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Fonseca A, Spytek M, Biecek P, Cordeiro C, Sepúlveda N. Antibody selection strategies and their impact in predicting clinical malaria based on multi-sera data. BioData Min 2024; 17:2. [PMID: 38273386 PMCID: PMC10811867 DOI: 10.1186/s13040-024-00354-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Nowadays, the chance of discovering the best antibody candidates for predicting clinical malaria has notably increased due to the availability of multi-sera data. The analysis of these data is typically divided into a feature selection phase followed by a predictive one where several models are constructed for predicting the outcome of interest. A key question in the analysis is to determine which antibodies should be included in the predictive stage and whether they should be included in the original or a transformed scale (i.e. binary/dichotomized). METHODS To answer this question, we developed three approaches for antibody selection in the context of predicting clinical malaria: (i) a basic and simple approach based on selecting antibodies via the nonparametric Mann-Whitney-Wilcoxon test; (ii) an optimal dychotomizationdichotomization approach where each antibody was selected according to the optimal cut-off via maximization of the chi-squared (χ2) statistic for two-way tables; (iii) a hybrid parametric/non-parametric approach that integrates Box-Cox transformation followed by a t-test, together with the use of finite mixture models and the Mann-Whitney-Wilcoxon test as a last resort. We illustrated the application of these three approaches with published serological data of 36 Plasmodium falciparum antigens for predicting clinical malaria in 121 Kenyan children. The predictive analysis was based on a Super Learner where predictions from multiple classifiers including the Random Forest were pooled together. RESULTS Our results led to almost similar areas under the Receiver Operating Characteristic curves of 0.72 (95% CI = [0.62, 0.82]), 0.80 (95% CI = [0.71, 0.89]), 0.79 (95% CI = [0.7, 0.88]) for the simple, dichotomization and hybrid approaches, respectively. These approaches were based on 6, 20, and 16 antibodies, respectively. CONCLUSIONS The three feature selection strategies provided a better predictive performance of the outcome when compared to the previous results relying on Random Forest including all the 36 antibodies (AUC = 0.68, 95% CI = [0.57;0.79]). Given the similar predictive performance, we recommended that the three strategies should be used in conjunction in the same data set and selected according to their complexity.
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Affiliation(s)
- André Fonseca
- FCT - Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
- CEAUL - Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Mikolaj Spytek
- Faculty of Mathematics & Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Przemysław Biecek
- Faculty of Mathematics & Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Clara Cordeiro
- FCT - Faculdade de Ciências e Tecnologia, Universidade do Algarve, Faro, Portugal
- CEAUL - Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Nuno Sepúlveda
- CEAUL - Centro de Estatística e Aplicações da Universidade de Lisboa, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
- Faculty of Mathematics & Information Science, Warsaw University of Technology, Warsaw, Poland.
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Drysdale M, Tan L, Martin A, Fuhrer IB, Duparc S, Sharma H. Plasmodium vivax in Children: Hidden Burden and Conspicuous Challenges, a Narrative Review. Infect Dis Ther 2023; 12:33-51. [PMID: 36378465 PMCID: PMC9868225 DOI: 10.1007/s40121-022-00713-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
There has been progress towards decreasing malaria prevalence globally; however, Plasmodium vivax has been less responsive to elimination efforts compared with Plasmodium falciparum. P. vivax malaria remains a serious public health concern in regions where it is the dominant species (South and South-East Asia, the Eastern Mediterranean region, and South America) and is increasingly recognized for its contribution to overall morbidity and mortality worldwide. The incidence of P. vivax decreases with increasing age owing to rapidly acquired clinical immunity and there is a disproportionate burden of P. vivax in infants and children, who remain highly vulnerable to severe disease, recurrence, and anemia with associated developmental impacts. Diagnosis is sometimes difficult owing to the sensitivity of diagnostic tests to detect low levels of parasitemia. Additionally, the propensity of P. vivax to relapse following reactivation of dormant hypnozoites in the liver contributes to disease recurrence in infants and children, and potentiates morbidity and transmission. The 8-aminoquinolines, primaquine and tafenoquine, provide radical cure (relapse prevention). However, the risk of hemolysis in patients with glucose-6-phosphate dehydrogenase (G6PD) deficiency necessitates testing prior to administration of 8-aminoquinolines, which has limited their uptake. Additional challenges include lack of availability of pediatric dose formulations and problems with adherence to primaquine owing to the length of treatment recommended. A paucity of data and studies specific to pediatric P. vivax malaria impacts the ability to deliver targeted interventions. It is imperative that P. vivax in infants and children be the focus of future research, control initiatives, and anti-malarial drug development.
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Affiliation(s)
| | - Lionel Tan
- GSK, 980 Great West Road, Brentford, TW8 9GS Middlesex UK
| | - Ana Martin
- GSK, 980 Great West Road, Brentford, TW8 9GS Middlesex UK
| | | | | | - Hema Sharma
- GSK, 980 Great West Road, Brentford, TW8 9GS Middlesex UK
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Sun Y, Shi X, Lu F, Fu H, Yin Y, Xu J, Jin C, Han ET, Huang X, Chen Y, Dong C, Cheng Y. Vesicular stomatitis virus-based vaccine targeting plasmodium blood-stage antigens elicits immune response and protects against malaria with protein booster strategy. Front Microbiol 2022; 13:1042414. [PMID: 36504817 PMCID: PMC9731671 DOI: 10.3389/fmicb.2022.1042414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022] Open
Abstract
Merozoite invasion of the erythrocytes in humans is a key step in the pathogenesis of malaria. The proteins involved in the merozoite invasion could be potential targets for the development of malaria vaccines. Novel viral-vector-based malaria vaccine regimens developed are currently under clinical trials. Vesicular stomatitis virus (VSV) is a single-stranded negative-strand RNA virus widely used as a vector for virus or cancer vaccines. Whether the VSV-based malarial vaccine is more effective than conventional vaccines based on proteins involved in parasitic invasion is still unclear. In this study, we have used the reverse genetics system to construct recombinant VSVs (rVSVs) expressing apical membrane protein 1 (AMA1), rhoptry neck protein 2 (RON2), and reticulocyte-binding protein homolog 5 (RH5), which are required for Plasmodium falciparum invasion. Our results showed that VSV-based viral vaccines significantly increased Plasmodium-specific IgG levels and lymphocyte proliferation. Also, VSV-PyAMA1 and VSV-PyRON2sp prime-boost regimens could significantly increase the levels of IL-2 and IFN-γ-producing by CD4+ and CD8+ T cells and suppress invasion in vitro. The rVSV prime-protein boost regimen significantly increase Plasmodium antigen-specific IgG levels in the serum of mice compared to the homologous rVSV prime-boost. Furthermore, the protective efficacy of rVSV prime protein boost immunization in the mice challenged with P. yoelii 17XL was better compared to traditional antigen immunization. Together, our results show that VSV vector is a novel strategy for malarial vaccine development and preventing the parasitic diseases.
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Affiliation(s)
- Yifan Sun
- Department of Laboratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China,Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiaodan Shi
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Feng Lu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Haitian Fu
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China,Department of Nuclear Medicine, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Yi Yin
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Jiahui Xu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, China
| | - Cheng Jin
- Department of Hepatobiliary Surgery, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Eun-taek Han
- Department of Medical Environmental Biology and Tropical Medicine, School of Medicine, Kangwon National University, Chuncheon, Gangwon-do, South Korea
| | - Xuan Huang
- Department of Laboratory Medicine, Affiliated Hospital of Jiangnan University, Wuxi, Jiangsu, China
| | - Yongquan Chen
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Chunsheng Dong
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou, Jiangsu, China,*Correspondence: Chunsheng Dong,
| | - Yang Cheng
- Laboratory of Pathogen Infection and Immunity, Department of Public Health and Preventive Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China,Yang Cheng,
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Zhou M, Varol A, Efferth T. Multi-omics approaches to improve malaria therapy. Pharmacol Res 2021; 167:105570. [PMID: 33766628 DOI: 10.1016/j.phrs.2021.105570] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/02/2021] [Accepted: 03/16/2021] [Indexed: 01/07/2023]
Abstract
Malaria contributes to the most widespread infectious diseases worldwide. Even though current drugs are commercially available, the ever-increasing drug resistance problem by malaria parasites poses new challenges in malaria therapy. Hence, searching for efficient therapeutic strategies is of high priority in malaria control. In recent years, multi-omics technologies have been extensively applied to provide a more holistic view of functional principles and dynamics of biological mechanisms. We briefly review multi-omics technologies and focus on recent malaria progress conducted with the help of various omics methods. Then, we present up-to-date advances for multi-omics approaches in malaria. Next, we describe resistance phenomena to established antimalarial drugs and underlying mechanisms. Finally, we provide insight into novel multi-omics approaches, new drugs and vaccine developments and analyze current gaps in multi-omics research. Although multi-omics approaches have been successfully used in malaria studies, they are still limited. Many gaps need to be filled to bridge the gap between basic research and treatment of malaria patients. Multi-omics approaches will foster a better understanding of the molecular mechanisms of Plasmodium that are essential for the development of novel drugs and vaccines to fight this disastrous disease.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ayşegül Varol
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University, Staudinger Weg 5, 55128 Mainz, Germany.
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5
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Longley RJ, White MT, Takashima E, Brewster J, Morita M, Harbers M, Obadia T, Robinson LJ, Matsuura F, Liu ZSJ, Li-Wai-Suen CSN, Tham WH, Healer J, Huon C, Chitnis CE, Nguitragool W, Monteiro W, Proietti C, Doolan DL, Siqueira AM, Ding XC, Gonzalez IJ, Kazura J, Lacerda M, Sattabongkot J, Tsuboi T, Mueller I. Development and validation of serological markers for detecting recent Plasmodium vivax infection. Nat Med 2020; 26:741-749. [DOI: 10.1038/s41591-020-0841-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/18/2020] [Indexed: 11/09/2022]
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Imported Malaria in Countries where Malaria Is Not Endemic: a Comparison of Semi-immune and Nonimmune Travelers. Clin Microbiol Rev 2020; 33:33/2/e00104-19. [PMID: 32161068 DOI: 10.1128/cmr.00104-19] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The continuous increase in long-distance travel and recent large migratory movements have changed the epidemiological characteristics of imported malaria in countries where malaria is not endemic (here termed non-malaria-endemic countries). While malaria was primarily imported to nonendemic countries by returning travelers, the proportion of immigrants from malaria-endemic regions and travelers visiting friends and relatives (VFRs) in malaria-endemic countries has continued to increase. VFRs and immigrants from malaria-endemic countries now make up the majority of malaria patients in many nonendemic countries. Importantly, this group is characterized by various degrees of semi-immunity to malaria, resulting from repeated exposure to infection and a gradual decline of protection as a result of prolonged residence in non-malaria-endemic regions. Most studies indicate an effect of naturally acquired immunity in VFRs, leading to differences in the parasitological features, clinical manifestation, and odds for severe malaria and clinical complications between immune VFRs and nonimmune returning travelers. There are no valid data indicating evidence for differing algorithms for chemoprophylaxis or antimalarial treatment in semi-immune versus nonimmune malaria patients. So far, no robust biomarkers exist that properly reflect anti-parasite or clinical immunity. Until they are found, researchers should rigorously stratify their study results using surrogate markers, such as duration of time spent outside a malaria-endemic country.
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van den Hoogen LL, Walk J, Oulton T, Reuling IJ, Reiling L, Beeson JG, Coppel RL, Singh SK, Draper SJ, Bousema T, Drakeley C, Sauerwein R, Tetteh KKA. Antibody Responses to Antigenic Targets of Recent Exposure Are Associated With Low-Density Parasitemia in Controlled Human Plasmodium falciparum Infections. Front Microbiol 2019; 9:3300. [PMID: 30700984 PMCID: PMC6343524 DOI: 10.3389/fmicb.2018.03300] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 12/18/2018] [Indexed: 12/05/2022] Open
Abstract
The majority of malaria infections in low transmission settings remain undetectable by conventional diagnostics. A powerful model to identify antibody responses that allow accurate detection of recent exposure to low-density infections is controlled human malaria infection (CHMI) studies in which healthy volunteers are infected with the Plasmodium parasite. We aimed to evaluate antibody responses in malaria-naïve volunteers exposed to a single CHMI using a custom-made protein microarray. All participants developed a blood-stage infection with peak parasite densities up to 100 parasites/μl in the majority of participants (50/54), while the remaining four participants had peak densities between 100 and 200 parasites/μl. There was a strong correlation between parasite density and antibody responses associated with the most reactive blood-stage targets 1 month after CHMI (Etramp 5, GLURP-R2, MSP4 and MSP1-19; Spearman’s ρ = 0.82, p < 0.001). Most volunteers developed antibodies against a potential marker of recent exposure: Etramp 5 (37/45, 82%). Our findings justify validation in endemic populations to define a minimum set of antigens needed to detect exposure to natural low-density infections.
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Affiliation(s)
- Lotus L van den Hoogen
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Jona Walk
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tate Oulton
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Isaie J Reuling
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - James G Beeson
- Burnet Institute, Melbourne, VIC, Australia.,Department of Medicine, The University of Melbourne, Melbourne, VIC, Australia.,Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Ross L Coppel
- Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Susheel K Singh
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark.,Department of International Health, Immunology and Microbiology, Centre for Medical Parasitology, University of Copenhagen, Copenhagen, Denmark
| | - Simon J Draper
- Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Teun Bousema
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Chris Drakeley
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Robert Sauerwein
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Kevin K A Tetteh
- Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, United Kingdom
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Ntege EH, Takashima E, Morita M, Nagaoka H, Ishino T, Tsuboi T. Blood-stage malaria vaccines: post-genome strategies for the identification of novel vaccine candidates. Expert Rev Vaccines 2017; 16:769-779. [PMID: 28604122 DOI: 10.1080/14760584.2017.1341317] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION An efficacious malaria vaccine is necessary to advance the current control measures towards malaria elimination. To-date, only RTS,S/AS01, a leading pre-erythrocytic stage vaccine completed phase 3 trials, but with an efficacy of 28-36% in children, and 18-26% in infants, that waned over time. Blood-stage malaria vaccines protect against disease, and are considered effective targets for the logical design of next generation vaccines to improve the RTS,S field efficacy. Therefore, novel blood-stage vaccine candidate discovery efforts are critical, albeit with several challenges including, high polymorphisms in vaccine antigens, poor understanding of targets of naturally protective immunity, and difficulties in the expression of high AT-rich plasmodial proteins. Areas covered: PubMed ( www.ncbi.nlm.nih.gov/pubmed ) was searched to review the progress and future prospects of malaria vaccine research and development. We focused on post-genome vaccine candidate discovery, malaria vaccine development, sequence diversity, pre-clinical and clinical trials. Expert commentary: Post-genome high-throughput technologies using wheat germ cell-free protein synthesis technology and immuno-profiling with sera from malaria patients with clearly defined outcomes are highlighted to overcome current challenges of malaria vaccine candidate discovery.
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Affiliation(s)
- Edward H Ntege
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Eizo Takashima
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Masayuki Morita
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Hikaru Nagaoka
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
| | - Tomoko Ishino
- b Division of Molecular Parasitology , Proteo-Science Center, Ehime University , Toon , Ehime , Japan
| | - Takafumi Tsuboi
- a Division of Malaria Research , Proteo-Science Center, Ehime University , Matsuyama , Ehime , Japan
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A Plasmodium vivax Plasmid DNA- and Adenovirus-Vectored Malaria Vaccine Encoding Blood-Stage Antigens AMA1 and MSP1 42 in a Prime/Boost Heterologous Immunization Regimen Partially Protects Aotus Monkeys against Blood-Stage Challenge. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2017; 24:CVI.00539-16. [PMID: 28179404 DOI: 10.1128/cvi.00539-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 02/06/2017] [Indexed: 01/30/2023]
Abstract
Malaria is caused by parasites of the genus Plasmodium, which are transmitted to humans by the bites of Anopheles mosquitoes. After the elimination of Plasmodium falciparum, it is predicted that Plasmodium vivax will remain an important cause of morbidity and mortality outside Africa, stressing the importance of developing a vaccine against P. vivax malaria. In this study, we assessed the immunogenicity and protective efficacy of two P. vivax antigens, apical membrane antigen 1 (AMA1) and the 42-kDa C-terminal fragment of merozoite surface protein 1 (MSP142) in a plasmid recombinant DNA prime/adenoviral (Ad) vector boost regimen in Aotus monkeys. Groups of 4 to 5 monkeys were immunized with plasmid DNA alone, Ad alone, prime/boost regimens with each antigen, prime/boost regimens with both antigens, and empty vector controls and then subjected to blood-stage challenge. The heterologous immunization regimen with the antigen pair was more protective than either antigen alone or both antigens delivered with a single vaccine platform, on the basis of their ability to induce the longest prepatent period and the longest time to the peak level of parasitemia, the lowest peak and mean levels of parasitemia, the smallest area under the parasitemia curve, and the highest self-cure rate. Overall, prechallenge MSP142 antibody titers strongly correlated with a decreased parasite burden. Nevertheless, a significant proportion of immunized animals developed anemia. In conclusion, the P. vivax plasmid DNA/Ad serotype 5 vaccine encoding blood-stage parasite antigens AMA1 and MSP142 in a heterologous prime/boost immunization regimen provided significant protection against blood-stage challenge in Aotus monkeys, indicating the suitability of these antigens and this regimen for further development.
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Editorial: Molecular Approaches to Malaria, 2016. Int J Parasitol 2017; 47:75. [DOI: 10.1016/j.ijpara.2017.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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