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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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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: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [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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Schmidt F, Muecksch F, Weisblum Y, Da Silva J, Bednarski E, Cho A, Wang Z, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. Plasma neutralization properties of the SARS-CoV-2 Omicron variant. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34931199 PMCID: PMC8687470 DOI: 10.1101/2021.12.12.21267646] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The Omicron SARS-CoV-2 variant has spread internationally and is responsible for rapidly increasing case numbers. The emergence of divergent variants in the context of a heterogeneous and evolving neutralizing antibody response in host populations might compromise protection afforded by vaccines or prior infection. METHODS We measured neutralizing antibody titers in 169 longitudinally collected plasma samples using pseudotypes bearing the Wuhan-hu-1 or the Omicron variant or a laboratory-designed neutralization-resistant SARS-CoV-2 spike (PMS20). Plasmas were obtained from convalescents who did or did not subsequently receive an mRNA vaccine, or naive individuals who received 3-doses of mRNA or 1-dose Ad26 vaccines. Samples were collected approximately 1, 5–6 and 12 months after initial vaccination or infection. RESULTS Like PMS20, the Omicron spike protein was substantially resistant to neutralization compared to Wuhan-hu-1. In convalescent plasma the median deficit in neutralizing activity against PMS20 or Omicron was 30- to 60-fold. Plasmas from recipients of 2 mRNA vaccine doses were 30- to 180- fold less potent against PMS20 and Omicron than Wuhan-hu-1. Notably, previously infected or two-mRNA dose vaccinated individuals who received additional mRNA vaccine dose(s) had 38 to 154-fold and 35 to 214-fold increases in neutralizing activity against Omicron and PMS20 respectively. CONCLUSIONS Omicron exhibits similar distribution of sequence changes and neutralization resistance as does a laboratory-designed neutralization-resistant spike protein, suggesting natural evolutionary pressure to evade the human antibody response. Currently available mRNA vaccine boosters, that may promote antibody affinity maturation, significantly ameliorate SARS-CoV-2 neutralizing antibody titers.
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Affiliation(s)
- Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Justin Da Silva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA.,Howard Hughes Medical Institute
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Schmidt F, Weisblum Y, Rutkowska M, Poston D, DaSilva J, Zhang F, Bednarski E, Cho A, Schaefer-Babajew DJ, Gaebler C, Caskey M, Nussenzweig MC, Hatziioannou T, Bieniasz PD. High genetic barrier to SARS-CoV-2 polyclonal neutralizing antibody escape. Nature 2021; 600:512-516. [PMID: 34544114 PMCID: PMC9241107 DOI: 10.1038/s41586-021-04005-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/07/2021] [Indexed: 11/08/2022]
Abstract
The number and variability of the neutralizing epitopes targeted by polyclonal antibodies in individuals who are SARS-CoV-2 convalescent and vaccinated are key determinants of neutralization breadth and the genetic barrier to viral escape1-4. Using HIV-1 pseudotypes and plasma selection experiments with vesicular stomatitis virus/SARS-CoV-2 chimaeras5, here we show that multiple neutralizing epitopes, within and outside the receptor-binding domain, are variably targeted by human polyclonal antibodies. Antibody targets coincide with spike sequences that are enriched for diversity in natural SARS-CoV-2 populations. By combining plasma-selected spike substitutions, we generated synthetic 'polymutant' spike protein pseudotypes that resisted polyclonal antibody neutralization to a similar degree as circulating variants of concern. By aggregating variant of concern-associated and antibody-selected spike substitutions into a single polymutant spike protein, we show that 20 naturally occurring mutations in the SARS-CoV-2 spike protein are sufficient to generate pseudotypes with near-complete resistance to the polyclonal neutralizing antibodies generated by individuals who are convalescent or recipients who received an mRNA vaccine. However, plasma from individuals who had been infected and subsequently received mRNA vaccination neutralized pseudotypes bearing this highly resistant SARS-CoV-2 polymutant spike, or diverse sarbecovirus spike proteins. Thus, optimally elicited human polyclonal antibodies against SARS-CoV-2 should be resilient to substantial future SARS-CoV-2 variation and may confer protection against potential future sarbecovirus pandemics.
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Affiliation(s)
- Fabian Schmidt
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Yiska Weisblum
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Magdalena Rutkowska
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
| | - Daniel Poston
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Justin DaSilva
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Fengwen Zhang
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Eva Bednarski
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA
| | - Alice Cho
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Christian Gaebler
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Marina Caskey
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | - Michel C Nussenzweig
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY, USA.
- Howard Hughes Medical Institute, The Rockefeller University, New York, NY, USA.
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Van Rompay KKA, Olstad KJ, Sammak RL, Dutra J, Watanabe JK, Usachenko JL, Immareddy R, Roh JW, Verma A, Shaan Lakshmanappa Y, Schmidt BA, Di Germanio C, Rizvi N, Stone M, Simmons G, Dumont LJ, Allen AM, Lockwood S, Pollard RE, de Assis RR, Yee JL, Nham PB, Ardeshir A, Deere JD, Patterson J, Jain A, Felgner PL, Iyer SS, Hartigan-O'Connor DJ, Busch MP, Reader JR. Early post-infection treatment of SARS-CoV-2 infected macaques with human convalescent plasma with high neutralizing activity reduces lung inflammation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.09.01.458520. [PMID: 34494025 DOI: 10.1101/2021.08.06.455491] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
UNLABELLED Early in the SARS-CoV-2 pandemic, there was a high level of optimism based on observational studies and small controlled trials that treating hospitalized patients with convalescent plasma from COVID-19 survivors (CCP) would be an important immunotherapy. However, as more data from controlled trials became available, the results became disappointing, with at best moderate evidence of efficacy when CCP with high titers of neutralizing antibodies was used early in infection. To better understand the potential therapeutic efficacy of CCP, and to further validate SARS-CoV-2 infection of macaques as a reliable animal model for testing such strategies, we inoculated 12 adult rhesus macaques with SARS-CoV-2 by intratracheal and intranasal routes. One day later, 8 animals were infused with pooled human CCP with a high titer of neutralizing antibodies (RVPN NT 50 value of 3,003), while 4 control animals received normal human plasma. Animals were monitored for 7 days. Animals treated with CCP had detectable levels of antiviral antibodies after infusion. In comparison to the control animals, they had similar levels of virus replication in the upper and lower respiratory tract, but had significantly reduced interstitial pneumonia, as measured by comprehensive lung histology. By highlighting strengths and weaknesses, data of this study can help to further optimize nonhuman primate models to provide proof-of-concept of intervention strategies, and guide the future use of convalescent plasma against SARS-CoV-2 and potentially other newly emerging respiratory viruses. AUTHOR SUMMARY The results of treating SARS-CoV-2 infected hospitalized patients with COVID-19 convalescent plasma (CCP), collected from survivors of natural infection, have been disappointing. The available data from various studies indicate at best moderate clinical benefits only when CCP with high titer of neutralizing antibodies was infused early in infection. The macaque model of SARS-CoV-2 infection can be useful to gain further insights in the value of CCP therapy. In this study, animals were infected with SARS-CoV-2 and the next day, were infused with pooled human convalescent plasma, selected to have a very high titer of neutralizing antibodies. While administration of CCP did not result in a detectable reduction in virus replication in the respiratory tract, it significantly reduced lung inflammation. These data, combined with the results of monoclonal antibody studies, emphasize the need to use products with high titers of neutralizing antibodies, and guide the future development of CCP-based therapies.
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Affiliation(s)
- Koen K A Van Rompay
- California National Primate Research Center, University of California, Davis, CA 95616
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA 95616
| | - Katherine J Olstad
- California National Primate Research Center, University of California, Davis, CA 95616
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA 95616
| | - Rebecca L Sammak
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Joseph Dutra
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
| | - Jennifer K Watanabe
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Jodie L Usachenko
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Ramya Immareddy
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Jamin W Roh
- Center for Immunology and Infectious Diseases, University of California, Davis, CA 95616
- Graduate Group in Immunology, University of California, Davis, CA 95616
| | - Anil Verma
- Center for Immunology and Infectious Diseases, University of California, Davis, CA 95616
| | | | - Brian A Schmidt
- Center for Immunology and Infectious Diseases, University of California, Davis, CA 95616
| | | | - Nabeela Rizvi
- Vitalant Research Institute, San Francisco, CA 94118
| | - Mars Stone
- Vitalant Research Institute, San Francisco, CA 94118
| | | | - Larry J Dumont
- Vitalant Research Institute, Denver, CO 80230; University of Colorado School of Medicine, Aurora, CO 80045
| | - A Mark Allen
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Sarah Lockwood
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Rachel E Pollard
- School of Veterinary Medicine, University of California, Davis, CA 95616
| | - Rafael Ramiro de Assis
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697
| | - JoAnn L Yee
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Peter B Nham
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Amir Ardeshir
- California National Primate Research Center, University of California, Davis, CA 95616
| | - Jesse D Deere
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
| | - Jean Patterson
- Translational Research Section, Virology Branch, DMID/NIAID/NIH, MD 20852
| | - Aarti Jain
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697
| | - Philip L Felgner
- Vaccine Research and Development Center, Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697
| | - Smita S Iyer
- California National Primate Research Center, University of California, Davis, CA 95616
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA 95616
- Center for Immunology and Infectious Diseases, University of California, Davis, CA 95616
| | - Dennis J Hartigan-O'Connor
- California National Primate Research Center, University of California, Davis, CA 95616
- Department of Medical Microbiology and Immunology, School of Medicine, University of California, Davis, CA 95616
| | - Michael P Busch
- Vitalant Research Institute, San Francisco, CA 94118
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA, 94118
| | - J Rachel Reader
- California National Primate Research Center, University of California, Davis, CA 95616
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA 95616
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Sequeiros-Borja CE, Surpeta B, Brezovsky J. Recent advances in user-friendly computational tools to engineer protein function. Brief Bioinform 2021; 22:bbaa150. [PMID: 32743637 PMCID: PMC8138880 DOI: 10.1093/bib/bbaa150] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/16/2020] [Indexed: 12/14/2022] Open
Abstract
Progress in technology and algorithms throughout the past decade has transformed the field of protein design and engineering. Computational approaches have become well-engrained in the processes of tailoring proteins for various biotechnological applications. Many tools and methods are developed and upgraded each year to satisfy the increasing demands and challenges of protein engineering. To help protein engineers and bioinformaticians navigate this emerging wave of dedicated software, we have critically evaluated recent additions to the toolbox regarding their application for semi-rational and rational protein engineering. These newly developed tools identify and prioritize hotspots and analyze the effects of mutations for a variety of properties, comprising ligand binding, protein-protein and protein-nucleic acid interactions, and electrostatic potential. We also discuss notable progress to target elusive protein dynamics and associated properties like ligand-transport processes and allosteric communication. Finally, we discuss several challenges these tools face and provide our perspectives on the further development of readily applicable methods to guide protein engineering efforts.
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Affiliation(s)
- Carlos Eduardo Sequeiros-Borja
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Bartłomiej Surpeta
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Jan Brezovsky
- Laboratory of Biomolecular Interactions and Transport, Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University and the International Institute of Molecular and Cell Biology in Warsaw
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