1
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Herder V, Caporale M, MacLean OA, Pintus D, Huang X, Nomikou K, Palmalux N, Nichols J, Scivoli R, Boutell C, Taggart A, Allan J, Malik H, Ilia G, Gu Q, Ronchi GF, Furnon W, Zientara S, Bréard E, Antonucci D, Capista S, Giansante D, Cocco A, Mercante MT, Di Ventura M, Da Silva Filipe A, Puggioni G, Sevilla N, Stewart ME, Ligios C, Palmarini M. Correlates of disease severity in bluetongue as a model of acute arbovirus infection. PLoS Pathog 2024; 20:e1012466. [PMID: 39150989 DOI: 10.1371/journal.ppat.1012466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 08/28/2024] [Accepted: 07/31/2024] [Indexed: 08/18/2024] Open
Abstract
Most viral diseases display a variable clinical outcome due to differences in virus strain virulence and/or individual host susceptibility to infection. Understanding the biological mechanisms differentiating a viral infection displaying severe clinical manifestations from its milder forms can provide the intellectual framework toward therapies and early prognostic markers. This is especially true in arbovirus infections, where most clinical cases are present as mild febrile illness. Here, we used a naturally occurring vector-borne viral disease of ruminants, bluetongue, as an experimental system to uncover the fundamental mechanisms of virus-host interactions resulting in distinct clinical outcomes. As with most viral diseases, clinical symptoms in bluetongue can vary dramatically. We reproduced experimentally distinct clinical forms of bluetongue infection in sheep using three bluetongue virus (BTV) strains (BTV-1IT2006, BTV-1IT2013 and BTV-8FRA2017). Infected animals displayed clinical signs varying from clinically unapparent, to mild and severe disease. We collected and integrated clinical, haematological, virological, and histopathological data resulting in the analyses of 332 individual parameters from each infected and uninfected control animal. We subsequently used machine learning to select the key viral and host processes associated with disease pathogenesis. We identified and experimentally validated five different fundamental processes affecting the severity of bluetongue: (i) virus load and replication in target organs, (ii) modulation of the host type-I IFN response, (iii) pro-inflammatory responses, (iv) vascular damage, and (v) immunosuppression. Overall, we showed that an agnostic machine learning approach can be used to prioritise the different pathogenetic mechanisms affecting the disease outcome of an arbovirus infection.
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Affiliation(s)
- Vanessa Herder
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Marco Caporale
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Oscar A MacLean
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Davide Pintus
- Istituto Zooprofilattico Sperimentale della Sardegna, Sassari, Italy
| | - Xinyi Huang
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Kyriaki Nomikou
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Natasha Palmalux
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Jenna Nichols
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Rosario Scivoli
- Istituto Zooprofilattico Sperimentale della Sardegna, Sassari, Italy
| | - Chris Boutell
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Aislynn Taggart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Jay Allan
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Haris Malik
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Georgios Ilia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Quan Gu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Stephan Zientara
- Laboratory for Animal Health, INRAE, Ecole Nationale Vétérinaire d'Alfort, ANSES, Maisons-Alfort, France
| | - Emmanuel Bréard
- Laboratory for Animal Health, INRAE, Ecole Nationale Vétérinaire d'Alfort, ANSES, Maisons-Alfort, France
| | - Daniela Antonucci
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Sara Capista
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Daniele Giansante
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Antonio Cocco
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Maria Teresa Mercante
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Mauro Di Ventura
- Istituto Zooprofilattico Sperimentale dell' Abruzzo e Molise "G. Caporale", Teramo, Italy
| | - Ana Da Silva Filipe
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Noemi Sevilla
- Centro de Investigación en Sanidad Animal. Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria. Consejo Superior de Investigaciones Científicas (CISA-INIA-CSIC). Valdeolmos, Madrid, Spain
| | - Meredith E Stewart
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Ciriaco Ligios
- Istituto Zooprofilattico Sperimentale della Sardegna, Sassari, Italy
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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2
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Chang YS, Huang K, Lee JM, Vagts CL, Ascoli C, Amin MR, Ghassemi M, Lora CM, Edafetanure-Ibeh R, Huang Y, Cherian RA, Sarup N, Warpecha SR, Hwang S, Goel R, Turturice BA, Schott C, Hernandez M, Chen Y, Jorgensen J, Wang W, Rasic M, Novak RM, Finn PW, Perkins DL. Altered transcriptomic immune responses of maintenance hemodialysis patients to the COVID-19 mRNA vaccine. eLife 2024; 13:e83641. [PMID: 38656290 PMCID: PMC11042800 DOI: 10.7554/elife.83641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
Background End-stage renal disease (ESRD) patients experience immune compromise characterized by complex alterations of both innate and adaptive immunity, and results in higher susceptibility to infection and lower response to vaccination. This immune compromise, coupled with greater risk of exposure to infectious disease at hemodialysis (HD) centers, underscores the need for examination of the immune response to the COVID-19 mRNA-based vaccines. Methods The immune response to the COVID-19 BNT162b2 mRNA vaccine was assessed in 20 HD patients and cohort-matched controls. RNA sequencing of peripheral blood mononuclear cells was performed longitudinally before and after each vaccination dose for a total of six time points per subject. Anti-spike antibody levels were quantified prior to the first vaccination dose (V1D0) and 7 d after the second dose (V2D7) using anti-spike IgG titers and antibody neutralization assays. Anti-spike IgG titers were additionally quantified 6 mo after initial vaccination. Clinical history and lab values in HD patients were obtained to identify predictors of vaccination response. Results Transcriptomic analyses demonstrated differing time courses of immune responses, with prolonged myeloid cell activity in HD at 1 wk after the first vaccination dose. HD also demonstrated decreased metabolic activity and decreased antigen presentation compared to controls after the second vaccination dose. Anti-spike IgG titers and neutralizing function were substantially elevated in both controls and HD at V2D7, with a small but significant reduction in titers in HD groups (p<0.05). Anti-spike IgG remained elevated above baseline at 6 mo in both subject groups. Anti-spike IgG titers at V2D7 were highly predictive of 6-month titer levels. Transcriptomic biomarkers after the second vaccination dose and clinical biomarkers including ferritin levels were found to be predictive of antibody development. Conclusions Overall, we demonstrate differing time courses of immune responses to the BTN162b2 mRNA COVID-19 vaccination in maintenance HD subjects comparable to healthy controls and identify transcriptomic and clinical predictors of anti-spike IgG titers in HD. Analyzing vaccination as an in vivo perturbation, our results warrant further characterization of the immune dysregulation of ESRD. Funding F30HD102093, F30HL151182, T32HL144909, R01HL138628. This research has been funded by the University of Illinois at Chicago Center for Clinical and Translational Science (CCTS) award UL1TR002003.
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Affiliation(s)
- Yi-Shin Chang
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
| | - Kai Huang
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
| | - Jessica M Lee
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Microbiology and Immunology, University of Illinois at ChicagoChicagoUnited States
| | - Christen L Vagts
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Christian Ascoli
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Md-Ruhul Amin
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Mahmood Ghassemi
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Claudia M Lora
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | | | - Yue Huang
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Ruth A Cherian
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Nandini Sarup
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Samantha R Warpecha
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Sunghyun Hwang
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Rhea Goel
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Benjamin A Turturice
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Microbiology and Immunology, University of Illinois at ChicagoChicagoUnited States
- Department of Medicine, Stanford UniversityPalo AltoUnited States
| | - Cody Schott
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Microbiology and Immunology, University of Illinois at ChicagoChicagoUnited States
- Department of Medicine, University of Colorado DenverAuroraUnited States
| | | | - Yang Chen
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Biological Sciences, University of Illinois at ChicagoChicagoUnited States
| | - Julianne Jorgensen
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
| | - Wangfei Wang
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
| | - Mladen Rasic
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
| | - Richard M Novak
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
| | - Patricia W Finn
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
- Department of Microbiology and Immunology, University of Illinois at ChicagoChicagoUnited States
| | - David L Perkins
- Department of Medicine, University of Illinois at ChicagoChicagoUnited States
- Department of Bioengineering, University of Illinois at ChicagoChicagoUnited States
- Department of Biological Sciences, University of Illinois at ChicagoChicagoUnited States
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3
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Chang YS, Huang K, Lee JM, Vagts CL, Ascoli C, Amin MR, Ghassemi M, Lora CM, Edafetanure-Ibeh R, Huang Y, Cherian RA, Sarup N, Warpecha SR, Hwang S, Goel R, Turturice BA, Schott C, Hernandez M, Chen Y, Joregensen J, Wang W, Rasic M, Novak RM, Finn PW, Perkins DL. Immune response to the mRNA COVID-19 vaccine in hemodialysis patients: cohort study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.19.23284792. [PMID: 36711520 PMCID: PMC9882629 DOI: 10.1101/2023.01.19.23284792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Background End-stage renal disease (ESRD) patients experience immune compromise characterized by complex alterations of both innate and adaptive immunity, and results in higher susceptibility to infection and lower response to vaccination. This immune compromise, coupled with greater risk of exposure to infectious disease at hemodialysis (HD) centers, underscores the need for examination of the immune response to the COVID-19 mRNA-based vaccines. Methods A transcriptomic analysis of the immune response to the Covid-19 BNT162b2 mRNA vaccine was assessed in 20 HD patients and cohort-matched controls. RNA sequencing of peripheral blood mononuclear cells (PBMCs) was performed longitudinally before and after each vaccination dose for a total of six time points per subject. Anti-spike antibody levels were quantified prior to the first vaccination dose (V1D0) and seven days after the second dose (V2D7) using anti-Spike IgG titers and antibody neutralization assays. Anti-spike IgG titers were additionally quantified six months after initial vaccination. Clinical history and lab values in HD patients were obtained to identify predictors of vaccination response. Results Transcriptomic analyses demonstrated differing time courses of immune responses, with predominant T cell activity in controls one week after the first vaccination dose, compared to predominant myeloid cell activity in HD at this time point. HD demonstrated decreased metabolic activity and decreased antigen presentation compared to controls after the second vaccination dose. Anti-spike IgG titers and neutralizing function were substantially elevated in both controls and HD at V2D7, with a small but significant reduction in titers in HD groups (p < 0.05). Anti-spike IgG remained elevated above baseline at six months in both subject groups. Anti-spike IgG titers at V2D7 were highly predictive of 6-month titer levels. Transcriptomic biomarkers after the second vaccination dose and clinical biomarkers including ferritin levels were found to be predictive of antibody development. Conclusion Overall, we demonstrate differing time courses of immune responses to the BTN162b2 mRNA COVID-19 vaccination in maintenance hemodialysis subjects (HD) comparable to healthy controls (HC) and identify transcriptomic and clinical predictors of anti-Spike IgG titers in HD. Analyzing vaccination as an in vivo perturbation, our results warrant further characterization of the immune dysregulation of end stage renal disease (ESRD). Funding F30HD102093, F30HL151182, T32HL144909, R01HL138628This research has been funded by the University of Illinois at Chicago Center for Clinical and Translational Science (CCTS) award UL1TR002003.
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Affiliation(s)
- Yi-Shin Chang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Kai Huang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jessica M Lee
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Christen L Vagts
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Christian Ascoli
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Md-Ruhul Amin
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mahmood Ghassemi
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Claudia M Lora
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | - Yue Huang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ruth A Cherian
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Nandini Sarup
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Samantha R Warpecha
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Sunghyun Hwang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Rhea Goel
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Benjamin A Turturice
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicine, Stanford University, Palo Alto, California, USA
| | - Cody Schott
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Medicine, University of Colorado Denver, Aurora, Colorado, USA
| | - Montserrat Hernandez
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Yang Chen
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Julianne Joregensen
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Wangfei Wang
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mladen Rasic
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Richard M Novak
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patricia W Finn
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - David L Perkins
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA
- Department of Biological Sciences, University of Illinois at Chicago, Chicago, Illinois, USA
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4
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Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. Front Genet 2022; 13:1067350. [PMID: 36482891 PMCID: PMC9725098 DOI: 10.3389/fgene.2022.1067350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in several biological processes, including the immune system response to pathogens and vaccines. The annotation and functional characterization of lncRNAs is more advanced in humans than in livestock species. Here, we take advantage of the increasing number of high-throughput functional experiments deposited in public databases in order to uniformly analyse, profile unannotated lncRNAs and integrate 422 ovine RNA-seq samples from the ovine immune system. We identified 12302 unannotated lncRNA genes with support from independent CAGE-seq and histone modification ChIP-seq assays. Unannotated lncRNAs showed low expression levels and sequence conservation across other mammal species. There were differences in expression levels depending on the genomic location-based lncRNA classification. Differential expression analyses between unstimulated and samples stimulated with pathogen infection or vaccination resulted in hundreds of lncRNAs with changed expression. Gene co-expression analyses revealed immune gene-enriched clusters associated with immune system activation and related to interferon signalling, antiviral response or endoplasmic reticulum stress. Besides, differential co-expression networks were constructed in order to find condition-specific relationships between coding genes and lncRNAs. Overall, using a diverse set of immune system samples and bioinformatic approaches we identify several ovine lncRNAs associated with the response to an external stimulus. These findings help in the improvement of the ovine lncRNA catalogue and provide sheep-specific evidence for the implication in the general immune response for several lncRNAs.
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5
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Liu W, McNeilly TN, Mitchell M, Burgess STG, Nisbet AJ, Matthews JB, Babayan SA. Vaccine-induced time- and age-dependent mucosal immunity to gastrointestinal parasite infection. NPJ Vaccines 2022; 7:78. [PMID: 35798788 PMCID: PMC9262902 DOI: 10.1038/s41541-022-00501-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/10/2022] Open
Abstract
Individuals vary broadly in their response to vaccination and subsequent challenge infection, with poor vaccine responders causing persistence of both infection and transmission in populations. Yet despite having substantial economic and societal impact, the immune mechanisms that underlie such variability, especially in infected tissues, remain poorly understood. Here, to characterise how antihelminthic immunity at the mucosal site of infection developed in vaccinated lambs, we inserted gastric cannulae into the abomasa of three-month- and six-month-old lambs and longitudinally analysed their local immune response during subsequent challenge infection. The vaccine induced broad changes in pre-challenge abomasal immune profiles and reduced parasite burden and egg output post-challenge, regardless of age. However, age affected how vaccinated lambs responded to infection across multiple immune pathways: adaptive immune pathways were typically age-dependent. Identification of age-dependent and age-independent protective immune pathways may help refine the formulation of vaccines, and indicate specificities of pathogen-specific immunity more generally.
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Affiliation(s)
- Wei Liu
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK
| | - Tom N McNeilly
- The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK.
| | - Mairi Mitchell
- The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK
| | - Stewart T G Burgess
- The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK
| | - Alasdair J Nisbet
- The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK
| | - Jacqueline B Matthews
- The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK.,Roslin Technologies Limited, Roslin Innovation Centre, University of Edinburgh, Easter Bush, Scotland, EH25 9RG, UK
| | - Simon A Babayan
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, Scotland, UK. .,The Moredun Research Institute, Pentlands Science Park, Scotland, EH26 0PZ, UK.
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6
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Bocard LV, Kick AR, Hug C, Lischer HEL, Käser T, Summerfield A. Systems Immunology Analyses Following Porcine Respiratory and Reproductive Syndrome Virus Infection and Vaccination. Front Immunol 2022; 12:779747. [PMID: 34975868 PMCID: PMC8716554 DOI: 10.3389/fimmu.2021.779747] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/23/2021] [Indexed: 11/13/2022] Open
Abstract
This study was initiated to better understand the nature of innate immune responses and the relatively weak and delayed immune response against porcine reproductive and respiratory syndrome virus (PRRSV). Following modified live virus (MLV) vaccination or infection with two PRRSV-2 strains, we analyzed the transcriptome of peripheral blood mononuclear cells collected before and at three and seven days after vaccination or infection. We used blood transcriptional modules (BTMs)-based gene set enrichment analyses. BTMs related to innate immune processes were upregulated by PRRSV-2 strains but downregulated by MLV. In contrast, BTMs related to adaptive immune responses, in particular T cells and cell cycle, were downregulated by PRRSV-2 but upregulated by MLV. In addition, we found differences between the PRRSV strains. Only the more virulent strain induced a strong platelet activation, dendritic cell activation, interferon type I and plasma cell responses. We also calculated the correlations of BTM with the neutralizing antibody and the T-cell responses. Early downregulation (day 0-3) of dendritic cell and B-cell BTM correlated to both CD4 and CD8 T-cell responses. Furthermore, a late (day 3-7) upregulation of interferon type I modules strongly correlated to helper and regulatory T-cell responses, while inflammatory BTM upregulation correlated more to CD8 T-cell responses. BTM related to T cells had positive correlations at three days but negative associations at seven days post-infection. Taken together, this work contributes to resolve the complexity of the innate and adaptive immune responses against PRRSV and indicates a fundamentally different immune response to the less immunogenic MLV compared to field strains which induced robust adaptive immune responses. The identified correlates of T-cell responses will facilitate a rational approach to improve the immunogenicity of MLV.
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Affiliation(s)
| | - Andrew Robert Kick
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States.,Department of Chemistry & Life Science, United States Military Academy, West Point, NY, United States
| | - Corinne Hug
- Institute of Virology and Immunology, Mittelhäusern, Switzerland
| | - Heidi Erika Lisa Lischer
- Interfaculty Bioinformatics Unit, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Tobias Käser
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Artur Summerfield
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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7
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Kim EY, Che Y, Dean HJ, Lorenzo-Redondo R, Stewart M, Keller CK, Whorf D, Mills D, Dulin NN, Kim T, Votoupal M, Walter M, Fernandez-Sesma A, Kim H, Wolinsky SM. Transcriptome-wide changes in gene expression, splicing, and lncRNAs in response to a live attenuated dengue virus vaccine. Cell Rep 2022; 38:110341. [PMID: 35139383 PMCID: PMC8994511 DOI: 10.1016/j.celrep.2022.110341] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/20/2021] [Accepted: 01/14/2022] [Indexed: 01/26/2023] Open
Abstract
The tetravalent dengue vaccine candidate, TAK-003, induces a functional antibody response, but the titers of antibodies against the four serotypes of the dengue virus (DENV) can vary. Here, through a transcriptomic analysis on whole blood collected from recipients of a two-dose schedule of TAK-003, we examine gene expression, splicing, and transcript isoform-level changes for both protein-coding and noncoding genes to broaden our understanding of the immune response. Our analysis reveals a dynamic pattern of vaccine-associated regulation of long noncoding RNAs (lncRNAs), differential splicing of interferon-stimulated gene exons, and gene expression changes related to multiple signaling pathways that detect viral infection. Co-expression networks isolate immune cell-type-related and interferon-response modules that represent specific biological processes that correlate with more robust antibody responses. These data provide insights into the early determinants of the variable immune response to the vaccine, highlighting the significance of splicing and isoform-level gene regulatory mechanisms in defining vaccine immunogenicity.
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Affiliation(s)
- Eun-Young Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Yan Che
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | | | - Ramon Lorenzo-Redondo
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Michael Stewart
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Caroline K Keller
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Daniel Whorf
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Dawson Mills
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Nikita N Dulin
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Tiffany Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Megan Votoupal
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Miriam Walter
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Ana Fernandez-Sesma
- Department of Microbiology and Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Heejin Kim
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA
| | - Steven M Wolinsky
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60011, USA.
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8
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Eloiflin RJ, Auray G, Python S, Rodrigues V, Seveno M, Urbach S, El Koulali K, Holzmuller P, Totte P, Libeau G, Bataille A, Summerfield A. Identification of Differential Responses of Goat PBMCs to PPRV Virulence Using a Multi-Omics Approach. Front Immunol 2021; 12:745315. [PMID: 34671358 PMCID: PMC8521192 DOI: 10.3389/fimmu.2021.745315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022] Open
Abstract
Peste des petits ruminants (PPR) is an acute transboundary infectious viral disease of small ruminants, mainly sheep and goats. Host susceptibility varies considerably depending on the PPR virus (PPRV) strain, the host species and breed. The effect of strains with different levels of virulence on the modulation of the immune system has not been thoroughly compared in an experimental setting so far. In this study, we used a multi-omics approach to investigate the host cellular factors involved in different infection phenotypes. Peripheral blood mononuclear cells (PBMCs) from Saanen goats were activated with a T-cell mitogen and infected with PPRV strains of different virulence: Morocco 2008 (high virulence), Ivory Coast 1989 (low virulence) and Nigeria 75/1 (live attenuated vaccine strain). Our results showed that the highly virulent strain replicated better than the other two in PBMCs and rapidly induced cell death and a stronger inhibition of lymphocyte proliferation. However, all the strains affected lymphocyte proliferation and induced upregulation of key antiviral genes and proteins, meaning a classical antiviral response is orchestrated regardless of the virulence of the PPRV strain. On the other hand, the highly virulent strain induced stronger inflammatory responses and activated more genes related to lymphocyte migration and recruitment, and inflammatory processes. Both transcriptomic and proteomic approaches were successful in detecting viral and antiviral effectors under all conditions. The present work identified key immunological factors related to PPRV virulence in vitro.
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Affiliation(s)
- Roger-Junior Eloiflin
- CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Montpellier, France.,ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France
| | - Gaël Auray
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Sylvie Python
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Valérie Rodrigues
- ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France.,CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Petit-Bourg, France
| | - Martial Seveno
- BCM (BioCampus Montpellier), Univ. Montpellier, CNRS (Centre national de la recherche scientifique), INSERM, Montpellier, France
| | - Serge Urbach
- IGF (Institut de Génomique Fonctionnelle), Univ. Montpellier, CNRS (Centre national de la recherche scientifique), INSERM, Montpellier, France
| | - Khadija El Koulali
- BCM (BioCampus Montpellier), Univ. Montpellier, CNRS (Centre national de la recherche scientifique), INSERM, Montpellier, France
| | - Philippe Holzmuller
- CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Montpellier, France.,ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France
| | - Philippe Totte
- CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Montpellier, France.,ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France
| | - Genevieve Libeau
- CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Montpellier, France.,ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France
| | - Arnaud Bataille
- CIRAD (Agricultural Research Centre for International Development), UMR (Unité Mixte de Recherche), ASTRE (Animal, Health, Territories, Risks and Ecosystems), Montpellier, France.,ASTRE (Animal, Health, Territories, Risks and Ecosystems), University of Montpellier, CIRAD (Agricultural Research Centre for International Development), INRAE (Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement), Montpellier, France
| | - Artur Summerfield
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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9
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Schijns V, Majhen D, van der Ley P, Thakur A, Summerfield A, Berisio R, Nativi C, Fernández-Tejada A, Alvarez-Dominguez C, Gizurarson S, Zamyatina A, Molinaro A, Rosano C, Jakopin Ž, Gursel I, McClean S. Rational Vaccine Design in Times of Emerging Diseases: The Critical Choices of Immunological Correlates of Protection, Vaccine Antigen and Immunomodulation. Pharmaceutics 2021; 13:501. [PMID: 33917629 PMCID: PMC8067490 DOI: 10.3390/pharmaceutics13040501] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 01/21/2023] Open
Abstract
Vaccines are the most effective medical intervention due to their continual success in preventing infections and improving mortality worldwide. Early vaccines were developed empirically however, rational design of vaccines can allow us to optimise their efficacy, by tailoring the immune response. Establishing the immune correlates of protection greatly informs the rational design of vaccines. This facilitates the selection of the best vaccine antigens and the most appropriate vaccine adjuvant to generate optimal memory immune T cell and B cell responses. This review outlines the range of vaccine types that are currently authorised and those under development. We outline the optimal immunological correlates of protection that can be targeted. Finally we review approaches to rational antigen selection and rational vaccine adjuvant design. Harnessing current knowledge on protective immune responses in combination with critical vaccine components is imperative to the prevention of future life-threatening diseases.
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Affiliation(s)
- Virgil Schijns
- Intravacc, Institute for Translational Vaccinology (Intravacc), Utrecht Science Park, 3721 MA Bilthoven, The Netherlands;
- Epitopoietic Research Corporation (ERC), 5374 RE Schaijk, The Netherlands
| | - Dragomira Majhen
- Laboratory for Cell Biology and Signalling, Division of Molecular Biology, Ruđer Bošković Instiute, HR-10000 Zagreb, Croatia;
| | - Peter van der Ley
- Intravacc, Institute for Translational Vaccinology (Intravacc), Utrecht Science Park, 3721 MA Bilthoven, The Netherlands;
| | - Aneesh Thakur
- Department of Pharmacy, University of Copenhagen, 2100 Copenhagen, Denmark;
| | - Artur Summerfield
- Institute of Virology and Immunology, 3147 Mittelhausern, Switzerland;
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3001 Bern, Switzerland
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, I-80134 Naples, Italy;
| | - Cristina Nativi
- Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy;
| | - Alberto Fernández-Tejada
- Chemical Immunology Laboratory, Center for Cooperative Research in Biosciences (CIC bioGUNE), Biscay Science and Technology Park, 48160 Derio-Bilbao, Spain;
- Ikerbasque, Basque Foundation for Science, 48009 Bilbao, Spain
| | - Carmen Alvarez-Dominguez
- Facultativo en plantilla (Research Faculty), Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain;
| | - Sveinbjörn Gizurarson
- Faculty of Pharmaceutical Sciences, University of Iceland, 107 Reykjavik, Iceland;
- Department of Pharmacy, College of Medicine, University of Malawi, Blantyre 3, Malawi
| | - Alla Zamyatina
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Napoli Federico II, Complesso Universitario Monte Santangelo, I-80126 Napoli, Italy;
- Department of Chemistry, School of Science, Osaka University, 1-1 Osaka University Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Camillo Rosano
- Proteomics and Mass Spectrometry Unit, IRCCS Policlinico San Martino, 16132 Genova-1, Italy;
| | - Žiga Jakopin
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubiljana, Slovenia;
| | - Ihsan Gursel
- Molecular Biology and Genetics Department, Science Faculty, Bilkent University, Bilkent, 06800 Ankara, Turkey;
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
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10
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Blanc F, Maroilley T, Revilla M, Lemonnier G, Leplat JJ, Billon Y, Ravon L, Bouchez O, Bidanel JP, Bed'Hom B, Pinard-van der Laan MH, Estellé J, Rogel-Gaillard C. Influence of genetics and the pre-vaccination blood transcriptome on the variability of antibody levels after vaccination against Mycoplasma hyopneumoniae in pigs. Genet Sel Evol 2021; 53:24. [PMID: 33731010 PMCID: PMC7972226 DOI: 10.1186/s12711-021-00614-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 02/16/2021] [Indexed: 12/13/2022] Open
Abstract
Background The impact of individual genetic and genomic variations on immune responses is an emerging lever investigated in vaccination strategies. In our study, we used genetic and pre-vaccination blood transcriptomic data to study vaccine effectiveness in pigs. Results A cohort of 182 Large White pigs was vaccinated against Mycoplasma hyopneumoniae (M. hyo) at weaning (28 days of age), with a booster 21 days later. Vaccine response was assessed by measuring seric M. hyo antibodies (Ab) at 0 (vaccination day), 21 (booster day), 28, 35, and 118 days post-vaccination (dpv). Inter-individual variability of M. hyo Ab levels was observed at all time points and the corresponding heritabilities ranged from 0.46 to 0.57. Ab persistence was higher in females than in males. Genome-wide association studies with a 658 K SNP panel revealed two genomic regions associated with variations of M. hyo Ab levels at 21 dpv at positions where immunity-related genes have been mapped, DAB2IP on chromosome 1, and ASAP1, CYRIB and GSDMC on chromosome 4. We studied covariations of Ab responses with the pre-vaccination blood transcriptome obtained by RNA-Seq for a subset of 82 pigs. Weighted gene correlation network and differential expression analyses between pigs that differed in Ab responses highlighted biological functions that were enriched in heme biosynthesis and platelet activation for low response at 21 dpv, innate antiviral immunity and dendritic cells for high response at 28 and 35 dpv, and cell adhesion and extracellular matrix for high response at 118 dpv. Sparse partial least squares discriminant analysis identified 101 genes that efficiently predicted divergent responders at all time points. We found weak negative correlations of M. hyo Ab levels with body weight traits, which revealed a trade-off that needs to be further explored. Conclusions We confirmed the influence of the host genetics on vaccine effectiveness to M. hyo and provided evidence that the pre-vaccination blood transcriptome co-varies with the Ab response. Our results highlight that both genetic markers and blood biomarkers could be used as potential predictors of vaccine response levels and more studies are required to assess whether they can be exploited in breeding programs.
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Affiliation(s)
- Fany Blanc
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Tatiana Maroilley
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Manuel Revilla
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Gaëtan Lemonnier
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Jean-Jacques Leplat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | | | | | - Jean-Pierre Bidanel
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Bertrand Bed'Hom
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Jordi Estellé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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11
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Contagious Bovine and Caprine Pleuropneumonia: a research community's recommendations for the development of better vaccines. NPJ Vaccines 2020; 5:66. [PMID: 32728480 PMCID: PMC7381681 DOI: 10.1038/s41541-020-00214-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 07/03/2020] [Indexed: 12/26/2022] Open
Abstract
Contagious bovine pleuropneumonia (CBPP) and contagious caprine pleuropneumonia (CCPP) are major infectious diseases of ruminants caused by mycoplasmas in Africa and Asia. In contrast with the limited pathology in the respiratory tract of humans infected with mycoplasmas, CBPP and CCPP are devastating diseases associated with high morbidity and mortality. Beyond their obvious impact on animal health, CBPP and CCPP negatively impact the livelihood and wellbeing of a substantial proportion of livestock-dependent people affecting their culture, economy, trade and nutrition. The causative agents of CBPP and CCPP are Mycoplasma mycoides subspecies mycoides and Mycoplasma capricolum subspecies capripneumoniae, respectively, which have been eradicated in most of the developed world. The current vaccines used for disease control consist of a live attenuated CBPP vaccine and a bacterin vaccine for CCPP, which were developed in the 1960s and 1980s, respectively. Both of these vaccines have many limitations, so better vaccines are urgently needed to improve disease control. In this article the research community prioritized biomedical research needs related to challenge models, rational vaccine design and protective immune responses. Therefore, we scrutinized the current vaccines as well as the challenge-, pathogenicity- and immunity models. We highlight research gaps and provide recommendations towards developing safer and more efficacious vaccines against CBPP and CCPP.
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12
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Wattegedera SR, Livingstone M, Maley S, Rocchi M, Lee S, Pang Y, Wheelhouse NM, Aitchison K, Palarea-Albaladejo J, Buxton D, Longbottom D, Entrican G. Defining immune correlates during latent and active chlamydial infection in sheep. Vet Res 2020; 51:75. [PMID: 32487248 PMCID: PMC7268686 DOI: 10.1186/s13567-020-00798-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Accepted: 05/11/2020] [Indexed: 12/31/2022] Open
Abstract
Ovine enzootic abortion (OEA) caused by the obligate intracellular bacterial pathogen Chlamydia abortus (C. abortus), is an endemic disease in most sheep-rearing countries worldwide. Following infection, C. abortus establishes a complex host-pathogen interaction with a latent phase in non-pregnant sheep followed by an active disease phase in the placenta during pregnancy leading to OEA. Improved knowledge of the host-pathogen interactions at these different phases of disease will accelerate the development of new diagnostic tests and vaccines to control OEA. Current evidence indicates that cellular immunity is essential for controlling C. abortus infection. We have previously described a model of mucosal (intranasal) infection of non-pregnant sheep with C. abortus that replicates the latent and active phases of OEA. We have investigated antigen-specific recall responses of peripheral blood mononuclear cells (PBMC) in sheep infected with C. abortus via the intranasal route to determine how these change during the latent and active phases of disease. By analysing cytokines associated with the major CD4+ve Thelper (Th) cell subsets (Interferon-gamma (IFN-γ)/Th1; Interleukin (IL)-4/Th2; IL-17A/Th17; IL-10/Tregulatory), we show that there is selective activation of PBMC producing IFN-γ and/or IL-10 during the latent phase following infection. These cytokines are also elevated during the active disease phase and while they are produced by sheep that are protected from OEA, they are also produced by sheep that abort, highlighting the difficulties in finding specific cellular immunological correlates of protection for complex intracellular pathogens.
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Affiliation(s)
- Sean R. Wattegedera
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Morag Livingstone
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Stephen Maley
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Mara Rocchi
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Susan Lee
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Yvonne Pang
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Nick M. Wheelhouse
- School of Applied Sciences, Napier University, Edinburgh, Scotland EH11 4BN UK
| | - Kevin Aitchison
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Javier Palarea-Albaladejo
- Biomathematics and Statistics Scotland, JCMB, The King’s Buildings, Peter Guthrie Tait Road, Edinburgh, Scotland EH9 3FD UK
| | - David Buxton
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - David Longbottom
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
| | - Gary Entrican
- Moredun Research Institute, International Research Centre, Pentlands Science Park, Bush Loan, Penicuik, Scotland EH26 0PZ UK
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland EH25 9RG UK
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13
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Jouneau L, Lefebvre DJ, Costa F, Romey A, Blaise-Boisseau S, Relmy A, Jaszczyszyn Y, Dard-Dascot C, Déjean S, Versillé N, Guitton E, Hudelet P, Curet M, De Clercq K, Bakkali-Kassimi L, Zientara S, Klonjkowski B, Schwartz-Cornil I. The antibody response induced FMDV vaccines in sheep correlates with early transcriptomic responses in blood. NPJ Vaccines 2020; 5:1. [PMID: 31908850 PMCID: PMC6941976 DOI: 10.1038/s41541-019-0151-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/29/2019] [Indexed: 11/09/2022] Open
Abstract
Foot and mouth disease (FMD) is a highly contagious viral disease with high economic impact, representing a major threat for cloven-hooved mammals worldwide. Vaccines based on adjuvanted inactivated virus (iFMDV) induce effective protective immunity implicating antibody (Ab) responses. To reduce the biosafety constraints of the manufacturing process, a non-replicative human adenovirus type 5 vector encoding FMDV antigens (Ad5-FMDV) has been developed. Here we compared the immunogenicity of iFMDV and Ad5-FMDV with and without the ISA206VG emulsion-type adjuvant in sheep. Contrasted Ab responses were obtained: iFMDV induced the highest Ab levels, Ad5-FMDV the lowest ones, and ISA206VG increased the Ad5-FMDV-induced Ab responses to protective levels. Each vaccine generated heterogeneous Ab responses, with high and low responders, the latter being considered as obstacles to vaccine effectiveness. A transcriptomic study on total blood responses at 24 h post-vaccination revealed several blood gene module activities correlating with long-term Ab responses. Downmodulation of T cell modules’ activities correlated with high responses to iFMDV and to Ad5-FMDV+ISA206VG vaccines as also found in other systems vaccinology studies in humans and sheep. The impact of cell cycle activity depended on the vaccine types, as it positively correlated with higher responses to iFMDV but negatively to non-adjuvanted Ad5-FMDV. Finally an elevated B cell activity at 24 h correlated with high Ab responses to the Ad5-FMDV+ISA206VG vaccine. This study provides insights into the early mechanisms driving the Ab response induced by different vaccine regimens including Ad5 vectors and points to T cell modules as early biomarker candidates of different vaccine-type efficacy across species. Foot and mouth disease virus (FMDV) is a serious pathogen of cloven hoofed mammals and is of high economic and veterinary importance. Inactivated vaccine (iFMDV) is effective but difficult to produce because of high biosafety level requirements; non-replicating adenovirus vectors carrying key FMDV antigens (Ad5-FMDV) might therefore represent an attractive alternative. Isabelle Schwartz-Cornil and colleagues use sheep to systematically compare vaccination with adjuvanted iFMDV, adjuvanted Ad5-FMDV, or non-adjuvanted Ad5-FMDV. All vaccines produce neutralizing antibody responses which are stable to at least one year, however the iFMDV group elicits the strongest response, followed by the adjuvanted Ad5-FMDV. Ad5-FMDV alone produces weak antibody titers. Blood transcriptomic analysis performed in the first 24 h following vaccination identifies a reduced T cell gene expression module as a correlate of high neutralizing antibody titers. Blood gene expression might therefore offer insights into the mechanistic underpinnings of humoral immunity as well as provide useful biomarker correlates of protection.
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Affiliation(s)
- Luc Jouneau
- Université Paris-Saclay, INRA, VIM, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | - David J Lefebvre
- Sciensano, Scientific Direction of Infectious Diseases in Animals, Service for Exotic Viruses and Particular Diseases, Groeselenberg 99, 1180 Brussels, Belgium
| | - Fleur Costa
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Aurore Romey
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Sandra Blaise-Boisseau
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Anthony Relmy
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Yan Jaszczyszyn
- 4Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Cloelia Dard-Dascot
- 4Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Sébastien Déjean
- 5Université de Toulouse, Université Paul Sabatier, CNRS, Institut de Mathématiques de Toulouse, UMR5219, 31062 Toulouse Cedex, France
| | | | - Edouard Guitton
- INRA, Plate-Forme d'Infectiologie Expérimentale (PFIE), UE1277, 37380 Nouzilly, France
| | - Pascal Hudelet
- 8Merial S.A.S., 29 Avenue Tony Garnier, 69007 Lyon, France
| | - Marianne Curet
- 8Merial S.A.S., 29 Avenue Tony Garnier, 69007 Lyon, France
| | - Kris De Clercq
- Sciensano, Scientific Direction of Infectious Diseases in Animals, Service for Exotic Viruses and Particular Diseases, Groeselenberg 99, 1180 Brussels, Belgium
| | - Labib Bakkali-Kassimi
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Stéphan Zientara
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
| | - Bernard Klonjkowski
- Université Paris-Est, ANSES, Ecole Nationale Vétérinaire d'Alfort, INRA, Laboratoire de santé animale, UMR Virologie, Maisons-Alfort, France
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14
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Maruyama SR, Carvalho B, González-Porta M, Rung J, Brazma A, Gustavo Gardinassi L, Ferreira BR, Banin TM, Veríssimo CJ, Katiki LM, de Miranda-Santos IKF. Blood transcriptome profile induced by an efficacious vaccine formulated with salivary antigens from cattle ticks. NPJ Vaccines 2019; 4:53. [PMID: 31871773 PMCID: PMC6920353 DOI: 10.1038/s41541-019-0145-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 11/13/2019] [Indexed: 12/11/2022] Open
Abstract
Ticks cause massive damage to livestock and vaccines are one sustainable alternative for the acaricide poisons currently heavily used to control infestations. An experimental vaccine adjuvanted with alum and composed by four recombinant salivary antigens mined with reverse vaccinology from a transcriptome of salivary glands from Rhipicephalus microplus ticks was previously shown to present an overall efficacy of 73.2% and cause a significant decrease of tick loads in artificially tick-infested, immunized heifers; this decrease was accompanied by increased levels of antigen-specific IgG1 and IgG2 antibodies, which were boosted during a challenge infestation. In order to gain insights into the systemic effects induced by the vaccine and by the tick challenge we now report the gene expression profile of these hosts' whole-blood leukocytes with RNA-seq followed by functional analyses. These analyses show that vaccination induced unique responses to infestations; genes upregulated in the comparisons were enriched for processes associated with chemotaxis, cell adhesion, T-cell responses and wound repair. Blood transcriptional modules were enriched for activation of dendritic cells, cell cycle, phosphatidylinositol signaling, and platelets. Together, the results indicate that by neutralizing the tick's salivary mediators of parasitism with vaccine-induced antibodies, the bovine host is able to mount normal homeostatic responses that hinder tick attachment and haematophagy and that the tick otherwise suppresses with its saliva.
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Affiliation(s)
- Sandra R. Maruyama
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP Brazil
- Present Address: Department of Genetics and Evolution, Center for Biological Sciences and Health, Federal University of São Carlos, São Carlos, SP Brazil
| | | | - Mar González-Porta
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
- Present Address: Illumina Centre, Cambridge, UK
| | - Johan Rung
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
- Present Address: Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Alvis Brazma
- European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Hinxton, UK
| | - Luiz Gustavo Gardinassi
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Beatriz R. Ferreira
- Ribeirão Preto School of Nursing, University of São Paulo, Ribeirão Preto, SP Brazil
| | - Tamy M. Banin
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, SP Brazil
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15
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Çokçalışkan C, Tuncer Göktuna P, Türkoğlu T, Uzunlu E, Gündüzalp C, Uzun EA, Sareyyüpoğlu B, Kürkçü A, Gülyaz V. Effect of simultaneous administration of foot-and-mouth disease (FMD) and anthrax vaccines on antibody response to FMD in sheep. Clin Exp Vaccine Res 2019; 8:103-109. [PMID: 31406691 PMCID: PMC6689499 DOI: 10.7774/cevr.2019.8.2.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 07/30/2019] [Indexed: 11/15/2022] Open
Abstract
Purpose Foot-and-mouth disease (FMD) and anthrax are important diseases in sheep. Vaccination is a favorable strategy against both infections. Simultaneous administration of vaccines does generally not impede the immune responses of each other, although there are some exceptions, and it may help reduce the labor and costs of vaccination as well as distress on animals. Although oil adjuvant FMD vaccine has been tried with live anthrax vaccine in cattle, there are no reports on the simultaneous use of both vaccines in sheep. Materials and Methods In this study, FMD seronegative sheep were used to investigate the impact of the simultaneous vaccination of FMD and anthrax on FMD antibody titers of sheep. Virus neutralization test and liquid phase blocking enzyme-linked immunosorbent assay were used to determine the antibody response to the FMD vaccine. Results The results demonstrated that both vaccines can be used simultaneously without any interference with the FMD response. Moreover, the simultaneous administration with anthrax vaccine had a stimulating effect on the early (day 7 post-vaccination) virus neutralization antibody response to the FMD vaccine. Conclusion The simultaneous use of the FMD and anthrax vaccines did not hinder the response to the FMD vaccine in sheep.
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Affiliation(s)
- Can Çokçalışkan
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Pelin Tuncer Göktuna
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Tunçer Türkoğlu
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Ergün Uzunlu
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Ceylan Gündüzalp
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Eylem Aras Uzun
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Beyhan Sareyyüpoğlu
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Ayça Kürkçü
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
| | - Veli Gülyaz
- Republic of Turkey Ministry of Agriculture and Forestry, Institute of Foot and Mouth Disease (SAP), Ankara, Turkey
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16
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Matthijs AMF, Auray G, Jakob V, García-Nicolás O, Braun RO, Keller I, Bruggman R, Devriendt B, Boyen F, Guzman CA, Michiels A, Haesebrouck F, Collin N, Barnier-Quer C, Maes D, Summerfield A. Systems Immunology Characterization of Novel Vaccine Formulations for Mycoplasma hyopneumoniae Bacterins. Front Immunol 2019; 10:1087. [PMID: 31178860 PMCID: PMC6543460 DOI: 10.3389/fimmu.2019.01087] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
We characterized five different vaccine candidates and a commercial vaccine in terms of safety, immunogenicity and using a systems vaccinology approach, with the aim to select novel vaccine candidates against Mycoplasma hyopneumoniae. Seven groups of six M. hyopneumoniae-free piglets were primo- and booster vaccinated with the different experimental bacterin formulations, the commercial vaccine Hyogen® as a positive control or PBS as a negative control. The experimental bacterin was formulated with cationic liposomes + c-di-AMP (Lipo_AMP), cationic liposomes + Toll-like receptor (TLR) 2/1, TLR7, and TLR9 ligands (TLR ligands; Lipo_TLR), micro-particles + TLR ligands (PLGA_TLR), squalene-in-water emulsion + TLR ligands (SWE_TLR), or DDA:TDB liposomes (Lipo_DDA:TDB). Lipo_DDA:TDB and Lipo_AMP were the most potent in terms of serum antibody induction, and Lipo_DDA:TDB, Lipo_AMP, and SWE_TLR significantly induced Th1 cytokine-secreting T-cells. Only PLGA_TLR appeared to induce Th17 cells, but was unable to induce serum antibodies. The transcriptomic analyses demonstrated that the induction of inflammatory and myeloid cell blood transcriptional modules (BTM) in the first 24 h after vaccination correlated well with serum antibodies, while negative correlations with the same modules were found 7 days post-vaccination. Furthermore, many cell cycle and T-cell BTM upregulated at day seven correlated positively with adaptive immune responses. When comparing the delivery of the identical TLR ligands with the three formulations, we found SWE_TLR to be more potent in the induction of an early innate immune response, while the liposomal formulation more strongly promoted late cell cycle and T-cell BTM. For the PLGA formulation we found signs of a delayed and weak perturbation of these BTM. Lipo_AMP was found to be the most potent vaccine at inducing a BTM profile similar to that correlating with adaptive immune response in this and other studies. Taken together, we identified four promising vaccine candidates able to induce M. hyopneumoniae-specific antibody and T-cell responses. In addition, we have adapted a systems vaccinology approach developed for human to pigs and demonstrated its capacity in identifying early immune signatures in the blood relating to adaptive immune responses. This approach represents an important step in a more rational design of efficacious vaccines for pigs.
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Affiliation(s)
- Anneleen M F Matthijs
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Gaël Auray
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Virginie Jakob
- Vaccine Formulation Laboratory, University of Lausanne, Epalinges, Switzerland
| | - Obdulio García-Nicolás
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Roman O Braun
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene Keller
- Interfaculty Bioinformatics Unit, Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland.,Department of Biomedical Research, University of Bern, Bern, Switzerland
| | - Rémy Bruggman
- Interfaculty Bioinformatics Unit, Swiss Institute of Bioinformatics, University of Bern, Bern, Switzerland
| | - Bert Devriendt
- Laboratory of Veterinary Immunology, Department of Virology, Parasitology and Immunology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Boyen
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Carlos A Guzman
- Department of Vaccinology and Applied Microbiology, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Annelies Michiels
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nicolas Collin
- Vaccine Formulation Laboratory, University of Lausanne, Epalinges, Switzerland
| | | | - Dominiek Maes
- Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Artur Summerfield
- Institute of Virology and Immunology, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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