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Blanvillain G, Lorch JM, Joudrier N, Bury S, Cuenot T, Franzen M, Martínez-Freiría F, Guiller G, Halpern B, Kolanek A, Kurek K, Lourdais O, Michon A, Musilová R, Schweiger S, Szulc B, Ursenbacher S, Zinenko O, Hoyt JR. Contribution of host species and pathogen clade to snake fungal disease hotspots in Europe. Commun Biol 2024; 7:440. [PMID: 38600171 PMCID: PMC11006896 DOI: 10.1038/s42003-024-06092-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Infectious diseases are influenced by interactions between host and pathogen, and the number of infected hosts is rarely homogenous across the landscape. Areas with elevated pathogen prevalence can maintain a high force of infection and may indicate areas with disease impacts on host populations. However, isolating the ecological processes that result in increases in infection prevalence and intensity remains a challenge. Here we elucidate the contribution of pathogen clade and host species in disease hotspots caused by Ophidiomyces ophidiicola, the pathogen responsible for snake fungal disease, in 21 species of snakes infected with multiple pathogen strains across 10 countries in Europe. We found isolated areas of disease hotspots in a landscape where infections were otherwise low. O. ophidiicola clade had important effects on transmission, and areas with multiple pathogen clades had higher host infection prevalence. Snake species further influenced infection, with most positive detections coming from species within the Natrix genus. Our results suggest that both host and pathogen identity are essential components contributing to increased pathogen prevalence.
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Affiliation(s)
- Gaëlle Blanvillain
- Biological Sciences Department, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
| | - Jeffrey M Lorch
- U.S. Geological Survey, National Wildlife Health Center, Madison, WI, USA
| | - Nicolas Joudrier
- Institute of Biology, University of Neuchâtel, Neuchâtel, Switzerland
- Institute of Animal Pathology, University of Bern, Bern, Switzerland
- Info fauna-Karch, Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour la protection des reptiles et des amphibiens de Suisse (karch), Neuchâtel, Switzerland
| | - Stanislaw Bury
- Department of Comparative Anatomy, Institute of Zoology and Biomedical Research, Jagiellonian University, Cracow, Poland
- NATRIX Herpetological Association, Wroclaw, Poland
| | - Thibault Cuenot
- LPO Bourgogne-Franche-Comté, Site de Franche-Comté, Maison de l'environnement de BFC, Besançon, France
| | - Michael Franzen
- Bavarian State Collection of Zoology (ZSM-SNSB), Munich, Germany
| | - Fernando Martínez-Freiría
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, University of Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | | | - Bálint Halpern
- MME BirdLife Hungary, Budapest, Hungary
- Department of Systematic Zoology and Ecology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN-ELTE-MTM, Integrative Ecology Research Group, Budapest, Hungary
| | - Aleksandra Kolanek
- NATRIX Herpetological Association, Wroclaw, Poland
- Department of Geoinformatics and Cartography, Institute of Geography and Regional Development, Faculty of Earth Sciences and Environmental Management, University of Wroclaw, Wroclaw, Poland
| | - Katarzyna Kurek
- Department of Wildlife Conservation, Institute of Nature Conservation Polish Academy of Science, Cracow, Poland
| | - Olivier Lourdais
- Centre d'Etudes Biologiques de Chizé, ULR CNRS UMR 7372, Villiers en Bois, France
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Alix Michon
- LPO Bourgogne-Franche-Comté, Site de Franche-Comté, Maison de l'environnement de BFC, Besançon, France
| | | | - Silke Schweiger
- First Zoological Department, Herpetological Collection, Natural History Museum, Vienna, Austria
| | - Barbara Szulc
- NATRIX Herpetological Association, Wroclaw, Poland
- Department of Genetics, Kazimierz Wielki University, Bydgoszcz, Poland
| | - Sylvain Ursenbacher
- Info fauna-Karch, Centre Suisse de Cartographie de la Faune (CSCF) and Centre de coordination pour la protection des reptiles et des amphibiens de Suisse (karch), Neuchâtel, Switzerland
- Department of Environmental Sciences, Section of Conservation Biology, University of Basel, Basel, Switzerland
- Balaton Limnological Research Institute, Tihany, Hungary
| | | | - Joseph R Hoyt
- Biological Sciences Department, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
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Igyártó BZ, Qin Z. The mRNA-LNP vaccines - the good, the bad and the ugly? Front Immunol 2024; 15:1336906. [PMID: 38390323 PMCID: PMC10883065 DOI: 10.3389/fimmu.2024.1336906] [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: 11/11/2023] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The mRNA-LNP vaccine has received much attention during the COVID-19 pandemic since it served as the basis of the most widely used SARS-CoV-2 vaccines in Western countries. Based on early clinical trial data, these vaccines were deemed safe and effective for all demographics. However, the latest data raise serious concerns about the safety and effectiveness of these vaccines. Here, we review some of the safety and efficacy concerns identified to date. We also discuss the potential mechanism of observed adverse events related to the use of these vaccines and whether they can be mitigated by alterations of this vaccine mechanism approach.
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Affiliation(s)
- Botond Z. Igyártó
- Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, PA, United States
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Jing S, Milne R, Wang H, Xue L. Vaccine hesitancy promotes emergence of new SARS-CoV-2 variants. J Theor Biol 2023; 570:111522. [PMID: 37210068 DOI: 10.1016/j.jtbi.2023.111522] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/30/2023] [Accepted: 05/03/2023] [Indexed: 05/22/2023]
Abstract
The successive emergence of SARS-CoV-2 mutations has led to an unprecedented increase in COVID-19 incidence worldwide. Currently, vaccination is considered to be the best available solution to control the ongoing COVID-19 pandemic. However, public opposition to vaccination persists in many countries, which can lead to increased COVID-19 caseloads and hence greater opportunities for vaccine-evasive mutant strains to arise. To determine the extent that public opinion regarding vaccination can induce or hamper the emergence of new variants, we develop a model that couples a compartmental disease transmission framework featuring two strains of SARS-CoV-2 with game theoretical dynamics on whether or not to vaccinate. We combine semi-stochastic and deterministic simulations to explore the effect of mutation probability, perceived cost of receiving vaccines, and perceived risks of infection on the emergence and spread of mutant SARS-CoV-2 strains. We find that decreasing the perceived costs of being vaccinated and increasing the perceived risks of infection (that is, decreasing vaccine hesitation) will decrease the possibility of vaccine-resistant mutant strains becoming established by about fourfold for intermediate mutation rates. Conversely, we find increasing vaccine hesitation to cause both higher probability of mutant strains emerging and more wild-type cases after the mutant strain has appeared. We also find that once a new variant has emerged, perceived risk of being infected by the original variant plays a much larger role than perceptions of the new variant in determining future outbreak characteristics. Furthermore, we find that rapid vaccination under non-pharmaceutical interventions is a highly effective strategy for preventing new variant emergence, due to interaction effects between non-pharmaceutical interventions and public support for vaccination. Our findings indicate that policies that combine combating vaccine-related misinformation with non-pharmaceutical interventions (such as reducing social contact) will be the most effective for avoiding the establishment of harmful new variants.
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Affiliation(s)
- Shuanglin Jing
- College of Mathematical Sciences, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
| | - Russell Milne
- Department of Mathematical and Statistical Sciences & Interdisciplinary Lab for Mathematical Ecology and Epidemiology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Hao Wang
- Department of Mathematical and Statistical Sciences & Interdisciplinary Lab for Mathematical Ecology and Epidemiology, University of Alberta, Edmonton, Alberta T6G 2R3, Canada.
| | - Ling Xue
- College of Mathematical Sciences, Harbin Engineering University, Harbin, Heilongjiang, 150001, China
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Del Amparo R, González-Vázquez LD, Rodríguez-Moure L, Bastolla U, Arenas M. Consequences of Genetic Recombination on Protein Folding Stability. J Mol Evol 2023; 91:33-45. [PMID: 36463317 PMCID: PMC9849154 DOI: 10.1007/s00239-022-10080-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/25/2022] [Indexed: 12/05/2022]
Abstract
Genetic recombination is a common evolutionary mechanism that produces molecular diversity. However, its consequences on protein folding stability have not attracted the same attention as in the case of point mutations. Here, we studied the effects of homologous recombination on the computationally predicted protein folding stability for several protein families, finding less detrimental effects than we previously expected. Although recombination can affect multiple protein sites, we found that the fraction of recombined proteins that are eliminated by negative selection because of insufficient stability is not significantly larger than the corresponding fraction of proteins produced by mutation events. Indeed, although recombination disrupts epistatic interactions, the mean stability of recombinant proteins is not lower than that of their parents. On the other hand, the difference of stability between recombined proteins is amplified with respect to the parents, promoting phenotypic diversity. As a result, at least one third of recombined proteins present stability between those of their parents, and a substantial fraction have higher or lower stability than those of both parents. As expected, we found that parents with similar sequences tend to produce recombined proteins with stability close to that of the parents. Finally, the simulation of protein evolution along the ancestral recombination graph with empirical substitution models commonly used in phylogenetics, which ignore constraints on protein folding stability, showed that recombination favors the decrease of folding stability, supporting the convenience of adopting structurally constrained models when possible for inferences of protein evolutionary histories with recombination.
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Affiliation(s)
- Roberto Del Amparo
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Luis Daniel González-Vázquez
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Laura Rodríguez-Moure
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain
| | - Ugo Bastolla
- Centre for Molecular Biology Severo Ochoa (CSIC-UAM), 28049 Madrid, Spain
| | - Miguel Arenas
- CINBIO, Universidade de Vigo, 36310 Vigo, Spain ,Departamento de Bioquímica, Genética e Inmunología, Universidade de Vigo, 36310 Vigo, Spain ,Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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Bull JJ, Antia R. Which 'imperfect vaccines' encourage the evolution of higher virulence? Evol Med Public Health 2022; 10:202-213. [PMID: 35539897 PMCID: PMC9081871 DOI: 10.1093/emph/eoac015] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Background and objectives Theory suggests that some types of vaccines against infectious pathogens may lead to the evolution of variants that cause increased harm, particularly when they infect unvaccinated individuals. This theory was supported by the observation that the use of an imperfect vaccine to control Marek's disease virus in chickens resulted in the virus evolving to be more lethal to unvaccinated birds. This raises the concern that the use of some other vaccines may lead to similar pernicious outcomes. We examine that theory with a focus on considering the regimes in which such outcomes are expected. Methodology We evaluate the plausibility of assumptions in the original theory. The previous theory rested heavily on a particular form of transmission-mortality-recovery trade-off and invoked other assumptions about the pathways of evolution. We review alternatives to mortality in limiting transmission and consider evolutionary pathways that were omitted in the original theory. Results The regime where the pernicious evolutionary outcome occurs is narrowed by our analysis but remains possible in various scenarios. We propose a more nuanced consideration of alternative models for the within-host dynamics of infections and for factors that limit virulence. Our analysis suggests imperfect vaccines against many pathogens will not lead to the evolution of pathogens with increased virulence in unvaccinated individuals. Conclusions and implications Evolution of greater pathogen mortality driven by vaccination remains difficult to predict, but the scope for such outcomes appears limited. Incorporation of mechanistic details into the framework, especially regarding immunity, may be requisite for prediction accuracy. Lay Summary A virus of chickens appears to have evolved high mortality in response to a vaccine that merely prevented disease symptoms. Theory has predicted this type of evolution in response to a variety of vaccines and other interventions such as drug treatment. Under what circumstances is this pernicious result likely to occur? Analysis of the theory in light of recent changes in our understanding of viral biology raises doubts that medicine-driven, pernicious evolution is likely to be common. But we are far from a mechanistic understanding of the interaction between pathogen and host that can predict when vaccines and other medical interventions will lead to the unwanted evolution of more virulent pathogens. So, while the regime where a pernicious result obtains may be limited, caution remains warranted in designing many types of interventions.
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Affiliation(s)
- James J Bull
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA,Department of Biological Sciences, University of Idaho, Moscow, ID 83844-3051, USA. E-mail:
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
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