as epitopes, suggesting that they may not be immunogenic regions. We present a set of epitopes that following in vitro validation provide a set of molecules to screen as potential vaccine candidates.
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Affiliation(s)
- Kevin Kariuki Wamae
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Kenya
- KEMRI-Wellcome Trust Collaborative Programme,Kilifi, Kenya; P.O. Box 230, Kilifi – 80108, Kenya
| | - Lynette Isabella Ochola-Oyier
- Centre for Biotechnology and Bioinformatics, University of Nairobi, Kenya
- KEMRI-Wellcome Trust Collaborative Programme,Kilifi, Kenya; P.O. Box 230, Kilifi – 80108, Kenya
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17
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Gandhi K, Thera MA, Coulibaly D, Traoré K, Guindo AB, Ouattara A, Takala-Harrison S, Berry AA, Doumbo OK, Plowe CV. Correction: Variation in the Circumsporozoite Protein of Plasmodium falciparum: Vaccine Development Implications. PLoS One 2016; 11:e0148240. [PMID: 26820850 PMCID: PMC4731568 DOI: 10.1371/journal.pone.0148240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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18
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Flanagan KL, Wilson KL, Plebanski M. Polymorphism in liver-stage malaria vaccine candidate proteins: immune evasion and implications for vaccine design. Expert Rev Vaccines 2015; 15:389-99. [PMID: 26610026 DOI: 10.1586/14760584.2016.1125785] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The pre-erythrocytic stage of infection by malaria parasites represents a key target for vaccines that aim to eradicate malaria. Two important broad immune evasion strategies that can interfere with vaccine efficacy include the induction of dendritic cell (DC) dysfunction and regulatory T cells (Tregs) by blood-stage malaria parasites, leading to inefficient priming of T cells targeting liver-stage infections. The parasite also uses 'surgical strike' strategies, whereby polymorphism in pre-erythrocytic antigens can interfere with host immunity. Specifically, we review how even single amino acid changes in T cell epitopes can lead to loss of binding to major histocompatibility complex (MHC), lack of cross-reactivity, or antagonism and immune interference, where simultaneous or sequential stimulation with related variants of the same T cell epitope can cause T cell anergy or the conversion of effector to immunosuppressive T cell phenotypes.
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Affiliation(s)
- Katie L Flanagan
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
| | - Kirsty L Wilson
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
| | - Magdalena Plebanski
- a Vaccine and Infectious Diseases Laboratory, Department of Immunology , Monash University , Melbourne , VIC , Australia
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19
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Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Ansong D, Aponte JJ, Asante KP, Bejon P, Birkett AJ, Bruls M, Connolly KM, D'Alessandro U, Dobaño C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi P, Kariuki S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ogutu BR, Otieno W, Otieno L, Otieno K, Owusu-Agyei S, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarlal J, Sogoloff B, Sorgho H, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF. Genetic Diversity and Protective Efficacy of the RTS,S/AS01 Malaria Vaccine. N Engl J Med 2015; 373:2025-2037. [PMID: 26488565 PMCID: PMC4762279 DOI: 10.1056/nejmoa1505819] [Citation(s) in RCA: 275] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND The RTS,S/AS01 vaccine targets the circumsporozoite protein of Plasmodium falciparum and has partial protective efficacy against clinical and severe malaria disease in infants and children. We investigated whether the vaccine efficacy was specific to certain parasite genotypes at the circumsporozoite protein locus. METHODS We used polymerase chain reaction-based next-generation sequencing of DNA extracted from samples from 4985 participants to survey circumsporozoite protein polymorphisms. We evaluated the effect that polymorphic positions and haplotypic regions within the circumsporozoite protein had on vaccine efficacy against first episodes of clinical malaria within 1 year after vaccination. RESULTS In the per-protocol group of 4577 RTS,S/AS01-vaccinated participants and 2335 control-vaccinated participants who were 5 to 17 months of age, the 1-year cumulative vaccine efficacy was 50.3% (95% confidence interval [CI], 34.6 to 62.3) against clinical malaria in which parasites matched the vaccine in the entire circumsporozoite protein C-terminal (139 infections), as compared with 33.4% (95% CI, 29.3 to 37.2) against mismatched malaria (1951 infections) (P=0.04 for differential vaccine efficacy). The vaccine efficacy based on the hazard ratio was 62.7% (95% CI, 51.6 to 71.3) against matched infections versus 54.2% (95% CI, 49.9 to 58.1) against mismatched infections (P=0.06). In the group of infants 6 to 12 weeks of age, there was no evidence of differential allele-specific vaccine efficacy. CONCLUSIONS These results suggest that among children 5 to 17 months of age, the RTS,S vaccine has greater activity against malaria parasites with the matched circumsporozoite protein allele than against mismatched malaria. The overall vaccine efficacy in this age category will depend on the proportion of matched alleles in the local parasite population; in this trial, less than 10% of parasites had matched alleles. (Funded by the National Institutes of Health and others.).
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20
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Affiliation(s)
- Christopher V Plowe
- From the Institute for Global Health and Howard Hughes Medical Institute, University of Maryland School of Medicine, Baltimore
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21
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Designing malaria vaccines to circumvent antigen variability. Vaccine 2015; 33:7506-12. [PMID: 26475447 PMCID: PMC4731100 DOI: 10.1016/j.vaccine.2015.09.110] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 09/29/2015] [Accepted: 09/30/2015] [Indexed: 12/12/2022]
Abstract
Prospects for malaria eradication will be greatly enhanced by an effective vaccine, but parasite genetic diversity poses a major impediment to malaria vaccine efficacy. In recent pre-clinical and field trials, vaccines based on polymorphic Plasmodium falciparum antigens have shown efficacy only against homologous strains, raising the specter of allele-specific immunity such as that which plagues vaccines against influenza and HIV. The most advanced malaria vaccine, RTS,S, targets relatively conserved epitopes on the P. falciparum circumsporozoite protein. After more than 40 years of development and testing, RTS,S, has shown significant but modest efficacy against clinical malaria in phase 2 and 3 trials. Ongoing phase 2 studies of an irradiated sporozoite vaccine will ascertain whether the full protection against homologous experimental malaria challenge conferred by high doses of a whole organism vaccine can provide protection against diverse strains in the field. Here we review and evaluate approaches being taken to design broadly cross-protective malaria vaccines.
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22
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RTS,S: Toward a first landmark on the Malaria Vaccine Technology Roadmap. Vaccine 2015; 33:7425-32. [PMID: 26431982 DOI: 10.1016/j.vaccine.2015.09.061] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 09/08/2015] [Accepted: 09/15/2015] [Indexed: 01/07/2023]
Abstract
The Malaria Vaccine Technology Roadmap calls for a 2015 landmark goal of a first-generation malaria vaccine that has protective efficacy against severe disease and death, lasting longer than one year. This review focuses on product development efforts over the last five years of RTS,S, a pre-erythrocytic, recombinant subunit, adjuvanted, candidate malaria vaccine designed with this goal of a first-generation malaria vaccine in mind. RTS,S recently completed a successful pivotal Phase III safety, efficacy and immunogenicity study. Although vaccine efficacy was found to be modest, a substantial number of cases of clinical malaria were averted over a 3-4 years period, particularly in settings of significant disease burden. European regulators have subsequently adopted a positive opinion under the Article 58 procedure for an indication of active immunization of children aged 6 weeks up to 17 months against malaria caused by Plasmodium falciparum and against hepatitis B. Further evaluations of the benefit, risk, feasibility and cost-effectiveness of RTS,S are now anticipated through policy and financing reviews at the global and national levels.
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