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Miellet WR, Mariman R, van Veldhuizen J, Badoux P, Wijmenga-Monsuur AJ, Litt D, Bosch T, Miller E, Fry NK, van Houten MA, Rots NY, Sanders EAM, Trzciński K. Impact of age on pneumococcal colonization of the nasopharynx and oral cavity: an ecological perspective. ISME COMMUNICATIONS 2024; 4:ycae002. [PMID: 38390521 PMCID: PMC10881297 DOI: 10.1093/ismeco/ycae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Pneumococcal carriage studies have suggested that pneumococcal colonization in adults is largely limited to the oral cavity and oropharynx. In this study, we used total abundance-based β-diversity (dissimilarity) and β-diversity components to characterize age-related differences in pneumococcal serotype composition of respiratory samples. quantitative PCR (qPCR) was applied to detect pneumococcal serotypes in nasopharyngeal samples collected from 946 toddlers and 602 adults, saliva samples collected from a subset of 653 toddlers, and saliva and oropharyngeal samples collected from a subset of 318 adults. Bacterial culture rates from nasopharyngeal samples were used to characterize age-related differences in rates of colonizing bacteria. Dissimilarity in pneumococcal serotype composition was low among saliva and nasopharyngeal samples from children. In contrast, respiratory samples from adults exhibited high serotype dissimilarity, which predominantly consisted of abundance gradients and was associated with reduced nasopharyngeal colonization. Age-related serotype dissimilarity was high among nasopharyngeal samples and relatively low for saliva samples. Reduced nasopharyngeal colonization by pneumococcal serotypes coincided with significantly reduced Moraxella catarrhalis and Haemophilus influenzae and increased Staphylococcus aureus nasopharyngeal colonization rates among adults. Findings from this study suggest that within-host environmental conditions, utilized in the upper airways by pneumococcus and other bacteria, undergo age-related changes. It may result in a host-driven ecological succession of bacterial species colonizing the nasopharynx and lead to competitive exclusion of pneumococcus from the nasopharynx but not from the oral habitat. This explains the poor performance of nasopharyngeal samples for pneumococcal carriage among adults and indicates that in adults saliva more accurately represents the epidemiology of pneumococcal carriage than nasopharyngeal samples.
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Affiliation(s)
- Willem R Miellet
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht (UMCU), Wilhelmina Children's Hospital, Utrecht, 3584 CX, The Netherlands
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Rob Mariman
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Janieke van Veldhuizen
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Paul Badoux
- Regional Laboratory of Public Health (Streeklab) Haarlem, Haarlem, 2035 RC, The Netherlands
| | - Alienke J Wijmenga-Monsuur
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - David Litt
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU) and Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | - Thijs Bosch
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Elizabeth Miller
- School of Hygiene and Tropical Medicine, Department of Infectious Disease Epidemiology, London, WC1E 7HT, United Kingdom
| | - Norman K Fry
- Respiratory and Vaccine Preventable Bacterial Reference Unit (RVPBRU) and Immunisation and Vaccine Preventable Diseases Division, UK Health Security Agency, London, NW9 5EQ, United Kingdom
| | | | - Nynke Y Rots
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Elisabeth A M Sanders
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht (UMCU), Wilhelmina Children's Hospital, Utrecht, 3584 CX, The Netherlands
- Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment (RIVM), Bilthoven, 3721 MA, The Netherlands
| | - Krzysztof Trzciński
- Department of Pediatric Immunology and Infectious Diseases, University Medical Center Utrecht (UMCU), Wilhelmina Children's Hospital, Utrecht, 3584 CX, The Netherlands
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2
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Miah SMS, Lelias S, Gutierrez AH, McAllister M, Boyle CM, Moise L, De Groot AS. A SARS-CoV-2 NSP7 homolog of a Treg epitope suppresses CD4+ and CD8+ T cell memory responses. Front Immunol 2023; 14:1290688. [PMID: 38124752 PMCID: PMC10731459 DOI: 10.3389/fimmu.2023.1290688] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 11/03/2023] [Indexed: 12/23/2023] Open
Abstract
Pathogens escape host defenses by T-cell epitope mutation or deletion (immune escape) and by simulating the appearance of human T cell epitopes (immune camouflage). We identified a highly conserved, human-like T cell epitope in non-structural protein 7 (NSP7) of SARS-CoV-2, RNA-dependent RNA polymerase (RdRp) hetero-tetramer complex. Remarkably, this T cell epitope has significant homology to a T regulatory cell epitope (Tregitope) previously identified in the Fc region of human immunoglobulin G (IgG) (Tregitope 289). We hypothesized that the SARS-CoV-2 NSP7 epitope (NSP7-289) may induce suppressive responses by engaging and activating pre-existing regulatory T cells. We therefore compared NSP7-289 and IgG Tregitopes (289 and 289z, a shorter version of 289 that isolates the shared NSP7 epitope) in vitro. Tregitope peptides 289, 289z and NSP7-289 bound to multiple HLA-DRB1 alleles in vitro and suppressed CD4+ and CD8+ T cell memory responses. Identification and in vitro validation of SARS-CoV-2 NSP7-289 provides further evidence of immune camouflage and suggests that pathogens can use human-like epitopes to evade immune response and potentially enhance host tolerance. Further exploration of the role of cross-conserved Tregs in human immune responses to pathogens such as SARS-CoV-2 is warranted.
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Affiliation(s)
| | | | | | | | | | | | - Anne S. De Groot
- EpiVax, Inc., Providence, RI, United States
- Center for Vaccines and Immunology, University of Georgia, Athens, GA, United States
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3
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Zinck CB, Thampy PR, Rego ROM, Brisson D, Ogden NH, Voordouw M. Borrelia burgdorferi strain and host sex influence pathogen prevalence and abundance in the tissues of a laboratory rodent host. Mol Ecol 2022; 31:5872-5888. [PMID: 36112076 DOI: 10.1111/mec.16694] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 01/13/2023]
Abstract
Experimental infections with different pathogen strains give insight into pathogen life history traits. The purpose of the present study was to compare variation in tissue infection prevalence and spirochete abundance among strains of Borrelia burgdorferi in a rodent host (Mus musculus, C3H/HeJ). Male and female mice were experimentally infected via tick bite with one of 12 strains. Ear tissue biopsies were taken at days 29, 59 and 89 postinfection, and seven tissues were collected at necropsy. The presence and abundance of spirochetes in the mouse tissues were measured by quantitative polymerase chain reaction. To determine the frequencies of our strains in nature, their multilocus sequence types were matched to published data sets. For the infected mice, 56.6% of the tissues were infected with B. burgdorferi. The mean spirochete load in the mouse necropsy tissues varied 4.8-fold between the strains. The mean spirochete load in the ear tissue biopsies decreased rapidly over time for some strains. The percentage of infected tissues in male mice (65.4%) was significantly higher compared to female mice (50.5%). The mean spirochete load in the seven tissues was 1.5× higher in male mice compared to female mice; this male bias was 15.3× higher in the ventral skin. Across the 11 strains, the mean spirochete loads in the infected mouse tissues were positively correlated with the strain-specific frequencies in their tick vector populations. The study suggests that laboratory-based estimates of pathogen abundance in host tissues can predict the strain composition of this important tick-borne pathogen in nature.
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Affiliation(s)
- Christopher B Zinck
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Prasobh Raveendran Thampy
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Ryan O M Rego
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Dustin Brisson
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nicholas H Ogden
- Public Health Risk Sciences, National Microbiology Laboratory, Public Health Agency of Canada, St Hyacinthe, Quebec, Canada
- Groupe de Recherche en Épidémiologie des Zoonoses et Santé Publique (GREZOSP), Faculté de Médecine Vétérinaire, and Centre de Recherche en Santé Publique (CReSP), Université de Montréal, Montreal, Quebec, Canada
| | - Maarten Voordouw
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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4
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López-Valiñas Á, Baioni L, Córdoba L, Darji A, Chiapponi C, Segalés J, Ganges L, Núñez JI. Evolution of Swine Influenza Virus H3N2 in Vaccinated and Nonvaccinated Pigs after Previous Natural H1N1 Infection. Viruses 2022; 14:v14092008. [PMID: 36146814 PMCID: PMC9505157 DOI: 10.3390/v14092008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 08/20/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Swine influenza viruses (SIV) produce a highly contagious and worldwide distributed disease that can cause important economic losses to the pig industry. Currently, this virus is endemic in farms and, although used limitedly, trivalent vaccine application is the most extended strategy to control SIV. The presence of pre-existing immunity against SIV may modulate the evolutionary dynamic of this virus. To better understand these dynamics, the viral variants generated in vaccinated and nonvaccinated H3N2 challenged pigs after recovery from a natural A(H1N1) pdm09 infection were determined and analyzed. In total, seventeen whole SIV genomes were determined, 6 from vaccinated, and 10 from nonvaccinated animals and their inoculum, by NGS. Herein, 214 de novo substitutions were found along all SIV segments, 44 of them being nonsynonymous ones with an allele frequency greater than 5%. Nonsynonymous substitutions were not found in NP; meanwhile, many of these were allocated in PB2, PB1, and NS1 proteins. Regarding HA and NA proteins, higher nucleotide diversity, proportionally more nonsynonymous substitutions with an allele frequency greater than 5%, and different domain allocations of mutants, were observed in vaccinated animals, indicating different evolutionary dynamics. This study highlights the rapid adaptability of SIV in different environments.
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Affiliation(s)
- Álvaro López-Valiñas
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
| | - Laura Baioni
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, 25124 Brescia, Italy
| | - Lorena Córdoba
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
| | - Ayub Darji
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
| | - Chiara Chiapponi
- WOAH Reference Laboratory for Swine Influenza, Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia-Romagna, 25124 Brescia, Italy
| | - Joaquim Segalés
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Llilianne Ganges
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
- WOAH Reference Laboratory for Classical Swine Fever, IRTA-CReSA, 08193 Barcelona, Spain
| | - José I. Núñez
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- Unitat Mixta d’Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193 Barcelona, Spain
- WOAH Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Barcelona, Spain
- Correspondence:
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5
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Nath A, Bhattacharjee R, Nandi A, Sinha A, Kar S, Manoharan N, Mitra S, Mojumdar A, Panda PK, Patro S, Dutt A, Ahuja R, Verma SK, Suar M. Phage delivered CRISPR-Cas system to combat multidrug-resistant pathogens in gut microbiome. Biomed Pharmacother 2022; 151:113122. [PMID: 35594718 DOI: 10.1016/j.biopha.2022.113122] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/08/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022] Open
Abstract
The Host-microbiome interactions that exist inside the gut microbiota operate in a synergistic and abnormal manner. Additionally, the normal homeostasis and functioning of gut microbiota are frequently disrupted by the intervention of Multi-Drug Resistant (MDR) pathogens. CRISPR-Cas (CRISPR-associated protein with clustered regularly interspersed short palindromic repeats) recognized as a prokaryotic immune system has emerged as an effective genome-editing tool to edit and delete specific microbial genes for the expulsion of bacteria through bactericidal action. In this review, we demonstrate many functioning CRISPR-Cas systems against the anti-microbial resistance of multiple pathogens, which infiltrate the gastrointestinal tract. Moreover, we discuss the advancement in the development of a phage-delivered CRISPR-Cas system for killing a gut MDR pathogen. We also discuss a combinatorial approach to use bacteriophage as a delivery system for the CRISPR-Cas gene for targeting a pathogenic community in the gut microbiome to resensitize the drug sensitivity. Finally, we discuss engineered phage as a plausible potential option for the CRISPR-Cas system for pathogenic killing and improvement of the efficacy of the system.
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Affiliation(s)
- Arijit Nath
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Rahul Bhattacharjee
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Aditya Nandi
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Adrija Sinha
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Sulagna Kar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | | | - Shirsajit Mitra
- KaviKrishna Laboratory, Indian Institute of Technology, Guwahati, Assam, India
| | - Abhik Mojumdar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Swadheena Patro
- KIIT School of Dental Sciences, KIIT University. Bhubaneswar 751024, Odisha
| | - Ateet Dutt
- Instituto de Investigaciones en Materiales, UNAM, CDMX, Mexico
| | - Rajeev Ahuja
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Suresh K Verma
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden.
| | - Mrutyunjay Suar
- KIIT School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India.
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6
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Shantal CJN, Juan CC, Lizbeth BUS, Carlos HGJ, Estela GPB. Candida glabrata is a successful pathogen: an artist manipulating the immune response. Microbiol Res 2022; 260:127038. [DOI: 10.1016/j.micres.2022.127038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 04/02/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023]
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7
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Lin YP, Tufts DM, Combs M, Dupuis AP, Marcinkiewicz AL, Hirsbrunner AD, Diaz AJ, Stout JL, Blom AM, Strle K, Davis AD, Kramer LD, Kolokotronis SO, Diuk-Wasser MA. Cellular and immunological mechanisms influence host-adapted phenotypes in a vector-borne microparasite. Proc Biol Sci 2022; 289:20212087. [PMID: 35193398 PMCID: PMC8864362 DOI: 10.1098/rspb.2021.2087] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Predicting pathogen emergence and spillover risk requires understanding the determinants of a pathogens' host range and the traits involved in host competence. While host competence is often considered a fixed species-specific trait, it may be variable if pathogens diversify across hosts. Balancing selection can lead to maintenance of pathogen polymorphisms (multiple-niche-polymorphism; MNP). The causative agent of Lyme disease, Borrelia burgdorferi (Bb), provides a model to study the evolution of host adaptation, as some Bb strains defined by their outer surface protein C (ospC) genotype, are widespread in white-footed mice and others are associated with non-rodent vertebrates (e.g. birds). To identify the mechanisms underlying potential strain × host adaptation, we infected American robins and white-footed mice, with three Bb strains of different ospC genotypes. Bb burdens varied by strain in a host-dependent fashion, and strain persistence in hosts largely corresponded to Bb survival at early infection stages and with transmission to larvae (i.e. fitness). Early survival phenotypes are associated with cell adhesion, complement evasion and/or inflammatory and antibody-mediated removal of Bb, suggesting directional selective pressure for host adaptation and the potential role of MNP in maintaining OspC diversity. Our findings will guide future investigations to inform eco-evolutionary models of host adaptation for microparasites.
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Affiliation(s)
- Yi-Pin Lin
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA,Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Danielle M. Tufts
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA,Infectious Diseases and Microbiology Department, University of Pittsburgh, Pittsburgh, PA, USA
| | - Matthew Combs
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
| | - Alan P. Dupuis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | | | | | - Alexander J. Diaz
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Jessica L. Stout
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Anna M. Blom
- Division of Medical Protein Chemistry, Department of Translational Medicine, Lund University, Malmo, Sweden
| | - Klemen Strle
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA,Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - April D. Davis
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA
| | - Laura D. Kramer
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA,Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA
| | - Sergios-Orestis Kolokotronis
- Department of Epidemiology and Biostatistics, School of Public Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA,Institute for Genomic Health, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA,Division of Infectious Diseases, Department of Medicine, College of Medicine, SUNY Downstate Health Sciences University, Brooklyn, NY, USA
| | - Maria A. Diuk-Wasser
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA
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8
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Miller ZR, Allesina S. Metapopulations with habitat modification. Proc Natl Acad Sci U S A 2021; 118:e2109896118. [PMID: 34857638 PMCID: PMC8670473 DOI: 10.1073/pnas.2109896118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 11/18/2022] Open
Abstract
Across the tree of life, organisms modify their local environment, rendering it more or less hospitable for other species. Despite the ubiquity of these processes, simple models that can be used to develop intuitions about the consequences of widespread habitat modification are lacking. Here, we extend the classic Levins metapopulation model to a setting where each of n species can colonize patches connected by dispersal, and when patches are vacated via local extinction, they retain a "memory" of the previous occupant-modeling habitat modification. While this model can exhibit a wide range of dynamics, we draw several overarching conclusions about the effects of modification and memory. In particular, we find that any number of species may potentially coexist, provided that each is at a disadvantage when colonizing patches vacated by a conspecific. This notion is made precise through a quantitative stability condition, which provides a way to unify and formalize existing conceptual models. We also show that when patch memory facilitates coexistence, it generically induces a positive relationship between diversity and robustness (tolerance of disturbance). Our simple model provides a portable, tractable framework for studying systems where species modify and react to a shared landscape.
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Affiliation(s)
- Zachary R Miller
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637;
| | - Stefano Allesina
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637
- Northwestern Institute on Complex Systems, Northwestern University, Evanston, IL 60208
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9
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Betti M, Bragazzi N, Heffernan J, Kong J, Raad A. Could a New COVID-19 Mutant Strain Undermine Vaccination Efforts? A Mathematical Modelling Approach for Estimating the Spread of B.1.1.7 Using Ontario, Canada, as a Case Study. Vaccines (Basel) 2021; 9:592. [PMID: 34204918 PMCID: PMC8227606 DOI: 10.3390/vaccines9060592] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/23/2022] Open
Abstract
Infections represent highly dynamic processes, characterized by evolutionary changes and events that involve both the pathogen and the host. Among infectious agents, viruses, such as Severe Acute Respiratory Syndrome-related Coronavirus type 2 (SARS-CoV-2), the infectious agent responsible for the currently ongoing Coronavirus disease 2019 (COVID-2019) pandemic, have a particularly high mutation rate. Taking into account the mutational landscape of an infectious agent, it is important to shed light on its evolution capability over time. As new, more infectious strains of COVID-19 emerge around the world, it is imperative to estimate when these new strains may overtake the wild-type strain in different populations. Therefore, we developed a general-purpose framework to estimate the time at which a mutant variant is able to take over a wild-type strain during an emerging infectious disease outbreak. In this study, we used COVID-19 as a case-study; however, the model is adaptable to any emerging pathogen. We devised a two-strain mathematical framework to model a wild- and a mutant-type viral population and fit cumulative case data to parameterize the model, using Ontario as a case study. We found that, in the context of under-reporting and the current case levels, a variant strain was unlikely to dominate until March/April 2021. The current non-pharmaceutical interventions in Ontario need to be kept in place longer even with vaccination in order to prevent another outbreak. The spread of a variant strain in Ontario will likely be observed by a widened peak of the daily reported cases. If vaccine efficacy is maintained across strains, then it is still possible to achieve high levels of immunity in the population by the end of 2021. Our findings have important practical implications in terms of public health as policy- and decision-makers are equipped with a mathematical tool that can enable the estimation of the take-over of a mutant strain of an emerging infectious disease.
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Affiliation(s)
- Mattew Betti
- Department of Mathematics and Computer Science, Mount Allison University, Sackville, NB E4L 1E2, Canada
| | - Nicola Bragazzi
- Department of Mathematics and Statistics, York University, Toronto, ON M3J 1P3, Canada; (N.B.); (J.H.); (J.K.); (A.R.)
- Laboratory for Industrial and Applied Mathematics, York University, Toronto, ON M3J 1P3, Canada
| | - Jane Heffernan
- Department of Mathematics and Statistics, York University, Toronto, ON M3J 1P3, Canada; (N.B.); (J.H.); (J.K.); (A.R.)
- Centre for Disease Modeling, York University, Toronto, ON M3J 1P3, Canada
| | - Jude Kong
- Department of Mathematics and Statistics, York University, Toronto, ON M3J 1P3, Canada; (N.B.); (J.H.); (J.K.); (A.R.)
- Centre for Disease Modeling, York University, Toronto, ON M3J 1P3, Canada
| | - Angie Raad
- Department of Mathematics and Statistics, York University, Toronto, ON M3J 1P3, Canada; (N.B.); (J.H.); (J.K.); (A.R.)
- Centre for Disease Modeling, York University, Toronto, ON M3J 1P3, Canada
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10
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Cámara M, Sánchez-Mata MC, Fernández-Ruiz V, Cámara RM, Cebadera E, Domínguez L. A Review of the Role of Micronutrients and Bioactive Compounds on Immune System Supporting to Fight against the COVID-19 Disease. Foods 2021; 10:foods10051088. [PMID: 34068930 PMCID: PMC8155867 DOI: 10.3390/foods10051088] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023] Open
Abstract
Micronutrients are critical for an adequate function of the immune system and play a vital role in promoting health and nutritional well-being. The present work is aimed at reviewing (1) the role of micronutrients in helping the immune system to fight against the COVID-19 disease through the diet with food or food supplements and (2) the potential use of food health claims regarding immune function according to the European Food Safety Authority (EFSA) requirements. Till date, there are some health claims authorized by the European Commission that refer to the role of certain essential nutrients (vitamins B6, B9, B12, A, D, C, and Cu, Fe, Se) to contribute to the proper functioning of the immune system. Vitamins D, C, Zn, and Se, have been thoroughly studied as a strategy to improve the immune system to fight against COVID-19 disease. From all the micronutrients, Vitamin D is the one with more scientific evidence suggesting positive effects against COVID-19 disease as it is linked to a reduction of infection rates, as well as an improved outcomes in patients. To validate scientific evidence, different clinical trials are ongoing currently, with promising preliminary results although inconclusive yet.
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Affiliation(s)
- Montaña Cámara
- Correspondence: ; Tel.: +34-91-394-1802; Fax: +34-91-394-1799
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11
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Harrow GL, Lees JA, Hanage WP, Lipsitch M, Corander J, Colijn C, Croucher NJ. Negative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures. THE ISME JOURNAL 2021; 15:1523-1538. [PMID: 33408365 PMCID: PMC8115253 DOI: 10.1038/s41396-020-00867-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 02/06/2023]
Abstract
Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.
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Affiliation(s)
- Gabrielle L Harrow
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Jukka Corander
- Department of Biostatistics, University of Oslo, Oslo, Norway
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Caroline Colijn
- Parasites & Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, W2 1PG, UK.
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12
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Temporal Dominance of B.1.1.7 over B.1.354 SARS-CoV-2 Variant: A Hypothesis Based on Areas of Variant Co-Circulation. Life (Basel) 2021; 11:life11050375. [PMID: 33921938 PMCID: PMC8143446 DOI: 10.3390/life11050375] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/17/2021] [Accepted: 04/19/2021] [Indexed: 11/29/2022] Open
Abstract
Some emergent SARS-CoV-2 variants raise concerns due to their altered biological properties. For both B.1.1.7 and B.1351 variants, named as variants of concern (VOC), increased transmissibility was reported, whereas B.1.351 was more resistant to multiple monoclonal antibodies (mAbs), as well as convalescent and vaccination sera. To test this hypothesis, we examined the proportion of VOC over time across different geographic areas where the two VOC, B.1.1.7 and B.1.351, co-circulate. Our comparative analysis was based on the number of SARS-CoV-2 sequences on GISAID database. We report that B.1.1.7 dominates over B.1.351 in geographic areas where both variants co-circulate and the B.1.1.7 was the first variant introduced in the population. The only areas where B.1.351 was detected at higher proportion were South Africa and Mayotte in Africa, where this strain was associated with increased community transmission before the detection of B.1.1.7. The dominance of B.1.1.7 over B.1.351 could be important since B.1.351 was more resistant to certain mAbs, as well as heterologous convalescent and vaccination sera, thus suggesting that it may be transmitted more effectively in people with pre-existing immunity to other VOC. This scenario would lessen the effectiveness of vaccine and urge the need to update them with new strains.
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13
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Lu G, Shan S, Zainab B, Ayaz Z, He J, Xie Z, Rashid U, Zhang D, Mehmood Abbasi A. Novel vaccine design based on genomics data analysis: A review. Scand J Immunol 2021; 93:e12986. [PMID: 33043473 DOI: 10.1111/sji.12986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/04/2020] [Accepted: 10/05/2020] [Indexed: 12/28/2022]
Abstract
Modification of pathogenic strains with the passage of time is responsible for evolution in the timeline of vaccine development for last 30 years. Recent advancements in computational vaccinology on the one hand and genome sequencing approaches on the other have generated new hopes in vaccine development. The aim of this review was to discuss the evolution of vaccines, their characteristics and limitations. In this review, we highlighted the evolution of vaccines, from first generation to the current status, pointing out how different vaccines have emerged and different approaches that are being followed up in the development of more rational vaccines against a wide range of diseases. Data were collected using Google Scholar, Web of Science, Science Direct, Web of Knowledge, Scopus and Science Hub, whereas computational tools such as NCBI, GeneMANIA and STRING were used to analyse the pathways of vaccine action. Innovative tools, such as computational tools, recombinant technologies and intra-dermal devices, are currently being investigated in order to improve the immunological response. New technologies enlightened the interactions of host proteins with pathogenic proteins for vaccine candidate development, but still there is a need of integrating transcriptomic and proteomic approaches. Although immunization with genomics data is a successful approach, its advantages must be assessed case by case and its applicability depends on the nature of the agent to be immunized, the nature of the antigen and the type of immune response required to achieve effective protection.
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Affiliation(s)
- Guangli Lu
- Institute of Business, School of Business, Henan University, Henan, China
| | - Sharui Shan
- The First Affiliated Hospital of Jinan University (Guangzhou Overseas Chinese Hospital), Guangzhou, China
- Department of Rehabilitation, The First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Bibi Zainab
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Zainab Ayaz
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Jialiang He
- School of Food and Bioengineering, Henan University of Science and Technology, Luoyang, China
| | - Zhenxing Xie
- Basic School of Medicine, Henan University, Kaifeng, China
| | - Umer Rashid
- Department of Chemistry, COMSATS University Islamabad, Islamabad, Pakistan
| | - Dalin Zhang
- Department of Biochemistry and Molecular Medicine, UC Davis Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Arshad Mehmood Abbasi
- Department of Environmental Sciences, COMSATS University Islamabad, Islamabad, Pakistan
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14
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A Paradigm Gap in Host–Pathogen Interaction Studies: Lesson from the COVID-19 Pandemic. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1353:47-70. [DOI: 10.1007/978-3-030-85113-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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15
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Burmeister AR, Hansen E, Cunningham JJ, Rego EH, Turner PE, Weitz JS, Hochberg ME. Fighting microbial pathogens by integrating host ecosystem interactions and evolution. Bioessays 2020; 43:e2000272. [PMID: 33377530 DOI: 10.1002/bies.202000272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 11/22/2020] [Accepted: 11/30/2020] [Indexed: 12/19/2022]
Abstract
Successful therapies to combat microbial diseases and cancers require incorporating ecological and evolutionary principles. Drawing upon the fields of ecology and evolutionary biology, we present a systems-based approach in which host and disease-causing factors are considered as part of a complex network of interactions, analogous to studies of "classical" ecosystems. Centering this approach around empirical examples of disease treatment, we present evidence that successful therapies invariably engage multiple interactions with other components of the host ecosystem. Many of these factors interact nonlinearly to yield synergistic benefits and curative outcomes. We argue that these synergies and nonlinear feedbacks must be leveraged to improve the study of pathogenesis in situ and to develop more effective therapies. An eco-evolutionary systems perspective has surprising and important consequences, and we use it to articulate areas of high research priority for improving treatment strategies.
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Affiliation(s)
- Alita R Burmeister
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA
| | - Elsa Hansen
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Jessica J Cunningham
- Department of Integrated Mathematical Oncology, Moffitt Cancer Center & Research Institute, Tampa, Florida, USA
| | - E Hesper Rego
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, Connecticut, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, Michigan, USA.,Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA.,School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Michael E Hochberg
- Institute of Evolutionary Sciences, University of Montpellier, Montpellier, France.,Santa Fe Institute, Santa Fe, New Mexico, USA
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16
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Rudenko O, Engelstädter J, Barnes AC. Evolutionary epidemiology of Streptococcus iniae: Linking mutation rate dynamics with adaptation to novel immunological landscapes. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104435. [PMID: 32569744 DOI: 10.1016/j.meegid.2020.104435] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 06/10/2020] [Accepted: 06/16/2020] [Indexed: 12/11/2022]
Abstract
Pathogens continuously adapt to changing host environments where variation in their virulence and antigenicity is critical to their long-term evolutionary success. The emergence of novel variants is accelerated in microbial mutator strains (mutators) deficient in DNA repair genes, most often from mismatch repair and oxidized-guanine repair systems (MMR and OG respectively). Bacterial MMR/OG mutants are abundant in clinical samples and show increased adaptive potential in experimental infection models, yet the role of mutators in the epidemiology and evolution of infectious disease is not well understood. Here we investigated the role of mutation rate dynamics in the evolution of a broad host range pathogen, Streptococcus iniae, using a set of 80 strains isolated globally over 40 years. We have resolved phylogenetic relationships using non-recombinant core genome variants, measured in vivo mutation rates by fluctuation analysis, identified variation in major MMR/OG genes and their regulatory regions, and phenotyped the major traits determining virulence in streptococci. We found that both mutation rate and MMR/OG genotype are remarkably conserved within phylogenetic clades but significantly differ between major phylogenetic lineages. Further, variation in MMR/OG loci correlates with occurrence of atypical virulence-associated phenotypes, infection in atypical hosts (mammals), and atypical (osseous) tissue of a vaccinated primary host. These findings suggest that mutators are likely to facilitate adaptations preceding major diversification events and may promote emergence of variation permitting colonization of a novel host tissue, novel host taxa (host jumps), and immune-escape in the vaccinated host.
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Affiliation(s)
- Oleksandra Rudenko
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Jan Engelstädter
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia
| | - Andrew C Barnes
- The University of Queensland, School of Biological Sciences, St Lucia Campus, Brisbane, Queensland 4072, Australia.
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17
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Liu T, Yang Q, Wei W, Wang K, Wang E. Toll/IL-1 receptor-containing proteins STIR-1, STIR-2 and STIR-3 synergistically assist Yersinia ruckeri SC09 immune escape. FISH & SHELLFISH IMMUNOLOGY 2020; 103:357-365. [PMID: 32461169 DOI: 10.1016/j.fsi.2020.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/29/2020] [Accepted: 05/03/2020] [Indexed: 06/11/2023]
Abstract
Immune escape is a common feature of bacteria, viruses, parasites and even cancer cells. Our earlier work on an integrative and conjugative element (ICEr2) of Yersinia ruckeri SC09 demonstrated contributory roles of stir-1, stir-2 and stir-3 in bacterial toxicity and ability to code for immune evasion. Here, we further examined the ability of stir-4 in ICE (r2) and its encoded STIR-4 protein to mediate immune evasion using comparative genomic analysis. Additionally, the mechanisms underlying the synergistic activities of STIR-1, STIR-2, STIR-3 and STIR-4 in immune evasion were examined. Our results showed that STIR-4 did not contribute to bacterial toxicity, either in vivo nor in vitro, or show the ability to assist in bacterial immune escape. STIR-1, STIR-2, and STIR-3 formed heterotrimers in bacteria while facilitating immune evasion, which we speculate may be essential to maintain their stability. This discovery also partially explains the previous finding that a single gene can mediate immune evasion. Our data provide further knowledge on the distribution of ICE (r2)-like elements in bacteria, validating the prevalence of large-scale gene transfer in pathogens and its potential for enhancing virulence levels. Further studies are necessary to establish the biological significance of the ICE (r2) component.
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Affiliation(s)
- Tao Liu
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qian Yang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Wenyan Wei
- Institute of Fisheries of Chengdu Agriculture and Forestry Academy, Chengdu, China
| | - Kaiyu Wang
- Department of Basic Veterinary, Veterinary Medicine College, Sichuan Agricultural University, Chengdu, Sichuan, China; Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China.
| | - Erlong Wang
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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18
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Zutshi S, Kumar S, Chauhan P, Bansode Y, Nair A, Roy S, Sarkar A, Saha B. Anti-Leishmanial Vaccines: Assumptions, Approaches, and Annulments. Vaccines (Basel) 2019; 7:vaccines7040156. [PMID: 31635276 PMCID: PMC6963565 DOI: 10.3390/vaccines7040156] [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: 08/27/2019] [Revised: 09/24/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022] Open
Abstract
Leishmaniasis is a neglected protozoan parasitic disease that occurs in 88 countries but a vaccine is unavailable. Vaccination with live, killed, attenuated (physically or genetically) Leishmania have met with limited success, while peptide-, protein-, or DNA-based vaccines showed promise only in animal models. Here, we critically assess several technical issues in vaccination and expectation of a host-protective immune response. Several studies showed that antigen presentation during priming and triggering of the same cells in infected condition are not comparable. Altered proteolytic processing, antigen presentation, protease-susceptible sites, and intracellular expression of pathogenic proteins during Leishmania infection may vary dominant epitope selection, MHC-II/peptide affinity, and may deter the reactivation of desired antigen-specific T cells generated during priming. The robustness of the memory T cells and their functions remains a concern. Presentation of the antigens by Leishmania-infected macrophages to antigen-specific memory T cells may lead to change in the T cells' functional phenotype or anergy or apoptosis. Although cells may be activated, the peptides generated during infection may be different and cross-reactive to the priming peptides. Such altered peptide ligands may lead to suppression of otherwise active antigen-specific T cells. We critically assess these different immunological issues that led to the non-availability of a vaccine for human use.
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Affiliation(s)
| | - Sunil Kumar
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Prashant Chauhan
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Yashwant Bansode
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Arathi Nair
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
| | - Somenath Roy
- Department of Human Physiology with Community Health, Vidyasagar University, Midnapore 721102, India.
| | - Arup Sarkar
- Department of Biotechnology, Trident Academy of Creative Technology, Bhubaneswar 751024, India.
| | - Bhaskar Saha
- National Centre for Cell Science, Ganeshkhind, Pune 411007, India.
- Department of Biotechnology, Trident Academy of Creative Technology, Bhubaneswar 751024, India.
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19
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Cliff OM, Sintchenko V, Sorrell TC, Vadlamudi K, McLean N, Prokopenko M. Network properties of salmonella epidemics. Sci Rep 2019; 9:6159. [PMID: 30992488 PMCID: PMC6467889 DOI: 10.1038/s41598-019-42582-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/03/2019] [Indexed: 12/20/2022] Open
Abstract
We examine non-typhoidal Salmonella (S. Typhimurium or STM) epidemics as complex systems, driven by evolution and interactions of diverse microbial strains, and focus on emergence of successful strains. Our findings challenge the established view that seasonal epidemics are associated with random sets of co-circulating STM genotypes. We use high-resolution molecular genotyping data comprising 17,107 STM isolates representing nine consecutive seasonal epidemics in Australia, genotyped by multiple-locus variable-number tandem-repeats analysis (MLVA). From these data, we infer weighted undirected networks based on distances between the MLVA profiles, depicting epidemics as networks of individual bacterial strains. The network analysis demonstrated dichotomy in STM populations which split into two distinct genetic branches, with markedly different prevalences. This distinction revealed the emergence of dominant STM strains defined by their local network topological properties, such as centrality, while correlating the development of new epidemics with global network features, such as small-world propensity.
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Affiliation(s)
- Oliver M Cliff
- Centre for Complex Systems, Faculty of Engineering and IT, University of Sydney, Sydney, NSW, 2006, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, NSW, 2145, Australia
- University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, NSW 2006 and Westmead Institute for Medical Research, Sydney, NSW, 2145, Australia
| | - Tania C Sorrell
- Centre for Infectious Diseases and Microbiology-Public Health, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Westmead Hospital, Sydney, NSW, 2145, Australia
- University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, NSW 2006 and Westmead Institute for Medical Research, Sydney, NSW, 2145, Australia
| | - Kiranmayi Vadlamudi
- Centre for Complex Systems, Faculty of Engineering and IT, University of Sydney, Sydney, NSW, 2006, Australia
| | - Natalia McLean
- Centre for Complex Systems, Faculty of Engineering and IT, University of Sydney, Sydney, NSW, 2006, Australia
| | - Mikhail Prokopenko
- Centre for Complex Systems, Faculty of Engineering and IT, University of Sydney, Sydney, NSW, 2006, Australia.
- University of Sydney Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, NSW 2006 and Westmead Institute for Medical Research, Sydney, NSW, 2145, Australia.
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20
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Ramaiah A, Nayak S, Rakshit S, Manson AL, Abeel T, Shanmugam S, Sahoo PN, John AJUK, Sundaramurthi JC, Narayanan S, D'Souza G, von Hoegen P, Ottenhoff THM, Swaminathan S, Earl AM, Vyakarnam A. Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. Front Immunol 2019; 10:195. [PMID: 30814998 PMCID: PMC6381025 DOI: 10.3389/fimmu.2019.00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/23/2019] [Indexed: 01/26/2023] Open
Abstract
Vaccines that confer protection through induction of adaptive T-cell immunity rely on understanding T-cell epitope (TCE) evolution induced by immune escape. This is poorly understood in tuberculosis (TB), an ancient, chronic disease, where CD4 T-cell immunity is of recognized importance. We probed 905 functionally validated, curated human CD4 T cell epitopes in 79 Mycobacterium tuberculosis (Mtb) whole genomes from India. This screen resulted in identifying 64 mutated epitopes in these strains initially using a computational pipeline and subsequently verified by single nucleotide polymorphism (SNP) analysis. SNP based phylogeny revealed the 79 Mtb strains to cluster to East African Indian (EAI), Central Asian Strain (CAS), and Beijing (BEI) lineages. Eighty-nine percent of the mutated T-cell epitopes (mTCEs) identified in the 79 Mtb strains from India has not previously been reported. These mTCEs were encoded by genes with high nucleotide diversity scores including seven mTCEs encoded by six antigens in the top 10% of rapidly divergent Mtb genes encoded by these strains. Using a T cell functional assay readout, we demonstrate 62% of mTCEs tested to significantly alter CD4 T-cell IFNγ and/or IL2 secretion with associated changes in predicted HLA-DR binding affinity: the gain of function mutations displayed higher predicted HLA-DR binding affinity and conversely mutations resulting in loss of function displayed lower predicted HLA-DR binding affinity. Most mutated antigens belonged to the cell wall/cell processes, and, intermediary metabolism and respiration families though all known Mtb proteins encoded mutations. Analysis of the mTCEs in an SNP database of 5,310 global Mtb strains identified 82% mTCEs to be significantly more prevalent in Mtb strains isolated from India, including 36 mTCEs identified exclusively in strains from India. These epitopes had a significantly higher predicted binding affinity to HLA-DR alleles that were highly prevalent in India compared to HLA-DR alleles rare in India, highlighting HLA-DR maybe an important driver of these mutations. This first evidence of region-specific TCE mutations potentially employed by Mtb to escape host immunity has important implications for TB vaccine design.
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Affiliation(s)
- Arunachalam Ramaiah
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Soumya Nayak
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Srabanti Rakshit
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Abigail L Manson
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Pravat Nalini Sahoo
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | | | | | - Sujatha Narayanan
- National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - George D'Souza
- Department of Pulmonary Medicine, St. John's Research Institute, Bangalore, India
| | | | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Ashlee M Earl
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Annapurna Vyakarnam
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India.,Department of Infectious Diseases, Faculty of Life Sciences & Medicine, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
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21
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Mostowy RJ, Holt KE. Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. Trends Microbiol 2018; 26:1008-1021. [PMID: 30037568 PMCID: PMC6249986 DOI: 10.1016/j.tim.2018.06.006] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/08/2018] [Accepted: 06/22/2018] [Indexed: 12/11/2022]
Abstract
Bacterial pathogens and commensals are surrounded by diverse surface polysaccharides which include capsules and lipopolysaccharides. These carbohydrates play a vital role in bacterial ecology and interactions with the environment. Here, we review recent rapid advancements in this field, which have improved our understanding of the roles, structures, and genetics of bacterial polysaccharide antigens. Genetic loci encoding the biosynthesis of these antigens may have evolved as bacterial diversity-generating machines, driven by selection from a variety of forces, including host immunity, bacteriophages, and cell-cell interactions. We argue that the high adaptive potential of polysaccharide antigens should be taken into account in the design of polysaccharide-targeting medical interventions like conjugate vaccines and phage-based therapies.
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Affiliation(s)
- Rafał J Mostowy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, UK.
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria, Australia; The London School of Hygiene and Tropical Medicine, London, United Kingdom
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22
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Felizardo AA, Caldas IS, Mendonça AAS, Gonçalves RV, Tana FL, Almeida LA, Novaes RD. Impact of Trypanosoma cruzi infection on nitric oxide synthase and arginase expression and activity in young and elderly mice. Free Radic Biol Med 2018; 129:227-236. [PMID: 30248443 DOI: 10.1016/j.freeradbiomed.2018.09.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Revised: 08/21/2018] [Accepted: 09/20/2018] [Indexed: 12/12/2022]
Abstract
Elderly organisms are more susceptible to infectious diseases. However, the impact of aging on antiparasitic mechanisms, especially the nitric oxide pathway, is poorly understood. Using an integrated in vivo and in vitro model, we compared the severity of Trypanosoma cruzi infection in young and elderly (8 or 72 weeks old) mice. Forty C57BL/6 mice were randomized into four groups: Y-inf, young infected; Yn-inf, young uninfected; A-inf, aged infected; An-inf, aged uninfected. Parasitemia was measured daily, and animals were euthanized after 15 days of infection. Trypanosoma cruzi-induced inflammatory processes were analyzed in blood and heart samples, as well as in bone marrow-derived macrophages (BMDMs) co-cultured with splenocytes isolated from young or elderly mice. Our results indicated upregulated IgG2b and IL-17 production in elderly animals, which was not sufficient to reduce parasitemia, parasitic load and myocarditis to levels observed in young animals. The higher susceptibility of elderly mice to T. cruzi infection was accompanied by reduced cardiac inducible nitric oxide synthase (iNOS) gene expression, nitric oxide (NO) and IFN-γ levels, as well as an antagonistic upregulation of arginase-1 expression and arginase activity. The same responses were observed when BMDMs co-cultured with splenocytes from elderly mice were stimulated with T. cruzi antigens. Our findings indicate that elderly mice were more susceptible to T. cruzi infection, which was potentially related to an attenuated response to antigenic stimulation, inhibition of iNOS gene expression and NO production, and antagonistic upregulation of arginase gene expression and activity, which created favorable conditions for heart parasitism and myocarditis development.
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Affiliation(s)
- Amanda A Felizardo
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil
| | - Ivo S Caldas
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil; Department of Pathology and Parasitology, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil
| | - Andréa A S Mendonça
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil; Department of Microbiology and Immunology, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil
| | - Reggiani V Gonçalves
- Department of Animal Biology, Federal University of Viçosa, Viçosa 36570-000, Minas Gerais, Brazil
| | - Fernanda L Tana
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil; Department of Microbiology and Immunology, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil
| | - Leonardo A Almeida
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil; Department of Microbiology and Immunology, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil
| | - Rômulo D Novaes
- Institute of Biomedical Sciences, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil; Department of Structural Biology, Federal University of Alfenas, Alfenas, 37130-001 Minas Gerais, Brazil.
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Klein LD, Huang J, Quinn EA, Martin MA, Breakey AA, Gurven M, Kaplan H, Valeggia C, Jasienska G, Scelza B, Lebrilla CB, Hinde K. Variation among populations in the immune protein composition of mother's milk reflects subsistence pattern. Evol Med Public Health 2018; 2018:230-245. [PMID: 30430010 PMCID: PMC6222208 DOI: 10.1093/emph/eoy031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 09/25/2018] [Indexed: 12/29/2022] Open
Abstract
LAY SUMMARY Adaptive immune proteins in mothers' milk are more variable than innate immune proteins across populations and subsistence strategies. These results suggest that the immune defenses in milk are shaped by a mother's environment throughout her life. BACKGROUND AND OBJECTIVES Mother's milk contains immune proteins that play critical roles in protecting the infant from infection and priming the infant's developing immune system during early life. The composition of these molecules in milk, particularly the acquired immune proteins, is thought to reflect a mother's immunological exposures throughout her life. In this study, we examine the composition of innate and acquired immune proteins in milk across seven populations with diverse disease and cultural ecologies. METHODOLOGY Milk samples (n = 164) were collected in Argentina, Bolivia, Nepal, Namibia, Philippines, Poland and the USA. Populations were classified as having one of four subsistence patterns: urban-industrialism, rural-shop, horticulturalist-forager or agro-pastoralism. Milk innate (lactalbumin, lactoferrin and lysozyme) and acquired (Secretory IgA, IgG and IgM) protein concentrations were determined using triple-quadrupole mass spectrometry. RESULTS Both innate and acquired immune protein composition in milk varied among populations, though the acquired immune protein composition of milk differed more among populations. Populations living in closer geographic proximity or having similar subsistence strategies (e.g. agro-pastoralists from Nepal and Namibia) had more similar milk immune protein compositions. Agro-pastoralists had different milk innate immune protein composition from horticulturalist-foragers and urban-industrialists. Acquired immune protein composition differed among all subsistence strategies except horticulturist-foragers and rural-shop. CONCLUSIONS AND IMPLICATIONS Our results reveal fundamental variation in milk composition that has not been previously explored in human milk research. Further study is needed to understand what specific aspects of the local environment influence milk composition and the effects this variation may have on infant health outcomes.
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Affiliation(s)
- Laura D Klein
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, USA
- Department of Anthropology, University of Illinois at Chicago, 1007 West Harrison Street, Chicago IL, USA
| | - Jincui Huang
- Chemistry Department, University of California Davis, 2465 Chemistry Annex, One Shields Avenue, Davis, CA, USA
| | - Elizabeth A Quinn
- Department of Anthropology, Washington University in St Louis, Campus Box 1114, One Brookings Drive, St Louis, MO, USA
| | - Melanie A Martin
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
- Department of Anthropology, University of Washington, 314 Denny Hall, Box 353100, Seattle, WA, USA
| | - Alicia A Breakey
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, USA
| | - Michael Gurven
- Department of Anthropology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Hillard Kaplan
- Department of Anthropology, University of New Mexico, MSC01-1040, 1 University of New Mexico, Albuquerque, NM, USA
| | - Claudia Valeggia
- Department of Anthropology, Yale University, 10 Sachem Street, New Haven, CT, USA
| | - Grazyna Jasienska
- Department of Environmental Health, Faculty of Health Sciences, Jagiellonian University Medical College, ul. Grzegorzecka 20, Krakow, Poland
| | - Brooke Scelza
- Department of Anthropology, University of California Los Angeles, 341 Haines Hall, Box 951553, Los Angeles, CA, USA
| | - Carlito B Lebrilla
- Chemistry Department, University of California Davis, 2465 Chemistry Annex, One Shields Avenue, Davis, CA, USA
| | - Katie Hinde
- Department of Human Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, MA, USA
- School of Human Evolution and Social Change
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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24
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Muñoz M, Camargo M, Ramírez JD. Estimating the Intra-taxa Diversity, Population Genetic Structure, and Evolutionary Pathways of Cryptococcus neoformans and Cryptococcus gattii. Front Genet 2018; 9:148. [PMID: 29740480 PMCID: PMC5928140 DOI: 10.3389/fgene.2018.00148] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 04/09/2018] [Indexed: 12/20/2022] Open
Abstract
Members of the Cryptococcus complex, includes Cryptococcus neoformans (most common fungal infection of the brain) and Cryptococcus gattii (high-impact emerging pathogen worldwide). Currently, the fungal multilocus sequence typing database (Fungal MLST Database) constitutes a valuable data repository of the genes used for molecular typing of these pathogens. We analyzed the data available in the Fungal MLST Database for seven housekeeping genes, with the aim to evaluate its contribution in the description of intra-taxa diversity, population genetic structure, and evolutionary patterns. Although the Fungal MLST Database has a greater number of reports for C. neoformans (n = 487) than for C. gattii (n = 344), similar results were obtained for both species in terms of allelic diversity. Phylogenetic reconstructions revealed grouping by molecular type in both species and allowed us to propose differences in evolutionary patterns (gradualism in the case of C. neoformans and punctuated evolution in the case of C. gattii). In addition, C. neoformans showed a population genetic structure consisting of 37 clonal complexes (CCs; CC1 being predominant), high crosslinking [without sequence type (ST) grouping by molecular type], marked divergence events in phylogenetic analysis, and few introgression events (mainly between VNI and VNIV). By contrast, C. gattii showed 50 CCs (with greater homogeneity in ST number by CC) and clustering by molecular type with marked crosslinking events in phylogenetic networks being less evident. Understanding relationships at the molecular level for species of the Cryptococcus complex, based on the sequences of the housekeeping genes, provides information for describing the evolutionary history of these emerging pathogens.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
- Centro de Tecnología en Salud (CETESA), Upqua SAS, Bogotá, Colombia
- Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Milena Camargo
- Centro de Tecnología en Salud (CETESA), Upqua SAS, Bogotá, Colombia
- Departamento de Biología Molecular e Inmunología, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Doctorado en Ciencias Biomédicas y Biológicas, Universidad del Rosario, Bogotá, Colombia
| | - Juan D. Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Bogotá, Colombia
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25
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How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin. Nat Commun 2018; 9:1386. [PMID: 29643370 PMCID: PMC5895760 DOI: 10.1038/s41467-018-03665-3] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/28/2018] [Indexed: 01/19/2023] Open
Abstract
Influenza virus can escape most antibodies with single mutations. However, rare antibodies broadly neutralize many viral strains. It is unclear how easily influenza virus might escape such antibodies if there was strong pressure to do so. Here, we map all single amino-acid mutations that increase resistance to broad antibodies to H1 hemagglutinin. Our approach not only identifies antigenic mutations but also quantifies their effect sizes. All antibodies select mutations, but the effect sizes vary widely. The virus can escape a broad antibody to hemagglutinin's receptor-binding site the same way it escapes narrow strain-specific antibodies: via single mutations with huge effects. In contrast, broad antibodies to hemagglutinin's stalk only select mutations with small effects. Therefore, among the antibodies we examine, breadth is an imperfect indicator of the potential for viral escape via single mutations. Antibodies targeting the H1 hemagglutinin stalk are quantifiably harder to escape than the other antibodies tested here.
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26
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Recurring infection with ecologically distinct HPV types can explain high prevalence and diversity. Proc Natl Acad Sci U S A 2017; 114:13573-13578. [PMID: 29208707 DOI: 10.1073/pnas.1714712114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The high prevalence of human papillomavirus (HPV), the most common sexually transmitted infection, arises from the coexistence of over 200 genetically distinct types. Accurately predicting the impact of vaccines that target multiple types requires understanding the factors that determine HPV diversity. The diversity of many pathogens is driven by type-specific or "homologous" immunity, which promotes the spread of variants to which hosts have little immunity. To test for homologous immunity and to identify mechanisms determining HPV transmission, we fitted nonlinear mechanistic models to longitudinal data on genital infections in unvaccinated men. Our results provide no evidence for homologous immunity, instead showing that infection with one HPV type strongly increases the risk of infection with that type for years afterward. For HPV16, the type responsible for most HPV-related cancers, an initial infection increases the 1-year probability of reinfection by 20-fold, and the probability of reinfection remains 14-fold higher 2 years later. This increased risk occurs in both sexually active and celibate men, suggesting that it arises from autoinoculation, episodic reactivation of latent virus, or both. Overall, our results suggest that high HPV prevalence and diversity can be explained by a combination of a lack of homologous immunity, frequent reinfections, weak competition between types, and variation in type fitness between host subpopulations. Because of the high risk of reinfection, vaccinating boys who have not yet been exposed may be crucial to reduce prevalence, but our results suggest that there may also be large benefits to vaccinating previously infected individuals.
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27
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Volgers C, Savelkoul PHM, Stassen FRM. Gram-negative bacterial membrane vesicle release in response to the host-environment: different threats, same trick? Crit Rev Microbiol 2017; 44:258-273. [PMID: 28741415 DOI: 10.1080/1040841x.2017.1353949] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Bacteria are confronted with a multitude of stressors when occupying niches within the host. These stressors originate from host defense mechanisms, other bacteria during niche competition or result from physiological challenges such as nutrient limitation. To counteract these stressors, bacteria have developed a stress-induced network to mount the adaptations required for survival. These stress-induced adaptations include the release of membrane vesicles from the bacterial envelope. Membrane vesicles can provide bacteria with a plethora of immediate and ultimate benefits for coping with environmental stressors. This review addresses how membrane vesicles aid Gram-negative bacteria to cope with host-associated stress factors, focusing on vesicle biogenesis and the physiological functions. As many of the pathways, that drive vesicle biogenesis, confer we propose that shedding of membrane vesicles by Gram-negative bacteria entails an integrated part of general stress responses.
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Affiliation(s)
- Charlotte Volgers
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands
| | - Paul H M Savelkoul
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands.,b Department of Medical Microbiology and Infection Control , VU University Medical Center , Amsterdam , The Netherlands
| | - Frank R M Stassen
- a Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM) , Maastricht University Medical Centre , Maastricht , The Netherlands
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28
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Cobey S, Hensley SE. Immune history and influenza virus susceptibility. Curr Opin Virol 2017; 22:105-111. [PMID: 28088686 DOI: 10.1016/j.coviro.2016.12.004] [Citation(s) in RCA: 165] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 12/14/2016] [Accepted: 12/20/2016] [Indexed: 12/25/2022]
Abstract
Antibody responses to influenza viruses are critical for protection, but the ways in which repeated viral exposures shape antibody evolution and effectiveness over time remain controversial. Early observations demonstrated that viral exposure history has a profound effect on the specificity and magnitude of antibody responses to a new viral strain, a phenomenon called 'original antigenic sin.' Although 'sin' might suppress some aspects of the immune response, so far there is little indication that hosts with pre-existing immunity are more susceptible to viral infections compared to naïve hosts. However, the tendency of the immune response to focus on previously recognized conserved epitopes when encountering new viral strains can create an opportunity cost when mutations arise in these conserved epitopes. Hosts with different exposure histories may continue to experience distinct patterns of infection over time, which may influence influenza viruses' continued antigenic evolution. Understanding the dynamics of B cell competition that underlie the development of antibody responses might help explain the low effectiveness of current influenza vaccines and lead to better vaccination strategies.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology & Evolution, The University of Chicago, Chicago, IL 19104, USA.
| | - Scott E Hensley
- Department of Microbiology, Perelman School of Medicine, The University of Pennsylvania, Philadelphia, PA 19104, USA.
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29
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Liu C, Shen Q, Zheng W, Lv Y, Chen X, Li X, Zhu Q, Guo X, Ge R, Li C. Poly(anhydride) nanoparticles act as effective adjuvants to elicit a persistent immune response. RSC Adv 2017. [DOI: 10.1039/c7ra11891k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
This research shows that p-OVA nanoparticles composed of poly(anhydride) and OVA have a strong ability to induce an OVA-specific immune response.
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Affiliation(s)
- Caixia Liu
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Qiuxai Shen
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Wenwen Zheng
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Yao Lv
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Xinyu Chen
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Xiaoheng Li
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Qiqi Zhu
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Xiaoling Guo
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Renshan Ge
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
| | - Chao Li
- The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University
- Wenzhou 325027
- P. R. China
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30
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Cobey S, Baskerville EB. Limits to Causal Inference with State-Space Reconstruction for Infectious Disease. PLoS One 2016; 11:e0169050. [PMID: 28030639 PMCID: PMC5193453 DOI: 10.1371/journal.pone.0169050] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 12/09/2016] [Indexed: 01/17/2023] Open
Abstract
Infectious diseases are notorious for their complex dynamics, which make it difficult to fit models to test hypotheses. Methods based on state-space reconstruction have been proposed to infer causal interactions in noisy, nonlinear dynamical systems. These “model-free” methods are collectively known as convergent cross-mapping (CCM). Although CCM has theoretical support, natural systems routinely violate its assumptions. To identify the practical limits of causal inference under CCM, we simulated the dynamics of two pathogen strains with varying interaction strengths. The original method of CCM is extremely sensitive to periodic fluctuations, inferring interactions between independent strains that oscillate with similar frequencies. This sensitivity vanishes with alternative criteria for inferring causality. However, CCM remains sensitive to high levels of process noise and changes to the deterministic attractor. This sensitivity is problematic because it remains challenging to gauge noise and dynamical changes in natural systems, including the quality of reconstructed attractors that underlie cross-mapping. We illustrate these challenges by analyzing time series of reportable childhood infections in New York City and Chicago during the pre-vaccine era. We comment on the statistical and conceptual challenges that currently limit the use of state-space reconstruction in causal inference.
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Affiliation(s)
- Sarah Cobey
- Ecology & Evolution, University of Chicago, Chicago, IL, United States of America
- * E-mail:
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31
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Abstract
The distinctive features of human influenza A phylogeny have inspired many mathematical and computational studies of viral infections spreading in a host population, but our understanding of the mechanisms that shape the coupled evolution of host immunity, disease incidence and viral antigenic properties is far from complete. In this paper we explore the epidemiology and the phylogeny of a rapidly mutating pathogen in a host population with a weak immune response, that allows re-infection by the same strain and provides little cross-immunity. We find that mutation generates explosive diversity and that, as diversity grows, the system is driven to a very high prevalence level. This is in stark contrast with the behavior of similar models where mutation gives rise to a large epidemic followed by disease extinction, under the assumption that infection with a strain provides lifelong immunity. For low mutation rates, the behavior of the system shows the main qualitative features of influenza evolution. Our results highlight the importance of heterogeneity in the human immune response for understanding influenza A phenomenology. They are meant as a first step toward computationally affordable, individual based models including more complex host-pathogen interactions.
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Affiliation(s)
- Tomás Aquino
- a Department of Civil & Environmental Engineering and Earth Sciences ; University of Notre Dame ; Notre Dame , IN USA
| | - Ana Nunes
- b BioISI Biosystems & Integrative Sciences Institute and Departamento de Física; Faculdade de Ciências da Universidade de Lisboa ; Lisboa , Portugal
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32
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Childs LM, Baskerville EB, Cobey S. Trade-offs in antibody repertoires to complex antigens. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0245. [PMID: 26194759 PMCID: PMC4528422 DOI: 10.1098/rstb.2014.0245] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Pathogens vary in their antigenic complexity. While some pathogens such as measles present a few relatively invariant targets to the immune system, others such as malaria display considerable antigenic diversity. How the immune response copes in the presence of multiple antigens, and whether a trade-off exists between the breadth and efficacy of antibody (Ab)-mediated immune responses, are unsolved problems. We present a theoretical model of affinity maturation of B-cell receptors (BCRs) during a primary infection and examine how variation in the number of accessible antigenic sites alters the Ab repertoire. Naive B cells with randomly generated receptor sequences initiate the germinal centre (GC) reaction. The binding affinity of a BCR to an antigen is quantified via a genotype-phenotype map, based on a random energy landscape, that combines local and distant interactions between residues. In the presence of numerous antigens or epitopes, B-cell clones with different specificities compete for stimulation during rounds of mutation within GCs. We find that the availability of many epitopes reduces the affinity and relative breadth of the Ab repertoire. Despite the stochasticity of somatic hypermutation, patterns of immunodominance are strongly shaped by chance selection of naive B cells with specificities for particular epitopes. Our model provides a mechanistic basis for the diversity of Ab repertoires and the evolutionary advantage of antigenically complex pathogens.
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Affiliation(s)
- Lauren M Childs
- Center for Communicable Disease Dynamics, Harvard T.H. Chan School of Public Health, Boston, MA, USA Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Sarah Cobey
- Ecology and Evolution, University of Chicago, Chicago, IL, USA
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33
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Homolka S, Ubben T, Niemann S. High Sequence Variability of the ppE18 Gene of Clinical Mycobacterium tuberculosis Complex Strains Potentially Impacts Effectivity of Vaccine Candidate M72/AS01E. PLoS One 2016; 11:e0152200. [PMID: 27011018 PMCID: PMC4806982 DOI: 10.1371/journal.pone.0152200] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 03/10/2016] [Indexed: 11/19/2022] Open
Abstract
The development of an effective vaccine is urgently needed to fight tuberculosis (TB) which is still the leading cause of death from a single infectious agent worldwide. One of the promising vaccine candidates M72/AS01E consists of two proteins subunits PepA and PPE18 coded by Rv0125 and Rv1196. However, preliminary data indicate a high level of sequence variability among clinical Mycobacterium tuberculosis complex (MTBC) strains that might have an impact on the vaccine efficacy. To further investigate this finding, we determined ppE18 sequence variability in a well-characterized reference collection of 71 MTBC strains from 23 phylogenetic lineages representing the global MTBC diversity. In total, 100 sequence variations consisting of 96 single nucleotide polymorphisms (SNPs), three insertions and one deletion were detected resulting in 141 variable positions distributed over the entire gene. The majority of SNPs detected were non-synonymous (n = 68 vs. n = 28 synonymous). Strains from animal adapted lineages, e.g., M. bovis, showed a significant higher diversity than the human pathogens such as M. tuberculosis Haarlem. SNP patterns specific for different lineages as well as for deeper branches in the phylogeny could be identified. The results of our study demonstrate a high variability of the ppE18 gene even in the N-terminal domains that is normally highly conserved in ppe genes. As the N-terminal region interacts with TLR2 receptor inducing a protective anti-inflammatory immune response, genetic heterogeneity has a potential impact on the vaccine efficiency, however, this has to be investigated in future studies.
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Affiliation(s)
- Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Schleswig-Holstein, Germany
| | - Tanja Ubben
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Schleswig-Holstein, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Schleswig-Holstein, Germany
- German Centre for Infection Research (DZIF), Partner Site Borstel, Schleswig-Holstein, Germany
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34
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Koelle K, Rasmussen DA. The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans. eLife 2015; 4:e07361. [PMID: 26371556 PMCID: PMC4611170 DOI: 10.7554/elife.07361] [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: 03/10/2015] [Accepted: 09/14/2015] [Indexed: 11/19/2022] Open
Abstract
Recent phylogenetic analyses indicate that RNA virus populations carry a significant deleterious mutation load. This mutation load has the potential to shape patterns of adaptive evolution via genetic linkage to beneficial mutations. Here, we examine the effect of deleterious mutations on patterns of influenza A subtype H3N2's antigenic evolution in humans. By first analyzing simple models of influenza that incorporate a mutation load, we show that deleterious mutations, as expected, act to slow the virus's rate of antigenic evolution, while making it more punctuated in nature. These models further predict three distinct molecular pathways by which antigenic cluster transitions occur, and we find phylogenetic patterns consistent with each of these pathways in influenza virus sequences. Simulations of a more complex phylodynamic model further indicate that antigenic mutations act in concert with deleterious mutations to reproduce influenza's spindly hemagglutinin phylogeny, co-circulation of antigenic variants, and high annual attack rates. DOI:http://dx.doi.org/10.7554/eLife.07361.001 Each year, up to 15% of the world's population experience symptoms of an influenza infection, also commonly known as flu. The most common culprit is a strain of the virus called influenza type A subtype H3N2. One reason that so many people become infected each year is that this virus evolves rapidly. Within a few years, proteins on the surface of the virus known as antigens become less recognizable to the immune system of a person who has been previously infected. This means that the person can become ill with the virus again because their immune system cannot mount an effective response to the evolved virus strain. Influenza virus strains evolve rapidly because their genetic material accumulates mutations quickly. Although some of these mutations are beneficial to the virus, other mutations are harmful and reduce the ability of the virus to spread. Sometimes beneficial mutations may occur alongside harmful ones, but it is not known how the harmful mutations affect the evolution of the virus. Here, Koelle and Rasmussen used computer models of H3N2 influenza to examine the effect of harmful mutations on the evolution of this virus population. The models show that harmful mutations limit how quickly the antigens can evolve. Also, the presence of these harmful mutations effectively acts as a sieve: they allow only large changes in the antigens to establish in the virus population. The models suggest that there are three routes by which large changes in the antigens on H3N2 viruses may occur. The first is by a single mutation that has a big effect on the antigens in viruses that only carry a few harmful mutations, but these large mutations would not happen very often. Another route may be through more common mutations that have only a small or moderate benefit, which would allow the virus to become more common in the population before it acquires a beneficial mutation with a much greater effect. The third possibility is that a large beneficial mutation may arise in viruses that have many harmful mutations. These harmful mutations may initially limit the ability of the virus to spread, but over time, some of these harmful mutations may then be lost. Koelle and Rasmussen found that the computer models could recreate the patterns of virus evolution that have been observed in real strains of H3N2. Researchers use predictions of influenza evolution to help them decide which virus strains should be included in flu vaccines each year. Koelle and Rasmussen findings indicate that harmful mutations should be considered when making these predictions. DOI:http://dx.doi.org/10.7554/eLife.07361.002
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Affiliation(s)
- Katia Koelle
- Department of Biology, Duke University, Durham, United States.,Fogarty International Center, National Institutes of Health, Bethesda, United States
| | - David A Rasmussen
- Department of Biology, Duke University, Durham, United States.,Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule Zürich, Basel, Switzerland
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Cobey S, Wilson P, Matsen FA. The evolution within us. Philos Trans R Soc Lond B Biol Sci 2015; 370:20140235. [PMID: 26194749 PMCID: PMC4528412 DOI: 10.1098/rstb.2014.0235] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2015] [Indexed: 01/05/2023] Open
Abstract
The B-cell immune response is a remarkable evolutionary system found in jawed vertebrates. B-cell receptors, the membrane-bound form of antibodies, are capable of evolving high affinity to almost any foreign protein. High germline diversity and rapid evolution upon encounter with antigen explain the general adaptability of B-cell populations, but the dynamics of repertoires are less well understood. These dynamics are scientifically and clinically important. After highlighting the remarkable characteristics of naive and experienced B-cell repertoires, especially biased usage of genes encoding the B-cell receptors, we contrast methods of sequence analysis and their attempts to explain patterns of B-cell evolution. These phylogenetic approaches are currently unlinked to explicit models of B-cell competition, which analyse repertoire evolution at the level of phenotype, the affinities and specificities to particular antigenic sites. The models, in turn, suggest how chance, infection history and other factors contribute to different patterns of immunodominance and protection between people. Challenges in rational vaccine design, specifically vaccines to induce broadly neutralizing antibodies to HIV, underscore critical gaps in our understanding of B cells' evolutionary and ecological dynamics.
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Affiliation(s)
- Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA
| | - Patrick Wilson
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA Committee on Immunology, University of Chicago, Chicago, IL 60637, USA Knapp Center for Lupus and Immunology Research, University of Chicago, Chicago, IL 60637, USA
| | - Frederick A Matsen
- Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Grad YH, Lipsitch M. Epidemiologic data and pathogen genome sequences: a powerful synergy for public health. Genome Biol 2014; 15:538. [PMID: 25418119 PMCID: PMC4282151 DOI: 10.1186/s13059-014-0538-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Epidemiologists aim to inform the design of public health interventions with evidence on the evolution, emergence and spread of infectious diseases. Sequencing of pathogen genomes, together with date, location, clinical manifestation and other relevant data about sample origins, can contribute to describing nearly every aspect of transmission dynamics, including local transmission and global spread. The analyses of these data have implications for all levels of clinical and public health practice, from institutional infection control to policies for surveillance, prevention and treatment. This review highlights the range of epidemiological questions that can be addressed from the combination of genome sequence and traditional ‘line lists’ (tables of epidemiological data where each line includes demographic and clinical features of infected individuals). We identify opportunities for these data to inform interventions that reduce disease incidence and prevalence. By considering current limitations of, and challenges to, interpreting these data, we aim to outline a research agenda to accelerate the genomics-driven transformation in public health microbiology.
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