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Ciubotariu II, Broyles BK, Xie S, Thimmapuram J, Mwenda MC, Mambwe B, Mulube C, Matoba J, Schue JL, Moss WJ, Bridges DJ, He Q, Carpi G. Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum. EBioMedicine 2024; 106:105227. [PMID: 39018754 DOI: 10.1016/j.ebiom.2024.105227] [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: 04/18/2024] [Revised: 06/18/2024] [Accepted: 06/18/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. METHODS We analysed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Database. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. FINDINGS Among the ten antigens analysed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. INTERPRETATION These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum. Based on our results, we recommend prioritising conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. FUNDING Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).
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Affiliation(s)
- Ilinca I Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Bradley K Broyles
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, IN, USA
| | | | - Mulenga C Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | | | - Jessica L Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - William J Moss
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | | | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA; Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, IN, USA.
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Ciubotariu II, Broyles BK, Xie S, Thimmapuram J, Mwenda MC, Mambwe B, Mulube C, Matoba J, Schue JL, Moss WJ, Bridges DJ, He Q, Carpi G. Diversity and selection analyses identify transmission-blocking antigens as the optimal vaccine candidates in Plasmodium falciparum. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.11.24307175. [PMID: 38766239 PMCID: PMC11100930 DOI: 10.1101/2024.05.11.24307175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Background A highly effective vaccine for malaria remains an elusive target, at least in part due to the under-appreciated natural parasite variation. This study aimed to investigate genetic and structural variation, and immune selection of leading malaria vaccine candidates across the Plasmodium falciparum's life cycle. Methods We analyzed 325 P. falciparum whole genome sequences from Zambia, in addition to 791 genomes from five other African countries available in the MalariaGEN Pf3k Rdatabase. Ten vaccine antigens spanning three life-history stages were examined for genetic and structural variations, using population genetics measures, haplotype network analysis, and 3D structure selection analysis. Findings Among the ten antigens analyzed, only three in the transmission-blocking vaccine category display P. falciparum 3D7 as the dominant haplotype. The antigens AMA1, CSP, MSP119 and CelTOS, are much more diverse than the other antigens, and their epitope regions are under moderate to strong balancing selection. In contrast, Rh5, a blood stage antigen, displays low diversity yet slightly stronger immune selection in the merozoite-blocking epitope region. Except for CelTOS, the transmission-blocking antigens Pfs25, Pfs48/45, Pfs230, Pfs47, and Pfs28 exhibit minimal diversity and no immune selection in epitopes that induce strain-transcending antibodies, suggesting potential effectiveness of 3D7-based vaccines in blocking transmission. Interpretations These findings offer valuable insights into the selection of optimal vaccine candidates against P. falciparum. Based on our results, we recommend prioritizing conserved merozoite antigens and transmission-blocking antigens. Combining these antigens in multi-stage approaches may be particularly promising for malaria vaccine development initiatives. Funding Purdue Department of Biological Sciences; Puskas Memorial Fellowship; National Institute of Allergy and Infectious Diseases (U19AI089680).
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Affiliation(s)
- Ilinca I. Ciubotariu
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Bradley K. Broyles
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Shaojun Xie
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, USA
| | | | - Mulenga C. Mwenda
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Brenda Mambwe
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | - Conceptor Mulube
- PATH-Malaria Control and Elimination Partnership in Africa (MACEPA), National Malaria Elimination Centre, Lusaka, Zambia
| | | | - Jessica L. Schue
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - William J. Moss
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | | | - Qixin He
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, West Lafayette, Indiana, USA
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Bell GJ, Gyaase S, Goel V, Adu B, Mensah B, Essone P, Dosoo D, Osei M, Niare K, Wiru K, Brandt K, Emch M, Ghansah A, Asante KP, Mvalo T, Agnandji ST, Juliano JJ, Bailey JA. Background malaria incidence and parasitemia during the three-dose RTS,S/AS01 vaccination series do not reduce magnitude of antibody response nor efficacy against the first case of malaria. BMC Infect Dis 2023; 23:716. [PMID: 37872492 PMCID: PMC10594884 DOI: 10.1186/s12879-023-08699-7] [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: 05/30/2023] [Accepted: 10/11/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND RTS,S/AS01 has been recommended by WHO for widespread implementation in medium to high malaria transmission settings. Previous analyses have noted lower vaccine efficacies in higher transmission settings, possibly due to the more rapid development of naturally acquired immunity in the control group. METHODS To investigate a reduced immune response to vaccination as a potential mechanism behind lower efficacy in high transmission areas, we examine initial vaccine antibody (anti-CSP IgG) response and vaccine efficacy against the first case of malaria (to exclude the effect of naturally acquired immunity) using data from three study areas (Kintampo, Ghana; Lilongwe, Malawi; Lambaréné, Gabon) from the 2009-2014 phase III trial (NCT00866619). Our key exposures are parasitemia during the vaccination series and background malaria incidence. We calculate vaccine efficacy (one minus hazard ratio) using a cox-proportional hazards model and allowing for the time-varying effect of RTS,S/AS01. RESULTS We find that antibody responses to the primary three-dose vaccination series were higher in Ghana than in Malawi and Gabon, but that neither antibody levels nor vaccine efficacy against the first case of malaria varied by background incidence or parasitemia during the primary vaccination series. CONCLUSIONS We find that vaccine efficacy is unrelated to infections during vaccination. Contributing to a conflicting literature, our results suggest that vaccine efficacy is also unrelated to infections before vaccination, meaning that control-group immunity is likely a major reason for lower efficacy in high transmission settings, not reduced immune responses to RTS,S/AS01. This may be reassuring for implementation in high transmission settings, though further studies are needed.
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Affiliation(s)
- Griffin J Bell
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | | | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Benedicta Mensah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | - Paulin Essone
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - David Dosoo
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Musah Osei
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Karamoko Niare
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
| | - Kenneth Wiru
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Katerina Brandt
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | - Tisungane Mvalo
- University of North Carolina Project, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jonathan J Juliano
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, USA
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, 02912, USA
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Hamilton A, Haghpanah F, Hasso-Agopsowicz M, Frost I, Lin G, Schueller E, Klein E, Laxminarayan R. Modeling of malaria vaccine effectiveness on disease burden and drug resistance in 42 African countries. COMMUNICATIONS MEDICINE 2023; 3:144. [PMID: 37833540 PMCID: PMC10576074 DOI: 10.1038/s43856-023-00373-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND The emergence of antimalarial drug resistance poses a major threat to effective malaria treatment and control. This study aims to inform policymakers and vaccine developers on the potential of an effective malaria vaccine in reducing drug-resistant infections. METHODS A compartmental model estimating cases, drug-resistant cases, and deaths averted from 2021 to 2030 with a vaccine against Plasmodium falciparum infection administered yearly to 1-year-olds in 42 African countries. Three vaccine efficacy (VE) scenarios and one scenario of rapidly increasing drug resistance are modeled. RESULTS When VE is constant at 40% for 4 years and then drops to 0%, 235.7 (Uncertainty Interval [UI] 187.8-305.9) cases per 1000 children, 0.6 (UI 0.4-1.0) resistant cases per 1000, and 0.6 (UI 0.5-0.9) deaths per 1000 are averted. When VE begins at 80% and drops 20 percentage points each year, 313.9 (UI 249.8-406.6) cases per 1000, 0.9 (UI 0.6-1.3) resistant cases per 1000, and 0.9 (UI 0.6-1.2) deaths per 1000 are averted. When VE remains 40% for 10 years, 384.7 (UI 311.7-496.5) cases per 1000, 1.0 (0.7-1.6) resistant cases per 1000, and 1.1 (UI 0.8-1.5) deaths per 1000 are averted. Assuming an effective vaccine and an increase in current levels of drug resistance to 80% by 2030, 10.4 (UI 7.3-15.8) resistant cases per 1000 children are averted. CONCLUSIONS Widespread deployment of a malaria vaccine could substantially reduce health burden in Africa. Maintaining VE longer may be more impactful than a higher initial VE that falls rapidly.
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Affiliation(s)
| | | | | | - Isabel Frost
- World Health Organization, Geneva, Switzerland
- Imperial College London, London, UK
| | - Gary Lin
- One Health Trust, Washington, D.C., USA
| | | | - Eili Klein
- One Health Trust, Washington, D.C., USA
- Johns Hopkins University, Department of Emergency Medicine, Baltimore, MD, USA
| | - Ramanan Laxminarayan
- One Health Trust, Washington, D.C., USA.
- One Health Trust, New Delhi, India.
- Princeton University, Princeton, NJ, USA.
- University of Washington, Seattle, WA, USA.
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Tukwasibwe S, Mboowa G, Sserwadda I, Nankabirwa JI, Arinaitwe E, Ssewanyana I, Taremwa Y, Tumusiime G, Kamya MR, Jagannathan P, Nakimuli A. Impact of high human genetic diversity in Africa on immunogenicity and efficacy of RTS,S/AS01 vaccine. Immunogenetics 2023; 75:207-214. [PMID: 37084013 PMCID: PMC10119520 DOI: 10.1007/s00251-023-01306-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/06/2023] [Indexed: 04/22/2023]
Abstract
In modern medicine, vaccination is one of the most effective public health strategies to prevent infectious diseases. Indisputably, vaccines have saved millions of lives by reducing the burden of many serious infections such as polio, tuberculosis, measles, pneumonia, and tetanus. Despite the recent recommendation by the World Health Organization (WHO) to roll out RTS,S/AS01, this malaria vaccine still faces major challenges of variability in its efficacy partly due to high genetic variation in humans and malaria parasites. Immune responses to malaria vary between individuals and populations. Human genetic variation in immune system genes is the probable cause for this heterogeneity. In this review, we will focus on human genetic factors that determine variable responses to vaccination and how variation in immune system genes affect the immunogenicity and efficacy of the RTS,S/AS01 vaccine.
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Affiliation(s)
- Stephen Tukwasibwe
- Infectious Diseases Research Collaboration, Kampala, Uganda.
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda.
- School of Medicine, Uganda Christian University, Kampala, Uganda.
| | - Gerald Mboowa
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ivan Sserwadda
- Infectious Diseases Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | | | | | - Yoweri Taremwa
- Infectious Diseases Research Collaboration, Kampala, Uganda
| | - Gerald Tumusiime
- School of Medicine, Uganda Christian University, Kampala, Uganda
| | - Moses R Kamya
- Infectious Diseases Research Collaboration, Kampala, Uganda
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
| | | | - Annettee Nakimuli
- School of Medicine, College of Health Sciences, Makerere University, Kampala, Uganda
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Bell GJ, Gyaase S, Goel V, Adu B, Mensah B, Essone P, Dosoo D, Osei M, Niare K, Wiru K, Brandt K, Emch M, Ghansah A, Asante KP, Mvalo T, Agnandji ST, Juliano JJ, Bailey JA. Malaria Transmission Intensity and Parasitemia during the Three-Dose RTS,S/AS01 Vaccination Series do not Reduce Magnitude of Antibody Response nor Efficacy Against the First Case of Malaria. RESEARCH SQUARE 2023:rs.3.rs-2960373. [PMID: 37292711 PMCID: PMC10246269 DOI: 10.21203/rs.3.rs-2960373/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Background RTS,S/AS01 has been recommended by WHO for widespread implementation in medium to high malaria transmission settings. Previous analyses have noted lower vaccine efficacies in higher transmission settings, possibly due to the more rapid development of naturally acquired immunity in the control group. Methods To investigate a reduced immune response to vaccination as a potential mechanism behind lower efficacy in high transmission areas, we examine initial vaccine antibody (anti-CSP IgG) response and vaccine efficacy against the first case of malaria to exclude the delayed malaria effect using data from three study areas (Kintampo, Ghana; Lilongwe, Malawi; Lambaréné, Gabon) from the 2009-2014 phase III trial (NCT00866619). Our key exposures are parasitemia during the vaccination series and malaria transmission intensity. We calculate vaccine efficacy (one minus hazard ratio) using a cox-proportional hazards model and allowing for the time-varying effect of RTS,S/AS01. Results We find that antibody responses to the primary three-dose vaccination series were higher in Ghana than in Malawi and Gabon, but that neither antibody levels nor vaccine efficacy against the first case of malaria varied by transmission intensity or parasitemia during the primary vaccination series. Conclusions We find that vaccine efficacy is unrelated to infections during vaccination. Contributing to a conflicting literature, our results suggest that vaccine efficacy is also unrelated to infections before vaccination, meaning that delayed malaria is likely the main reason for lower efficacy in high transmission settings, not reduced immune responses. This may be reassuring for implementation in high transmission settings, though further studies are needed.
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Bell GJ, Goel V, Essone P, Dosoo D, Adu B, Mensah BA, Gyaase S, Wiru K, Mougeni F, Osei M, Minsoko P, Sinai C, Niaré K, Juliano JJ, Hudgens M, Ghansah A, Kamthunzi P, Mvalo T, Agnandji ST, Bailey JA, Asante KP, Emch M. Malaria Transmission Intensity Likely Modifies RTS, S/AS01 Efficacy Due to a Rebound Effect in Ghana, Malawi, and Gabon. J Infect Dis 2022; 226:1646-1656. [PMID: 35899811 PMCID: PMC10205900 DOI: 10.1093/infdis/jiac322] [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: 05/20/2022] [Accepted: 07/26/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND RTS,S/AS01 is the first malaria vaccine to be approved and recommended for widespread implementation by the World Health Organization (WHO). Trials reported lower vaccine efficacies in higher-incidence sites, potentially due to a "rebound" in malaria cases in vaccinated children. When naturally acquired protection in the control group rises and vaccine protection in the vaccinated wanes concurrently, malaria incidence can become greater in the vaccinated than in the control group, resulting in negative vaccine efficacies. METHODS Using data from the 2009-2014 phase III trial (NCT00866619) in Lilongwe, Malawi; Kintampo, Ghana; and Lambaréné, Gabon, we evaluate this hypothesis by estimating malaria incidence in each vaccine group over time and in varying transmission settings. After estimating transmission intensities using ecological variables, we fit models with 3-way interactions between vaccination, time, and transmission intensity. RESULTS Over time, incidence decreased in the control group and increased in the vaccine group. Three-dose efficacy in the lowest-transmission-intensity group (0.25 cases per person-year [CPPY]) decreased from 88.2% to 15.0% over 4.5 years, compared with 81.6% to -27.7% in the highest-transmission-intensity group (3 CPPY). CONCLUSIONS These findings suggest that interventions, including the fourth RTS,S dose, that protect vaccinated individuals during the potential rebound period should be implemented for high-transmission settings.
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Affiliation(s)
- Griffin J Bell
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Varun Goel
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Paulin Essone
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - David Dosoo
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Bright Adu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Kenneth Wiru
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Fabrice Mougeni
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Musah Osei
- Kintampo Health Research Centre, Kintampo, Ghana
| | - Pamela Minsoko
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
| | - Cyrus Sinai
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Karamoko Niaré
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | - Jonathan J Juliano
- Division of Infectious Diseases, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Michael Hudgens
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Legon, Ghana
| | | | | | - Selidji Todagbe Agnandji
- Centre de Recherches Médicales de Lambaréné, Lambaréné, Gabon
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jeffrey A Bailey
- Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island, USA
| | | | - Michael Emch
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina, USA
- Carolina Population Center, University of North Carolina, Chapel Hill, North Carolina, USA
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Naung MT, Martin E, Munro J, Mehra S, Guy AJ, Laman M, Harrison GLA, Tavul L, Hetzel M, Kwiatkowski D, Mueller I, Bahlo M, Barry AE. Global diversity and balancing selection of 23 leading Plasmodium falciparum candidate vaccine antigens. PLoS Comput Biol 2022; 18:e1009801. [PMID: 35108259 PMCID: PMC8843232 DOI: 10.1371/journal.pcbi.1009801] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 02/14/2022] [Accepted: 01/03/2022] [Indexed: 12/30/2022] Open
Abstract
Investigation of the diversity of malaria parasite antigens can help prioritize and validate them as vaccine candidates and identify the most common variants for inclusion in vaccine formulations. Studies of vaccine candidates of the most virulent human malaria parasite, Plasmodium falciparum, have focused on a handful of well-known antigens, while several others have never been studied. Here we examine the global diversity and population structure of leading vaccine candidate antigens of P. falciparum using the MalariaGEN Pf3K (version 5.1) resource, comprising more than 2600 genomes from 15 malaria endemic countries. A stringent variant calling pipeline was used to extract high quality antigen gene 'haplotypes' from the global dataset and a new R-package named VaxPack was used to streamline population genetic analyses. In addition, a newly developed algorithm that enables spatial averaging of selection pressure on 3D protein structures was applied to the dataset. We analysed the genes encoding 23 leading and novel candidate malaria vaccine antigens including csp, trap, eba175, ama1, rh5, and CelTOS. Our analysis shows that current malaria vaccine formulations are based on rare haplotypes and thus may have limited efficacy against natural parasite populations. High levels of diversity with evidence of balancing selection was detected for most of the erythrocytic and pre-erythrocytic antigens. Measures of natural selection were then mapped to 3D protein structures to predict targets of functional antibodies. For some antigens, geographical variation in the intensity and distribution of these signals on the 3D structure suggests adaptation to different human host or mosquito vector populations. This study provides an essential framework for the diversity of P. falciparum antigens to be considered in the design of the next generation of malaria vaccines.
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Affiliation(s)
- Myo T. Naung
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
| | - Elijah Martin
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Jacob Munro
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Somya Mehra
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
| | - Andrew J. Guy
- School of Science, RMIT University, Melbourne, Victoria, Australia
| | - Moses Laman
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - G. L. Abby Harrison
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Livingstone Tavul
- Vector Borne Diseases Unit, Papua New Guinea Institute of Medical Research, Madang, Papua New Guinea
| | - Manuel Hetzel
- Swiss Tropical Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Dominic Kwiatkowski
- Sanger Institute, Hinxton, United Kingdom
- Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Ivo Mueller
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Division of Parasites and Insect Vectors, Pasteur Institute, Paris, France
| | - Melanie Bahlo
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
| | - Alyssa E. Barry
- Population Health and Immunity Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Carlton, Victoria, Australia
- Institute of Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Geelong, Victoria, Australia
- Life Sciences Discipline, Burnet Institute, Melbourne, Victoria, Australia
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9
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Voinson M, Nunn CL, Goldberg A. Primate malarias as a model for cross-species parasite transmission. eLife 2022; 11:e69628. [PMID: 35086643 PMCID: PMC8798051 DOI: 10.7554/elife.69628] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 01/14/2022] [Indexed: 12/16/2022] Open
Abstract
Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.
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Affiliation(s)
- Marina Voinson
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | - Charles L Nunn
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
- Duke Global Health, Duke UniversityDurhamUnited States
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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