1
|
Bastide P, Rocu P, Wirtz J, Hassler GW, Chevenet F, Fargette D, Suchard MA, Dellicour S, Lemey P, Guindon S. Modeling the velocity of evolving lineages and predicting dispersal patterns. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.06.597755. [PMID: 38895258 PMCID: PMC11185746 DOI: 10.1101/2024.06.06.597755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Accurate estimation of the dispersal velocity or speed of evolving organisms is no mean feat. In fact, existing probabilistic models in phylogeography or spatial population genetics generally do not provide an adequate framework to define velocity in a relevant manner. For instance, the very concept of instantaneous speed simply does not exist under one of the most popular approaches that models the evolution of spatial coordinates as Brownian trajectories running along a phylogeny [30]. Here, we introduce a new family of models - the so-called "Phylogenetic Integrated Velocity" (PIV) models - that use Gaussian processes to explicitly model the velocity of evolving lineages instead of focusing on the fluctuation of spatial coordinates over time. We describe the properties of these models and show an increased accuracy of velocity estimates compared to previous approaches. Analyses of West Nile virus data in the U.S.A. indicate that PIV models provide sensible predictions of the dispersal of evolving pathogens at a one-year time horizon. These results demonstrate the feasibility and relevance of predictive phylogeography in monitoring epidemics in time and space.
Collapse
Affiliation(s)
- Paul Bastide
- IMAG, Université de Montpellier, CNRS, Montpellier, France
| | - Pauline Rocu
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier. CNRS - UMR 5506. Montpellier, France
| | - Johannes Wirtz
- CEFE, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Gabriel W Hassler
- Department of Economics, Sociology, and Statistics, RAND, Santa Monica, CA, USA
| | | | - Denis Fargette
- PHIM, IRD, INRAE, CIRAD, Université de Montpellier, Montpellier, France
| | - Marc A Suchard
- Department of Biostatistics, Jonathan and Karin Fielding School of Public Health, University of California, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
- Department of Computational Medicine, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA, USA
| | - Simon Dellicour
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven, Belgium
| | - Stéphane Guindon
- Laboratoire d'Informatique, de Robotique et de Microélectronique de Montpellier. CNRS - UMR 5506. Montpellier, France
| |
Collapse
|
2
|
Cantoni D, Mayora-Neto M, Derveni M, da Costa K, Del Rosario J, Ameh VO, Sabeta CT, Auld B, Hamlet A, Jones IM, Wright E, Scott SD, Giotis ES, Banyard AC, Temperton N. Serological evidence of virus infection in Eidolon helvum fruit bats: implications for bushmeat consumption in Nigeria. Front Public Health 2023; 11:1283113. [PMID: 38106901 PMCID: PMC10723585 DOI: 10.3389/fpubh.2023.1283113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/02/2023] [Indexed: 12/19/2023] Open
Abstract
Introduction The Eidolon helvum fruit bat is one of the most widely distributed fruit bats in Africa and known to be a reservoir for several pathogenic viruses that can cause disease in animals and humans. To assess the risk of zoonotic spillover, we conducted a serological survey of 304 serum samples from E. helvum bats that were captured for human consumption in Makurdi, Nigeria. Methods Using pseudotyped viruses, we screened 304 serum samples for neutralizing antibodies against viruses from the Coronaviridae, Filoviridae, Orthomyxoviridae and Paramyxoviridae families. Results We report the presence of neutralizing antibodies against henipavirus lineage GH-M74a virus (odds ratio 6.23; p < 0.001), Nipah virus (odds ratio 4.04; p = 0.00031), bat influenza H17N10 virus (odds ratio 7.25; p < 0.001) and no significant association with Ebola virus (odds ratio 0.56; p = 0.375) in this bat cohort. Conclusion The data suggest a potential risk of zoonotic spillover including the possible circulation of highly pathogenic viruses in E. helvum populations. These findings highlight the importance of maintaining sero-surveillance of E. helvum, and the necessity for further, more comprehensive investigations to monitor changes in virus prevalence, distribution over time, and across different geographic locations.
Collapse
Affiliation(s)
- Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Martin Mayora-Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Mariliza Derveni
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kelly da Costa
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Joanne Del Rosario
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Veronica O. Ameh
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - Claude T. Sabeta
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
- World Organisation for Animal Health Rabies Reference Laboratory, Agricultural Research Council-Onderstepoort Veterinary Research, Onderstepoort, South Africa
| | - Bethany Auld
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Arran Hamlet
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Ian M. Jones
- School of Biological Sciences, University of Reading, Reading, United Kingdom
| | - Edward Wright
- Viral Pseudotype Unit, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Simon D. Scott
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| | - Efstathios S. Giotis
- Department of Infectious Diseases, Imperial College London, London, United Kingdom
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | | | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, Universities of Kent and Greenwich, Chatham, United Kingdom
| |
Collapse
|
3
|
Ben Geoffrey AS, Gracia J. A Bayesian walker coupled with a computational workflow that generates the micro-evolution of SARS-CoV-2 and makes predictions of new mutations that can emerge. J Biomol Struct Dyn 2023:1-9. [PMID: 37771150 DOI: 10.1080/07391102.2023.2263798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 09/22/2023] [Indexed: 09/30/2023]
Abstract
In this work, a Bayesian walker was constructed that generates mutations that are more prone as per UNIPROT variant data. The Bayesian walker was used to search the mutational landscape of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2) and a computational workflow was followed to evaluate whether a particular mutation would satisfy natural selection's fitness criteria. For SARS-CoV-2, the empirical known fitness criteria derived from SARS-CoV-2 micro-evolution data is 3-fold criteria. Mutations that have emerged on the Spike protein of SARS-CoV-2 are ones that preserve the structural integrity of the Spike, retain, or increase infectivity and are Immune evasive as per literature reports. Based on the molecular mechanism of infectivity and Immune evasion of SARS-CoV-2, a molecular modelling workflow was adopted to investigate the evolutionary feasibility of the mutations generated by the walker, to check whether the mutations satisfy the 3-fold fitness criteria for SARS-CoV-2 micro-evolution. It was found that the walker (mutation generator) coupled with the computational workflow to evaluate the evolutionary fitness of the generated mutations, re-generated the mutants corresponding to the Alpha, Beta and Gamma variants of SARS-CoV-2 demonstrating the ability of the methodology to generate the micro-evolution of SARS-CoV-2. Having demonstrated the ability of the methodology to generate the micro-evolution of SARS-CoV-2, the computational methodology was used to make predictions for new mutants that could emerge.Communicated by Ramaswamy H. Sarma.
Collapse
|
4
|
Colom MS, Vucinic J, Adolf-Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Complete Combinatorial Mutational Enumeration of a protein functional site enables sequence-landscape mapping and identifies highly-mutated variants that retain activity. RESEARCH SQUARE 2023:rs.3.rs-2248327. [PMID: 36482980 PMCID: PMC9727770 DOI: 10.21203/rs.3.rs-2248327/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Understanding how proteins evolve under selective pressure is a longstanding challenge. The immensity of the search space has limited efforts to systematically evaluate the impact of multiple simultaneous mutations, so mutations have typically been assessed individually. However, epistasis, or the way in which mutations interact, prevents accurate prediction of combinatorial mutations based on measurements of individual mutations. Here, we use artificial intelligence to define the entire functional sequence landscape of a protein binding site in silico, and we call this approach Complete Combinatorial Mutational Enumeration (CCME). By leveraging CCME, we are able to construct a comprehensive map of the evolutionary connectivity within this functional sequence landscape. As a proof of concept, we applied CCME to the ACE2 binding site of the SARS-CoV-2 spike protein receptor binding domain. We selected representative variants from across the functional sequence landscape for testing in the laboratory. We identified variants that retained functionality to bind ACE2 despite changing over 40% of evaluated residue positions, and the variants now escape binding and neutralization by monoclonal antibodies. This work represents a crucial initial stride towards achieving precise predictions of pathogen evolution, opening avenues for proactive mitigation.
Collapse
Affiliation(s)
- Mireia Solà Colom
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Jelena Vucinic
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Jared Adolf-Bryfogle
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
| | - James W. Bowman
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Sébastien Verel
- Université Littoral Côte d’Opale; UR 4491, LISIC, F-62100 Calais, France
| | - Isabelle Moczygemba
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| | - Thomas Schiex
- Université Fédérale de Toulouse; ANITI, INRAE-UR 875, 31000 Toulouse, France
| | - David Simoncini
- Université Fédérale de Toulouse; ANITI, IRIT-CNRS UMR 5505, Université Toulouse Capitole, 31000 Toulouse, France
| | - Christopher D. Bahl
- Institute for Protein Innovation; Boston, Massachusetts, 02115, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Harvard Medical School; Boston, Massachusetts, 02115, USA
- current address: AI Proteins; Boston, Massachusetts, 02215, USA
| |
Collapse
|
5
|
Qin L, Ding S, He Z. Compositional biases and evolution of the largest plant RNA virus order Patatavirales. Int J Biol Macromol 2023; 240:124403. [PMID: 37076075 DOI: 10.1016/j.ijbiomac.2023.124403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/13/2023] [Accepted: 03/25/2023] [Indexed: 04/21/2023]
Abstract
Patatavirales is the largest order of plant RNA viruses and exclusively contains the family Potyviridae, accounting for 30 % of all known plant viruses. The composition bias of animal RNA viruses and several plant RNA viruses has been determined. However, the comprehensive nucleic acid composition, codon pair usage patterns, dinucleotide preference and codon pair preference of plant RNA viruses have not been investigated to date. In this study, integrated analysis and discussion of the nucleic acid composition, codon usage patterns, dinucleotide composition and codon pair bias of potyvirids were performed using 3732 complete genome coding sequences. The nucleic acid composition of potyvirids was significantly enriched in A/U. Interestingly, the A/U-rich nucleotide composition of Patatavirales is essential for determining the preferred A-ended and U-ended codons and the overexpression of UpG and CpA dinucleotides. The codon usage patterns and codon pair bias of potyvirids were significantly correlated with their nucleic acid composition. Additionally, the codon usage pattern, dinucleotide composition and codon-pair bias of potyvirids are more dependent on the classification of the virus compared with their hosts. Our analysis provides a better understanding of future research on the origin and evolution patterns of the order Patatavirales.
Collapse
Affiliation(s)
- Lang Qin
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China
| | - Zhen He
- College of Plant Protection, Yangzhou University, Wenhui East Road No.48, Yangzhou 225009, Jiangsu Province, PR China.
| |
Collapse
|
6
|
Sun B, Ni M, Liu H, Liu D. Viral intra-host evolutionary dynamics revealed via serial passage of Japanese encephalitis virus in vitro. Virus Evol 2023; 9:veac103. [PMID: 37205166 PMCID: PMC10185921 DOI: 10.1093/ve/veac103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/04/2022] [Accepted: 03/21/2023] [Indexed: 12/02/2023] Open
Abstract
Analyses of viral inter- and intra-host mutations could better guide the prevention and control of infectious diseases. For a long time, studies on viral evolution have focused on viral inter-host variations. Next-generation sequencing has accelerated the investigations of viral intra-host diversity. However, the theoretical basis and dynamic characteristics of viral intra-host mutations remain unknown. Here, using serial passages of the SA14-14-2 vaccine strain of Japanese encephalitis virus (JEV) as the in vitro model, the distribution characteristics of 1,788 detected intra-host single-nucleotide variations (iSNVs) and their mutated frequencies from 477 deep-sequenced samples were analyzed. Our results revealed that in adaptive (baby hamster kidney (BHK)) cells, JEV is under a nearly neutral selection pressure, and both non-synonymous and synonymous mutations represent an S-shaped growth trend over time. A higher positive selection pressure was observed in the nonadaptive (C6/36) cells, and logarithmic growth in non-synonymous iSNVs and linear growth in synonymous iSNVs were observed over time. Moreover, the mutation rates of the NS4B protein and the untranslated region (UTR) of the JEV are significantly different between BHK and C6/36 cells, suggesting that viral selection pressure is regulated by different cellular environments. In addition, no significant difference was detected in the distribution of mutated frequencies of iSNVs between BHK and C6/36 cells.
Collapse
Affiliation(s)
- Bangyao Sun
- School of Medical Laboratory, Weifang Medical University, Baotong West Street, Weifang 261053, China
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| | - Ming Ni
- Beijing Institute of Radiation Medicine, Taiping Road 27#, Beijing 100850, China
| | - Haizhou Liu
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
| | - Di Liu
- CAS Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- Computational Virology Group, Center for Bacteria and Viruses Resources and Bioinformation, Wuhan Institute of Virology, Chinese Academy of Sciences, Xiaohongshan 44#, Wuhan 430000, China
- University of Chinese Academy of Sciences, Yuquan Road 19#, Beijing 100049, China
| |
Collapse
|
7
|
Delgado MS, López-Galíndez C, Moran F. Viral Fitness Landscapes Based on Self-organizing Maps. Curr Top Microbiol Immunol 2023; 439:95-119. [PMID: 36592243 DOI: 10.1007/978-3-031-15640-3_2] [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] [Indexed: 01/03/2023]
Abstract
The creation of fitness maps from viral populations especially in the case of RNA viruses, with high mutation rates producing quasispecies, is complex since the mutant spectrum is in a very high-dimensional space. In this work, a new approach is presented using a class of neural networks, Self-Organized Maps (SOM), to represent realistic fitness landscapes in two RNA viruses: Human Immunodeficiency Virus type 1 (HIV-1) and Hepatitis C Virus (HCV). This methodology has proven to be very effective in the classification of viral quasispecies, using as criterium the mutant sequences in the population. With HIV-1, the fitness landscapes are constructed by representing the experimentally determined fitness on the sequence map. This approach permitted the depiction of the evolutionary paths of the variants subjected to processes of fitness loss and gain in cell culture. In the case of HCV, the efficiency was measured as a function of the frequency of each haplotype in the population by ultra-deep sequencing. The fitness landscapes obtained provided information on the efficiency of each variant in the quasispecies environment, that is, in relation to the entire spectrum of mutants. With the SOM maps, it is possible to determine the evolutionary dynamics of the different haplotypes.
Collapse
Affiliation(s)
- M Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos (ETSISI), Universidad Politécnica de Madrid, 28031, Madrid, Spain.
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en Retrovirus, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Federico Moran
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, 28040, Madrid, Spain
| |
Collapse
|
8
|
He Z, Qin L, Xu X, Ding S. Evolution and host adaptability of plant RNA viruses: Research insights on compositional biases. Comput Struct Biotechnol J 2022; 20:2600-2610. [PMID: 35685354 PMCID: PMC9160401 DOI: 10.1016/j.csbj.2022.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 01/23/2023] Open
Abstract
During recent decades, many new emerging or re-emerging RNA viruses have been found in plants through the development of deep-sequencing technology and big data analysis. These findings largely changed our understanding of the origin, evolution and host range of plant RNA viruses. There is evidence that their genetic composition originates from viruses, and host populations play a key role in the evolution and host adaptability of plant RNA viruses. In this mini-review, we describe the state of our understanding of the evolution of plant RNA viruses in view of compositional biases and explore how they adapt to the host. It appears that adenine rich (A-rich) coding sequences, low CpG and UpA dinucleotide frequencies and lower codon usage patterns were found in the vast majority of plant RNA viruses. The codon usage pattern of plant RNA viruses was influenced by both natural selection and mutation pressure, and natural selection mostly from hosts was the dominant factor. The codon adaptation analyses support that plant RNA viruses probably evolved a dynamic balance between codon adaptation and deoptimization to maintain efficient replication cycles in multiple hosts with various codon usage patterns. In the future, additional combinations of computational and experimental analyses of the nucleotide composition and codon usage of plant RNA viruses should be addressed.
Collapse
Affiliation(s)
- Zhen He
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
- Corresponding author.
| | - Lang Qin
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Xiaowei Xu
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| | - Shiwen Ding
- School of Horticulture and Plant Protection, Yangzhou University, Wenhui East Road No. 48, Yangzhou 225009, Jiangsu Province, PR China
| |
Collapse
|
9
|
Abstract
The twenty-first century has witnessed a wave of severe infectious disease outbreaks, not least the COVID-19 pandemic, which has had a devastating impact on lives and livelihoods around the globe. The 2003 severe acute respiratory syndrome coronavirus outbreak, the 2009 swine flu pandemic, the 2012 Middle East respiratory syndrome coronavirus outbreak, the 2013-2016 Ebola virus disease epidemic in West Africa and the 2015 Zika virus disease epidemic all resulted in substantial morbidity and mortality while spreading across borders to infect people in multiple countries. At the same time, the past few decades have ushered in an unprecedented era of technological, demographic and climatic change: airline flights have doubled since 2000, since 2007 more people live in urban areas than rural areas, population numbers continue to climb and climate change presents an escalating threat to society. In this Review, we consider the extent to which these recent global changes have increased the risk of infectious disease outbreaks, even as improved sanitation and access to health care have resulted in considerable progress worldwide.
Collapse
|
10
|
Majewska AA, Huang T, Han B, Drake JM. Predictors of zoonotic potential in helminths. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200356. [PMID: 34538139 PMCID: PMC8450625 DOI: 10.1098/rstb.2020.0356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Helminths are parasites that cause disease at considerable cost to public health and present a risk for emergence as novel human infections. Although recent research has elucidated characteristics conferring a propensity to emergence in other parasite groups (e.g. viruses), the understanding of factors associated with zoonotic potential in helminths remains poor. We applied an investigator-directed learning algorithm to a global dataset of mammal helminth traits to identify factors contributing to spillover of helminths from wild animal hosts into humans. We characterized parasite traits that distinguish between zoonotic and non-zoonotic species with 91% accuracy. Results suggest that helminth traits relating to transmission (e.g. definitive and intermediate hosts) and geography (e.g. distribution) are more important to discriminating zoonotic from non-zoonotic species than morphological or epidemiological traits. Whether or not a helminth causes infection in companion animals (cats and dogs) is the most important predictor of propensity to cause human infection. Finally, we identified helminth species with high modelled propensity to cause zoonosis (over 70%) that have not previously been considered to be of risk. This work highlights the importance of prioritizing studies on the transmission of helminths that infect pets and points to the risks incurred by close associations with these animals. This article is part of the theme issue 'Infectious disease macroecology: parasite diversity and dynamics across the globe'.
Collapse
Affiliation(s)
- Ania A Majewska
- Odum School of Ecology and the Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA.,Biology Department, Emory University, Atlanta, GA, USA
| | - Tao Huang
- Cary Institute of Ecosystem Studies, Millbrook, NY, USA.,Ecology, Evolution, and Behavior, Boise State University, Boise, ID, USA
| | - Barbara Han
- Cary Institute of Ecosystem Studies, Millbrook, NY, USA
| | - John M Drake
- Odum School of Ecology and the Center for Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| |
Collapse
|
11
|
Imrie RM, Roberts KE, Longdon B. Between virus correlations in the outcome of infection across host species: Evidence of virus by host species interactions. Evol Lett 2021; 5:472-483. [PMID: 34621534 PMCID: PMC8484721 DOI: 10.1002/evl3.247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 06/15/2021] [Accepted: 06/28/2021] [Indexed: 12/24/2022] Open
Abstract
Virus host shifts are a major source of outbreaks and emerging infectious diseases, and predicting the outcome of novel host and virus interactions remains a key challenge for virus research. The evolutionary relationships between host species can explain variation in transmission rates, virulence, and virus community composition between hosts, but it is unclear if correlations exist between related viruses in infection traits across novel hosts. Here, we measure correlations in viral load of four Cripavirus isolates across experimental infections of 45 Drosophilidae host species. We find positive correlations between every pair of viruses tested, suggesting that some host clades show broad susceptibility and could act as reservoirs and donors for certain types of viruses. Additionally, we find evidence of virus by host species interactions, highlighting the importance of both host and virus traits in determining the outcome of virus host shifts. Of the four viruses tested here, those that were more closely related tended to be more strongly correlated, providing tentative evidence that virus evolutionary relatedness may be a useful proxy for determining the likelihood of novel virus emergence, which warrants further research.
Collapse
Affiliation(s)
- Ryan M. Imrie
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| | - Katherine E. Roberts
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| | - Ben Longdon
- Centre for Ecology and Conservation, Biosciences, College of Life and Environmental SciencesUniversity of ExeterPenrynTR10 9FEUnited Kingdom
| |
Collapse
|
12
|
Villarreal LP, Witzany G. Social Networking of Quasi-Species Consortia drive Virolution via Persistence. AIMS Microbiol 2021; 7:138-162. [PMID: 34250372 PMCID: PMC8255905 DOI: 10.3934/microbiol.2021010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022] Open
Abstract
The emergence of cooperative quasi-species consortia (QS-C) thinking from the more accepted quasispecies equations of Manfred Eigen, provides a conceptual foundation from which concerted action of RNA agents can now be understood. As group membership becomes a basic criteria for the emergence of living systems, we also start to understand why the history and context of social RNA networks become crucial for survival and function. History and context of social RNA networks also lead to the emergence of a natural genetic code. Indeed, this QS-C thinking can also provide us with a transition point between the chemical world of RNA replicators and the living world of RNA agents that actively differentiate self from non-self and generate group identity with membership roles. Importantly the social force of a consortia to solve complex, multilevel problems also depend on using opposing and minority functions. The consortial action of social networks of RNA stem-loops subsequently lead to the evolution of cellular organisms representing a tree of life.
Collapse
|
13
|
Yousefi B, Valizadeh S, Ghaffari H, Vahedi A, Karbalaei M, Eslami M. A global treatments for coronaviruses including COVID-19. J Cell Physiol 2020; 235:9133-9142. [PMID: 32394467 PMCID: PMC7273044 DOI: 10.1002/jcp.29785] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/03/2020] [Indexed: 02/06/2023]
Abstract
In late December 2019 in Wuhan, China, several patients with viral pneumonia were identified as 2019 novel coronavirus (2019‐nCoV). So far, there are no specific treatments for patients with coronavirus disease‐19 (COVID‐19), and the treatments available today are based on previous experience with similar viruses such as severe acute respiratory syndrome‐related coronavirus (SARS‐CoV), Middle East respiratory syndrome coronavirus (MERS‐CoV), and Influenza virus. In this article, we have tried to reach a therapeutic window of drugs available to patients with COVID‐19. Cathepsin L is required for entry of the 2019‐nCoV virus into the cell as target teicoplanin inhibits virus replication. Angiotensin‐converting‐enzyme 2 (ACE2) in soluble form as a recombinant protein can prevent the spread of coronavirus by restricting binding and entry. In patients with COVID‐19, hydroxychloroquine decreases the inflammatory response and cytokine storm, but overdose causes toxicity and mortality. Neuraminidase inhibitors such as oseltamivir, peramivir, and zanamivir are invalid for 2019‐nCoV and are not recommended for treatment but protease inhibitors such as lopinavir/ritonavir (LPV/r) inhibit the progression of MERS‐CoV disease and can be useful for patients of COVID‐19 and, in combination with Arbidol, has a direct antiviral effect on early replication of SARS‐CoV. Ribavirin reduces hemoglobin concentrations in respiratory patients, and remdesivir improves respiratory symptoms. Use of ribavirin in combination with LPV/r in patients with SARS‐CoV reduces acute respiratory distress syndrome and mortality, which has a significant protective effect with the addition of corticosteroids. Favipiravir increases clinical recovery and reduces respiratory problems and has a stronger antiviral effect than LPV/r. currently, appropriate treatment for patients with COVID‐19 is an ACE2 inhibitor and a clinical problem reducing agent such as favipiravir in addition to hydroxychloroquine and corticosteroids.
Collapse
Affiliation(s)
- Bahman Yousefi
- Department of Immunology, Semnan University of Medical Sciences, Semnan, Iran
| | - Saeid Valizadeh
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Hadi Ghaffari
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Azadeh Vahedi
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran
| | - Mohsen Karbalaei
- Department of Microbiology and Virology, School of Medicine, Jiroft University of Medical Sciences, Jiroft, Iran
| | - Majid Eslami
- Department of Bacteriology and Virology, Semnan University of Medical Sciences, Semnan, Iran.,Cancer Research Center, Semnan University of Medical Sciences, Semnan, Iran
| |
Collapse
|
14
|
Epidemiology and evolutionary analysis of Torque teno sus virus. Vet Microbiol 2020; 244:108668. [PMID: 32402339 DOI: 10.1016/j.vetmic.2020.108668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 11/20/2022]
Abstract
Single stranded (ss) DNA viruses are increasingly being discovered due to the ongoing development of modern technologies in exploring the virosphere. Characterized by high rates of recombination and nucleotide substitutions, it could be comparable to RNA virus ones. Torque teno sus virus (TTSuV) is a standard ssDNA virus with a high population diversity, whose evolution is still obscure, further, it is frequently found in co-infections with other viruses threatening the porcine industry and therefore share the same host and epidemiological context. Here, we implement and describe approach to integrate viral nucleotide sequence analysis, surveillance data, and a structural approach to examine the evolution of TTSuVs, we collected samples from pigs displaying respiratory signs in China and revealed a high prevalence of TTSuV1 and TTSuVk2, frequently as part of co-infections with porcine circoviruses (PCVs), especially in spleen and lung. In addition, thirty six strains sequenced were obtained to investigate their genetic diversity in China. The evolutionary history of TTSuVs were unveiled as following: At the nucleotide sequence level, TTSuVs ORF1 was confirmed to be a robust phylogenetic maker to study evolution comparably to full genomes. Additionally, extensive recombination discovered within TTSuVk2a (also 5 out of the 36 sequenced strains in this study revealed to be recombination). Then, pairwise distance, phylogenetic trees, and amino acid analysis confirmed TTSuVs species, and allowed to define circulating genotypes (TTSuV1a-1, 1a-2, 1b-1, 1b-2, 1b-3, and k2a-1, k2a-2, k2b). Selection analysis uncovered seven and six positive selected sites in TTSuV1 and TTSuVk2, respectively. At the protein structure level, mapping of sites onto the three-dimensional structure revealed that several positive selected sites locate into potential epitopes, which might related to the potential escaping from host immune response. Our result could assist future studies on swine ssDNA virus classification, surveillance and control.
Collapse
|
15
|
Faber MS, Van Leuven JT, Ederer MM, Sapozhnikov Y, Wilson ZL, Wichman HA, Whitehead TA, Miller CR. Saturation Mutagenesis Genome Engineering of Infective ΦX174 Bacteriophage via Unamplified Oligo Pools and Golden Gate Assembly. ACS Synth Biol 2020; 9:125-131. [PMID: 31825605 PMCID: PMC7055157 DOI: 10.1021/acssynbio.9b00411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Here we present a novel protocol for the construction of saturation single-site-and massive multisite-mutant libraries of a bacteriophage. We segmented the ΦX174 genome into 14 nontoxic and nonreplicative fragments compatible with Golden Gate assembly. We next used nicking mutagenesis with oligonucleotides prepared from unamplified oligo pools with individual segments as templates to prepare near-comprehensive single-site mutagenesis libraries of genes encoding the F capsid protein (421 amino acids scanned) and G spike protein (172 amino acids scanned). Libraries possessed greater than 99% of all 11 860 programmed mutations. Golden Gate cloning was then used to assemble the complete ΦX174 mutant genome and generate libraries of infective viruses. This protocol will enable reverse genetics experiments for studying viral evolution and, with some modifications, can be applied for engineering therapeutically relevant bacteriophages with larger genomes.
Collapse
Affiliation(s)
- Matthew S. Faber
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - James T. Van Leuven
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho 83844, United States
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Martina M. Ederer
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Yesol Sapozhnikov
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Zoë L. Wilson
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Holly A. Wichman
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho 83844, United States
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Timothy A. Whitehead
- Department of Chemical & Biological Engineering, University of Colorado, Boulder, Colorado 80303, United States
- Department of Chemical Engineering & Materials Science, Michigan State University, East Lansing, Michigan 48824, United States
| | - Craig R. Miller
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, Idaho 83844, United States
- Department of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
| |
Collapse
|
16
|
Ryt-Hansen P, Pedersen AG, Larsen I, Krog JS, Kristensen CS, Larsen LE. Acute Influenza A virus outbreak in an enzootic infected sow herd: Impact on viral dynamics, genetic and antigenic variability and effect of maternally derived antibodies and vaccination. PLoS One 2019; 14:e0224854. [PMID: 31725751 PMCID: PMC6855628 DOI: 10.1371/journal.pone.0224854] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Influenza A virus (IAV) is a highly contagious pathogen in pigs. Swine IAV (swIAV) infection causes respiratory disease and is thereby a challenge for animal health, animal welfare and the production economy. In Europe, the most widespread strategy for controlling swIAV is implementation of sow vaccination programs, to secure delivery of protective maternally derived antibodies (MDAs) to the newborn piglets. In this study we report a unique case, where a persistently swIAV (A/sw/Denmark/P5U4/2016(H1N1)) infected herd experienced an acute outbreak with a new swIAV subtype (A/sw/Denmark/HB4280U1/2017(H1N2)) and subsequently decided to implement a mass sow vaccination program. Clinical registrations, nasal swabs and blood samples were collected from four different batches of pigs before and after vaccination. Virus isolation, sequencing of the virus strain and hemagglutinin inhibition (HI) tests were performed on samples collected before and during the outbreak and after implementation of mass sow vaccination. After implementation of the sow mass vaccination, the time of infection was delayed and the viral load significantly decreased. An increased number of pigs, however, tested positive at two consecutive sampling times indicating prolonged shedding. In addition, a significantly smaller proportion of the 10–12 weeks old pigs were seropositive by the end of the study, indicating an impaired induction of antibodies against swIAV in the presence of MDAs. Sequencing of the herd strains revealed major differences in the hemagglutinin gene of the strain isolated before- and during the acute outbreak despite that, the two strains belonged to the same HA lineage. The HI tests confirmed a limited degree of cross-reaction between the two strains. Furthermore, the sequencing results of the hemagglutinin gene obtained before and after implementation of mass sow vaccination revealed an increased substitution rate and an increase in positively selected sites in the globular head of the hemagglutinin after vaccination.
Collapse
Affiliation(s)
- Pia Ryt-Hansen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- * E-mail:
| | - Anders Gorm Pedersen
- Department of Health Technology, Section for Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Inge Larsen
- University of Copenhagen, Dpt. of Veterinary and Animal Sciences, Frederiksberg C, Denmark
| | - Jesper Schak Krog
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | - Lars Erik Larsen
- National Veterinary Institute, Technical University of Denmark, Kongens Lyngby, Denmark
- University of Copenhagen, Dpt. of Veterinary and Animal Sciences, Frederiksberg C, Denmark
| |
Collapse
|
17
|
Population Genomics of GII.4 Noroviruses Reveal Complex Diversification and New Antigenic Sites Involved in the Emergence of Pandemic Strains. mBio 2019; 10:mBio.02202-19. [PMID: 31551337 PMCID: PMC6759766 DOI: 10.1128/mbio.02202-19] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Noroviruses are an important cause of viral gastroenteritis around the world. An obstacle delaying the development of norovirus vaccines is inadequate understanding of the role of norovirus diversity in immunity. Using a population genomics approach, we identified new residues on the viral capsid protein (VP1) from GII.4 noroviruses, the predominant genotype, that appear to be involved in the emergence and antigenic topology of GII.4 variants. Careful monitoring of the substitutions in those residues involved in the diversification and emergence of new viruses could help in the early detection of future novel variants with pandemic potential. Therefore, this novel information on the antigenic diversification could facilitate GII.4 norovirus vaccine design. GII.4 noroviruses are a major cause of acute gastroenteritis. Their dominance has been partially explained by the continuous emergence of antigenically distinct variants. To gain insights into the mechanisms of viral emergence and population dynamics of GII.4 noroviruses, we performed large-scale genomics, structural, and mutational analyses of the viral capsid protein (VP1). GII.4 noroviruses exhibited a periodic replacement of predominant variants with accumulation of amino acid substitutions. Genomic analyses revealed (i) a large proportion (87%) of conserved residues; (ii) variable residues that map on the previously determined antigenic sites; and (iii) variable residues that map outside the antigenic sites. Residues in the third pattern category formed motifs on the surface of VP1, which suggested extensions of previously predicted and new uncharacterized antigenic sites. The role of two motifs (C and G) in the antigenic makeup of the GII.4 capsid protein was confirmed with monoclonal antibodies and carbohydrate blocking assays. Amino acid profiles from antigenic sites (A, C, D, E, and G) correlated with the circulation patterns of GII.4 variants, with three of them (A, C, and G) containing residues (352, 357, 368, and 378) linked with the diversifying selective pressure on the emergence of new GII.4 variants. Notably, the emergence of each variant was followed by stochastic diversification with minimal changes that did not progress toward the next variant. This report provides a methodological framework for antigenic characterization of viruses and expands our understanding of the dynamics of GII.4 noroviruses and could facilitate the design of cross-reactive vaccines.
Collapse
|
18
|
Jácome R, Carrasco-Hernández R, Campillo-Balderas JA, López-Vidal Y, Lazcano A, Wenzel RP, Ponce de León S. A yellow flag on the horizon: The looming threat of yellow fever to North America. Int J Infect Dis 2019; 87:143-150. [PMID: 31382047 DOI: 10.1016/j.ijid.2019.07.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/26/2019] [Accepted: 07/26/2019] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVES Yellow fever virus historically was a frequent threat to American and European coasts. Medical milestones such as the discovery of mosquitoes as vectors and subsequently an effective vaccine significantly reduced its incidence, in spite of which, thousands of cases of this deathly disease still occur regularly in Sub-Saharan Africa and the Amazonian basin in South America, which are usually not reported. An urban outbreak in Angola, consecutive years of increasing incidence near major Brazilian cities, and imported cases in China, South America and Europe, have brought this virus back to the global spotlight. The aim of this article is to underline that the preventive YFV measures, such as vaccination, need to be carefully revised in order to minimize the risks of new YFV outbreaks, especially in urban or immunologically vulnerable places. Furthermore, this article highlights the diverse factors that have favored the spread of other Aedes spp.-associated arboviral diseases like Dengue, Chikungunya and Zika, to northern latitudes causing epidemics in the United States and Europe, emphasizing the possibility that YFV might follow the path of these viruses unless enhanced surveillance and efficient control systems are urgently initiated.
Collapse
Affiliation(s)
- Rodrigo Jácome
- Laboratorio de Origen de la Vida, Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico
| | - R Carrasco-Hernández
- División de Investigación, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico
| | - José Alberto Campillo-Balderas
- Laboratorio de Origen de la Vida, Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico
| | - Yolanda López-Vidal
- Programa de Inmunología Molecular Microbiana, Facultad de Medicina, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico
| | - Antonio Lazcano
- Laboratorio de Origen de la Vida, Facultad de Ciencias, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico; Miembro de El Colegio Nacional, Mexico
| | | | - Samuel Ponce de León
- Programa Universitario de Investigación en Salud, Universidad Nacional Autónoma de México, Av. Universidad 3000, C.P. 04510, Mexico City, Mexico.
| |
Collapse
|
19
|
Qiu X, Duvvuri VR, Bahl J. Computational Approaches and Challenges to Developing Universal Influenza Vaccines. Vaccines (Basel) 2019; 7:E45. [PMID: 31141933 PMCID: PMC6631137 DOI: 10.3390/vaccines7020045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/15/2019] [Accepted: 05/23/2019] [Indexed: 12/25/2022] Open
Abstract
The traditional design of effective vaccines for rapidly-evolving pathogens, such as influenza A virus, has failed to provide broad spectrum and long-lasting protection. With low cost whole genome sequencing technology and powerful computing capabilities, novel computational approaches have demonstrated the potential to facilitate the design of a universal influenza vaccine. However, few studies have integrated computational optimization in the design and discovery of new vaccines. Understanding the potential of computational vaccine design is necessary before these approaches can be implemented on a broad scale. This review summarizes some promising computational approaches under current development, including computationally optimized broadly reactive antigens with consensus sequences, phylogenetic model-based ancestral sequence reconstruction, and immunomics to compute conserved cross-reactive T-cell epitopes. Interactions between virus-host-environment determine the evolvability of the influenza population. We propose that with the development of novel technologies that allow the integration of data sources such as protein structural modeling, host antibody repertoire analysis and advanced phylodynamic modeling, computational approaches will be crucial for the development of a long-lasting universal influenza vaccine. Taken together, computational approaches are powerful and promising tools for the development of a universal influenza vaccine with durable and broad protection.
Collapse
Affiliation(s)
- Xueting Qiu
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Venkata R Duvvuri
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
| | - Justin Bahl
- Center for Ecology of Infectious Diseases, Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA.
- Department of Epidemiology and Biostatistics, College of Public Health, University of Georgia, Athens, GA 30606, USA.
- Duke-NUS Graduate Medical School, Singapore 169857, Singapore.
| |
Collapse
|
20
|
Galbreath KE, Hoberg EP, Cook JA, Armién B, Bell KC, Campbell ML, Dunnum JL, Dursahinhan AT, Eckerlin RP, Gardner SL, Greiman SE, Henttonen H, Jiménez FA, Koehler AVA, Nyamsuren B, Tkach VV, Torres-Pérez F, Tsvetkova A, Hope AG. Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites. J Mammal 2019; 100:382-393. [PMID: 31043762 PMCID: PMC6479512 DOI: 10.1093/jmammal/gyz048] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023] Open
Abstract
Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.
Collapse
Affiliation(s)
- Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI, USA
| | - Eric P Hoberg
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Joseph A Cook
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Blas Armién
- Instituto Conmemorativo Gorgas de Estudios de la Salud, Panama City, Panama
| | - Kayce C Bell
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Mariel L Campbell
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Jonathan L Dunnum
- Biology Department and Museum of Southwestern Biology, University of New Mexico, CERIA Building, Albuquerque, NM, USA
| | - Altangerel T Dursahinhan
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Ralph P Eckerlin
- Mathematics, Science and Engineering Division, Northern Virginia Community College, Annandale, VA, USA
| | - Scott L Gardner
- Harold W. Manter Laboratory of Parasitology, Division of Parasitology, University of Nebraska State Museum, W Nebraska Hall University of Nebraska–Lincoln, Lincoln, NE, USA
| | - Stephen E Greiman
- Biology Department, Georgia Southern University, Statesboro, GA, USA
| | | | - F Agustín Jiménez
- Department of Zoology, Southern Illinois University, Carbondale, IL, USA
| | - Anson V A Koehler
- Department of Veterinary Biosciences, The University of Melbourne, Cnr Flemington Road and Park Drive, Parkville, Victoria, Australia
| | | | - Vasyl V Tkach
- Biology Department, University of North Dakota, Grand Forks, ND, USA
| | - Fernando Torres-Pérez
- Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Albina Tsvetkova
- Institute of Ecology and Evolution A.N. Severtsov RAS, Saratov Branch, Saratov, Russia
| | - Andrew G Hope
- Division of Biology, Kansas State University, Manhattan, KS, USA
| |
Collapse
|
21
|
Titcomb GC, Jerde CL, Young HS. High-Throughput Sequencing for Understanding the Ecology of Emerging Infectious Diseases at the Wildlife-Human Interface. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00126] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
22
|
Abstract
The deterministic force of natural selection and stochastic influence of drift shape RNA virus evolution. New deep-sequencing and microfluidics technologies allow us to quantify the effect of mutations and trace the evolution of viral populations with single-genome and single-nucleotide resolution. Such experiments can reveal the topography of the genotype-fitness landscapes that shape the path of viral evolution. By combining historical analyses, like phylogenetic approaches, with high-throughput and high-resolution evolutionary experiments, we can observe parallel patterns of evolution that drive important phenotypic transitions. These developments provide a framework for quantifying and anticipating potential evolutionary events. Here, we examine emerging technologies that can map the selective landscapes of viruses, focusing on their application to pathogenic viruses. We identify areas where these technologies can bolster our ability to study the evolution of viruses and to anticipate and possibly intervene in evolutionary events and prevent viral disease.
Collapse
Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, E200 Clark Center, 318 Campus Drive, Stanford, CA 94305, USA; Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, 600 16th Street, GH-S572, UCSF Box 2280, San Francisco, CA 94143-2280, USA.
| |
Collapse
|
23
|
Host-Specific Glycans Are Correlated with Susceptibility to Infection by Lagoviruses, but Not with Their Virulence. J Virol 2018; 92:JVI.01759-17. [PMID: 29187537 DOI: 10.1128/jvi.01759-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 11/16/2017] [Indexed: 11/20/2022] Open
Abstract
Rabbit hemorrhagic disease virus (RHDV) and European brown hare syndrome virus (EBHSV) are two lagoviruses from the family Caliciviridae that cause fatal diseases in two leporid genera, Oryctolagus and Lepus, respectively. In the last few years, several examples of host jumps of lagoviruses among leporids were recorded. In addition, a new pathogenic genotype of RHDV emerged, and many nonpathogenic strains of lagoviruses have been described. The molecular mechanisms behind host shifts and the emergence of virulence are unknown. Since RHDV uses glycans of the histo-blood group antigen type as attachment factors to initiate infection, we studied if glycan specificities of the new pathogenic RHDV genotype, nonpathogenic lagoviruses, and EBHSV potentially play a role in determining the host range and virulence of lagoviruses. We observed binding to A, B, or H antigens of the histo-blood group family for all strains known to primarily infect European rabbits (Oryctolagus cuniculus), which have recently been classified as GI strains. However, we could not explain the emergence of virulence, since similar glycan specificities were found in several pathogenic and nonpathogenic strains. In contrast, EBHSV, recently classified as GII.1, bound to terminal β-linked N-acetylglucosamine residues of O-glycans. Expression of these attachment factors in the upper respiratory and digestive tracts in three lagomorph species (Oryctolagus cuniculus, Lepus europaeus, and Sylvilagus floridanus) showed species-specific patterns regarding susceptibility to infection by these viruses, indicating that species-specific glycan expression is likely a major contributor to lagovirus host specificity and range.IMPORTANCE Lagoviruses constitute a genus of the family Caliciviridae comprising highly pathogenic viruses, RHDV and EBHSV, that infect rabbits and hares, respectively. Recently, nonpathogenic strains were discovered and new pathogenic strains have emerged. In addition, host jumps between lagomorphs have been observed. The mechanisms responsible for the emergence of pathogenicity and host species range are unknown. Previous studies showed that RHDV strains attach to glycans expressed in the upper respiratory and digestive tracts of rabbits, the likely portals of virus entry. Here, we studied the glycan-binding properties of novel pathogenic and nonpathogenic strains looking for a link between glycan binding and virulence or between glycan specificity and host range. We found that glycan binding did not correlate with virulence. However, expression of glycan motifs in the upper respiratory and digestive tracts of lagomorphs revealed species-specific patterns associated with the host ranges of the virus strains, suggesting that glycan diversity contributes to lagovirus host ranges.
Collapse
|
24
|
Carrasco-Hernandez R, Jácome R, López Vidal Y, Ponce de León S. Are RNA Viruses Candidate Agents for the Next Global Pandemic? A Review. ILAR J 2017; 58:343-358. [PMID: 28985316 PMCID: PMC7108571 DOI: 10.1093/ilar/ilx026] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 07/14/2017] [Accepted: 07/15/2017] [Indexed: 12/16/2022] Open
Abstract
Pathogenic RNA viruses are potentially the most important group involved in zoonotic disease transmission, and they represent a challenge for global disease control. Their biological diversity and rapid adaptive rates have proved to be difficult to overcome and to anticipate by modern medical technology. Also, the anthropogenic change of natural ecosystems and the continuous population growth are driving increased rates of interspecies contacts and the interchange of pathogens that can develop into global pandemics. The combination of molecular, epidemiological, and ecological knowledge of RNA viruses is therefore essential towards the proper control of these emergent pathogens. This review outlines, throughout different levels of complexity, the problems posed by RNA viral diseases, covering some of the molecular mechanisms allowing them to adapt to new host species-and to novel pharmaceutical developments-up to the known ecological processes involved in zoonotic transmission.
Collapse
Affiliation(s)
- R Carrasco-Hernandez
- R. Carrasco-Hernandez, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Rodrigo Jácome
- Rodrigo Jácome, MD, PhD, is a postdoctoral research fellow at the Microbiome Laboratory in the Postgraduate Division of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Yolanda López Vidal
- Yolanda López-Vidal, MD, PhD, is an associate professor “C” and is responsible for the Program of Microbial Molecular Immunology in the Department of Microbiology and Parasitology of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| | - Samuel Ponce de León
- Samuel Ponce-de-León, MD, MSc, is an associate professor “C”, is responsible for the Microbiome Laboratory and Coordinator of the University Program for Health Research of the Faculty of Medicine at the Universidad Nacional Autónoma de México, CDMX
| |
Collapse
|
25
|
Wong AHM, Tomlinson ACA, Zhou D, Satkunarajah M, Chen K, Sharon C, Desforges M, Talbot PJ, Rini JM. Receptor-binding loops in alphacoronavirus adaptation and evolution. Nat Commun 2017; 8:1735. [PMID: 29170370 PMCID: PMC5701055 DOI: 10.1038/s41467-017-01706-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 10/06/2017] [Indexed: 02/08/2023] Open
Abstract
RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding. Coronaviruses have a relatively high mutation rate, potentially allowing fast adaptation to changing pressures. Here, Wong et al. provide the structure of the receptor-binding domain (RBD) of the human coronavirus HCoV-229E and its receptor and analyze the evolution of the RBD over the past 50 years.
Collapse
Affiliation(s)
- Alan H M Wong
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Aidan C A Tomlinson
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Dongxia Zhou
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Malathy Satkunarajah
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Kevin Chen
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Chetna Sharon
- Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, 531 Boulevard des Prairies, Laval, Québec, Canada, H7V 1B7
| | - James M Rini
- Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8. .,Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.
| |
Collapse
|
26
|
McColl KA, Sunarto A, Slater J, Bell K, Asmus M, Fulton W, Hall K, Brown P, Gilligan D, Hoad J, Williams LM, Crane MSJ. Cyprinid herpesvirus 3 as a potential biological control agent for carp (Cyprinus carpio) in Australia: susceptibility of non-target species. JOURNAL OF FISH DISEASES 2017; 40:1141-1153. [PMID: 28026008 DOI: 10.1111/jfd.12591] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/20/2016] [Accepted: 10/21/2016] [Indexed: 06/06/2023]
Abstract
Carp (Cyprinus carpio L.) is a pest species in Australian waterways, and cyprinid herpesvirus 3 (CyHV-3) is being considered as a potential biological control (biocontrol) agent. An important consideration for any such agent is its target specificity. In this study, the susceptibility to CyHV-3 of a range of non-target species (NTS) was tested. The NTS were as follows: 13 native Australian, and one introduced, fish species; a lamprey species; a crustacean; two native amphibian species (tadpole and mature stages); two native reptilian species; chickens; and laboratory mice. Animals were exposed to 100-1000 times the approximate minimum amount of CyHV-3 required to cause disease in carp by intraperitoneal and/or bath challenge, and then examined clinically each day over the course of 28 days post-challenge. There were no clinical signs, mortalities or histological evidence consistent with a viral infection in a wide taxonomic range of NTS. Furthermore, there was no molecular evidence of infection with CyHV-3, and, in particular, all RT-PCRs for viral mRNA were negative. As a consequence, the results encourage further investigation of CyHV-3 as a potential biocontrol agent that is specific for carp.
Collapse
Affiliation(s)
- K A McColl
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - A Sunarto
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - J Slater
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - K Bell
- K&C Global Fisheries, Sale, Vic., Australia
| | - M Asmus
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW, Australia
| | - W Fulton
- Department of Primary Industries, Fisheries Research Branch, Queenscliff, Vic., Australia
| | - K Hall
- Department of Primary Industries, Fisheries Research Branch, Queenscliff, Vic., Australia
| | - P Brown
- The Murray-Darling Freshwater Research Centre and La Trobe University, Mildura, Vic., Australia
| | - D Gilligan
- Department of Primary Industries, Narrandera Fisheries Centre, Narrandera, NSW, Australia
| | - J Hoad
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - L M Williams
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| | - M St J Crane
- CSIRO-Australian Animal Health Laboratory, Geelong, Vic., Australia
| |
Collapse
|
27
|
Transmission and evolution of tick-borne viruses. Curr Opin Virol 2016; 21:67-74. [PMID: 27569396 DOI: 10.1016/j.coviro.2016.08.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 02/05/2023]
Abstract
Ticks transmit a diverse array of viruses such as tick-borne encephalitis virus, Powassan virus, and Crimean-Congo hemorrhagic fever virus that are reemerging in many parts of the world. Most tick-borne viruses (TBVs) are RNA viruses that replicate using error-prone polymerases and produce genetically diverse viral populations that facilitate their rapid evolution and adaptation to novel environments. This article reviews the mechanisms of virus transmission by tick vectors, the molecular evolution of TBVs circulating in nature, and the processes shaping viral diversity within hosts to better understand how these viruses may become public health threats. In addition, remaining questions and future directions for research are discussed.
Collapse
|
28
|
Birch M, Bolker BM. Evolutionary Stability of Minimal Mutation Rates in an Evo-epidemiological Model. Bull Math Biol 2015; 77:1985-2003. [PMID: 26507879 DOI: 10.1007/s11538-015-0112-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 10/02/2015] [Indexed: 10/22/2022]
Abstract
We consider the evolution of mutation rate in a seasonally forced, deterministic, compartmental epidemiological model with a transmission-virulence trade-off. We model virulence as a quantitative genetic trait in a haploid population and mutation as continuous diffusion in the trait space. There is a mutation rate threshold above which the pathogen cannot invade a wholly susceptible population. The evolutionarily stable (ESS) mutation rate is the one which drives the lowest average density, over the course of one forcing period, of susceptible individuals at steady state. In contrast with earlier eco-evolutionary models in which higher mutation rates allow for better evolutionary tracking of a dynamic environment, numerical calculations suggest that in our model the minimum average susceptible population, and hence the ESS, is achieved by a pathogen strain with zero mutation. We discuss how this result arises within our model and how the model might be modified to obtain a nonzero optimum.
Collapse
Affiliation(s)
- Michael Birch
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON, L8S 4K1, Canada.
| | - Benjamin M Bolker
- Department of Mathematics and Statistics, McMaster University, Hamilton, ON, L8S 4K1, Canada
| |
Collapse
|
29
|
Alonso WJ, McCormick BJJ, Miller MA, Schuck-Paim C, Asrar GR. Beyond crystal balls: crosscutting solutions in global health to prepare for an unpredictable future. BMC Public Health 2015; 15:955. [PMID: 26400682 PMCID: PMC4581487 DOI: 10.1186/s12889-015-2285-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 09/15/2015] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Efforts in global heath need to deal not only with current challenges, but also to anticipate new scenarios, which sometimes unfold at lightning speed. Predictive modeling is frequently used to assist planning, but outcomes depend heavily on a subset of critical assumptions, which are mostly hampered by our limited knowledge about the many factors, mechanisms and relationships that determine the dynamics of disease systems, by a lack of data to parameterize and validate models, and by uncertainties about future scenarios. DISCUSSION We propose a shift from a focus on the prediction of individual disease patterns to the identification and mitigation of broader fragilities in public health systems. Modeling capabilities should be used to perform "stress tests" on how interrelated fragilities respond when faced with a range of possible or plausible threats of different nature and intensity. This system should be able to reveal crosscutting solutions with the potential to address not only one threat, but multiple areas of vulnerability to future health risks. Actionable knowledge not based on a narrow subset of threats and conditions can better guide policy, build societal resilience and ensure effective prevention in an uncertain world.
Collapse
Affiliation(s)
- Wladimir Jimenez Alonso
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA.
- Origem Scientifica, São Paulo, São Paulo, Brazil.
| | | | - Mark A Miller
- Fogarty International Center, National Institutes of Health, Bethesda, Maryland, 20892, USA.
| | | | - Ghassem R Asrar
- Joint Global Change Research Institute, University of Maryland, College Park, MD, 20740, USA.
| |
Collapse
|
30
|
|
31
|
Stapleford KA, Coffey LL, Lay S, Bordería AV, Duong V, Isakov O, Rozen-Gagnon K, Arias-Goeta C, Blanc H, Beaucourt S, Haliloğlu T, Schmitt C, Bonne I, Ben-Tal N, Shomron N, Failloux AB, Buchy P, Vignuzzi M. Emergence and transmission of arbovirus evolutionary intermediates with epidemic potential. Cell Host Microbe 2015; 15:706-16. [PMID: 24922573 DOI: 10.1016/j.chom.2014.05.008] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 03/19/2014] [Accepted: 04/22/2014] [Indexed: 01/14/2023]
Abstract
The high replication and mutation rates of RNA viruses can result in the emergence of new epidemic variants. Thus, the ability to follow host-specific evolutionary trajectories of viruses is essential to predict and prevent epidemics. By studying the spatial and temporal evolution of chikungunya virus during natural transmission between mosquitoes and mammals, we have identified viral evolutionary intermediates prior to emergence. Analysis of virus populations at anatomical barriers revealed that the mosquito midgut and salivary gland pose population bottlenecks. By focusing on virus subpopulations in the saliva of multiple mosquito strains, we recapitulated the emergence of a recent epidemic strain of chikungunya and identified E1 glycoprotein mutations with potential to emerge in the future. These mutations confer fitness advantages in mosquito and mammalian hosts by altering virion stability and fusogenic activity. Thus, virus evolutionary trajectories can be predicted and studied in the short term before new variants displace currently circulating strains.
Collapse
Affiliation(s)
- Kenneth A Stapleford
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Lark L Coffey
- Center for Vectorborne Diseases, Department of Pathology, Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis, One Shields Avenue, 5327 VM3A, Davis, CA 95616, USA
| | - Sreyrath Lay
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Antonio V Bordería
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Veasna Duong
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Ofer Isakov
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Kathryn Rozen-Gagnon
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Camilo Arias-Goeta
- Arboviruses and Insect Vectors Lab, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Stéphanie Beaucourt
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Türkan Haliloğlu
- Department of Chemical Engineering and Polymer Research Center, Boğaziçi University, Bebek 34342, Istanbul, Turkey
| | - Christine Schmitt
- Ultrastructural Microscopy Platform, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Isabelle Bonne
- Ultrastructural Microscopy Platform, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Noam Shomron
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Anna-Bella Failloux
- Arboviruses and Insect Vectors Lab, Institut Pasteur, 25 rue du Dr Roux, 75724 Paris Cedex 15, France
| | - Philippe Buchy
- Virology Unit, Institut Pasteur in Cambodia 5, Monivong Boulevard, PO Box 983, Phnom Penh, Cambodia
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, Centre National de la Recherche Scientifique UMR 3569, 28 rue du Dr Roux, 75724 Paris Cedex 15, France.
| |
Collapse
|
32
|
Expected Effect of Deleterious Mutations on Within-Host Adaptation of Pathogens. J Virol 2015; 89:9242-51. [PMID: 26109724 DOI: 10.1128/jvi.00832-15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 06/20/2015] [Indexed: 01/09/2023] Open
Abstract
UNLABELLED Adaptation is a common theme in both pathogen emergence, for example, in zoonotic cross-species transmission, and pathogen control, where adaptation might limit the effect of the immune response and antiviral treatment. When such evolution requires deleterious intermediate mutations, fitness ridges and valleys arise in the pathogen's fitness landscape. The effect of deleterious intermediate mutations on within-host pathogen adaptation is examined with deterministic calculations, appropriate for pathogens replicating in large populations with high error rates. The effect of deleterious intermediate mutations on pathogen adaptation is smaller than their name might suggest: when two mutations are required and each individual single mutation is fully deleterious, the pathogen can jump across the fitness valley by obtaining two mutations at once, leading to a proportion of adapted mutants that is 20-fold lower than that in the situation where the fitness of all mutants is neutral. The negative effects of deleterious intermediates are typically substantially smaller and outweighed by the fitness advantages of the adapted mutant. Moreover, requiring a specific mutation order has a substantially smaller effect on pathogen adaptation than the effect of all intermediates being deleterious. These results can be rationalized when the number of routes of mutation available to the pathogen is calculated, providing a simple approach to estimate the effect of deleterious mutations. The calculations discussed here are applicable when the effect of deleterious mutations on the within-host adaptation of pathogens is assessed, for example, in the context of zoonotic emergence, antigenic escape, and drug resistance. IMPORTANCE Adaptation is critical for pathogens after zoonotic transmission into a new host species or to achieve antigenic immune escape and drug resistance. Using a deterministic approach, the effects of deleterious intermediate mutations on pathogen adaptation were calculated while avoiding commonly made simplifications that do not apply to large pathogen populations replicating with high mutation rates. Perhaps unexpectedly, pathogen adaptation does not halt when the intermediate mutations are fully deleterious. The negative effects of deleterious mutations are substantially outweighed by the fitness gains of adaptation. To gain an understanding of the effect of deleterious mutations on pathogen adaptation, a simple approach that counts the number of routes available to the pathogen with and without deleterious intermediate mutations is introduced. This methodology enables a straightforward calculation of the proportion of the pathogen population that will cross a fitness valley or traverse a fitness ridge, without reverting to more complicated mathematical models.
Collapse
|
33
|
Holmes EC, Zhang YZ. The evolution and emergence of hantaviruses. Curr Opin Virol 2015; 10:27-33. [PMID: 25562117 DOI: 10.1016/j.coviro.2014.12.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/25/2014] [Accepted: 12/17/2014] [Indexed: 12/20/2022]
Abstract
Hantaviruses are a major class of zoonotic pathogens and cause a variety of severe diseases in humans. For most of the last 50 years rodents have been considered to be the primary hosts of hantaviruses, with hantavirus evolution thought to reflect a process of virus-rodent co-divergence over a time-scale of millions of years, with occasional spill-over into humans. However, recent discoveries have revealed that hantaviruses infect a more diverse range of mammalian hosts, particularly Chiroptera (bats) and Soricomorpha (moles and shrews), and that cross-species transmission at multiple scales has played an important role in hantavirus evolution. As a consequence, the evolution and emergence of hantaviruses is more complex than previously anticipated, and may serve as a realistic model for other viral groups.
Collapse
Affiliation(s)
- Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia; State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China.
| | - Yong-Zhen Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Department of Zoonoses, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, China
| |
Collapse
|
34
|
Pernet O, Schneider BS, Beaty SM, LeBreton M, Yun TE, Park A, Zachariah TT, Bowden TA, Hitchens P, Ramirez CM, Daszak P, Mazet J, Freiberg AN, Wolfe ND, Lee B. Evidence for henipavirus spillover into human populations in Africa. Nat Commun 2014; 5:5342. [PMID: 25405640 PMCID: PMC4237230 DOI: 10.1038/ncomms6342] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Accepted: 09/19/2014] [Indexed: 02/06/2023] Open
Abstract
Zoonotic transmission of lethal henipaviruses (HNVs) from their natural fruit bat reservoirs to humans has only been reported in Australia and South/Southeast Asia. However, a recent study discovered numerous HNV clades in African bat samples. To determine the potential for HNV spillover events among humans in Africa, here we examine well-curated sets of bat (Eidolon helvum, n=44) and human (n=497) serum samples from Cameroon for Nipah virus (NiV) cross-neutralizing antibodies (NiV-X-Nabs). Using a vesicular stomatitis virus (VSV)-based pseudoparticle seroneutralization assay, we detect NiV-X-Nabs in 48% and 3–4% of the bat and human samples, respectively. Seropositive human samples are found almost exclusively in individuals who reported butchering bats for bushmeat. Seropositive human sera also neutralize Hendra virus and Gh-M74a (an African HNV) pseudoparticles, as well as live NiV. Butchering bat meat and living in areas undergoing deforestation are the most significant risk factors associated with seropositivity. Evidence for HNV spillover events warrants increased surveillance efforts. Henipaviruses (HNVs) infect bats in Asia and Africa, but transmission to humans (often with lethal consequences) is known only in Asia. Here the authors show that 3% of human serum samples from certain areas in Cameroon contain antibodies against HNV, indicating spillover into the human population.
Collapse
Affiliation(s)
- Olivier Pernet
- Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA
| | - Bradley S Schneider
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Shannon M Beaty
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Matthew LeBreton
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Tatyana E Yun
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Arnold Park
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Trevor T Zachariah
- Brevard Zoo Veterinary Services, Brevard Zoo, Melbourne, 32940 Florida, USA
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN UK
| | - Peta Hitchens
- Department of Medicine and Epidemiology, School of Veterinary Medicine, UC Davis, Davis, California 95616, USA
| | - Christina M Ramirez
- Department of Biostatistics, School of Public Health, UCLA, Los Angeles, California 90095, USA
| | - Peter Daszak
- EcoHealth Alliance, New York, New York 10001, USA
| | - Jonna Mazet
- Department of Medicine and Epidemiology, School of Veterinary Medicine, UC Davis, Davis, California 95616, USA
| | - Alexander N Freiberg
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas 77555, USA
| | - Nathan D Wolfe
- Global Viral/Metabiota Laboratory Sciences, San Francisco, California 90104, USA
| | - Benhur Lee
- 1] Department of Microbiology, Immunology and Molecular Genetics, David Geffen School of Medicine at UCLA, Los Angeles, California 90095, USA [2] Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| |
Collapse
|
35
|
Abstract
Emerging viral diseases are often the product of a host shift, where a pathogen jumps from its original host into a novel species. Phylogenetic studies show that host shifts are a frequent event in the evolution of most pathogens, but why pathogens successfully jump between some host species but not others is only just becoming clear. The susceptibility of potential new hosts can vary enormously, with close relatives of the natural host typically being the most susceptible. Often, pathogens must adapt to successfully infect a novel host, for example by evolving to use different cell surface receptors, to escape the immune response, or to ensure they are transmitted by the new host. In viruses there are often limited molecular solutions to achieve this, and the same sequence changes are often seen each time a virus infects a particular host. These changes may come at a cost to other aspects of the pathogen's fitness, and this may sometimes prevent host shifts from occurring. Here we examine how these evolutionary factors affect patterns of host shifts and disease emergence.
Collapse
Affiliation(s)
- Ben Longdon
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| | | | - Colin A. Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - John J. Welch
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Francis M. Jiggins
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
36
|
Viral biocontrol: grand experiments in disease emergence and evolution. Trends Microbiol 2014; 23:83-90. [PMID: 25455418 DOI: 10.1016/j.tim.2014.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 10/08/2014] [Accepted: 10/10/2014] [Indexed: 02/05/2023]
Abstract
Although viral emergence is commonly associated with cross-species transmission, the processes and determinants of viral evolution in a novel host environment are poorly understood. We address key questions in virus emergence and evolution using data generated from two unique natural experiments: the deliberate release of myxoma virus (MYXV) and rabbit hemorrhagic disease virus (RHDV) as biological control (biocontrol) agents against the European rabbit in Australia, and which have been of enormous benefit to Australia's ecosystem and agricultural industries. Notably, although virulence evolution in MYXV and RHDV followed different trajectories, a strongly parallel evolutionary process was observed in Australia and Europe. These biocontrol agents were also characterized by a lack of transmission to nontarget host species, suggesting that there are major barriers to successful emergence.
Collapse
|
37
|
Emergence of rice yellow mottle virus in eastern Uganda: Recent and singular interplay between strains in East Africa and in Madagascar. Virus Res 2014; 195:64-72. [PMID: 25245592 DOI: 10.1016/j.virusres.2014.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2014] [Revised: 09/10/2014] [Accepted: 09/12/2014] [Indexed: 11/22/2022]
Abstract
Epidemics of rice yellow mottle virus (RYMV) have developed recently in eastern Uganda, close to Lake Victoria in East Africa. Unexpectedly, all isolates from the affected area belonged to a single strain (named S4ug), a strain that is different from the S4lv strain that has been prevalent in the Lake Victoria basin for the past five decades. Interestingly, the S4ug strain is most closely related at the genomic level (except ORF1) to the strain present in Madagascar (S4mg), 2000km away. The minor parent of the S4mg recombinant strain could not be detected. Molecular clock dating analysis indicated that the singular sequence of events - that associated the emergence of a new strain (S4ug), a modular recombination between closely related strains (S4mg and S4ug) and a long distance transmission (S4mg) - occurred recently, within the past few decades. This finding is at variance with the process of gradual strain dispersal and diversification over two centuries throughout Africa that was previously established.
Collapse
|
38
|
Elsworth P, Cooke BD, Kovaliski J, Sinclair R, Holmes EC, Strive T. Increased virulence of rabbit haemorrhagic disease virus associated with genetic resistance in wild Australian rabbits (Oryctolagus cuniculus). Virology 2014; 464-465:415-423. [PMID: 25146599 DOI: 10.1016/j.virol.2014.06.037] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 06/10/2014] [Accepted: 06/12/2014] [Indexed: 01/14/2023]
Abstract
The release of myxoma virus (MYXV) and Rabbit Haemorrhagic Disease Virus (RHDV) in Australia with the aim of controlling overabundant rabbits has provided a unique opportunity to study the initial spread and establishment of emerging pathogens, as well as their co-evolution with their mammalian hosts. In contrast to MYXV, which attenuated shortly after its introduction, rapid attenuation of RHDV has not been observed. By studying the change in virulence of recent field isolates at a single field site we show, for the first time, that RHDV virulence has increased through time, likely because of selection to overcome developing genetic resistance in Australian wild rabbits. High virulence also appears to be favoured as rabbit carcasses, rather than diseased animals, are the likely source of mechanical insect transmission. These findings not only help elucidate the co-evolutionary interaction between rabbits and RHDV, but reveal some of the key factors shaping virulence evolution.
Collapse
Affiliation(s)
- Peter Elsworth
- Robert Wicks Pest Animal Research Centre, Biosecurity Queensland, Department of Agriculture, Fisheries and Forestry, Toowoomba, Queensland, Australia; Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia
| | - Brian D Cooke
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; University of Canberra, Institute for Applied Ecology, ACT, Canberra, Australia
| | - John Kovaliski
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; Biosecurity South Australia, Adelaide, South Australia, Australia
| | - Ronald Sinclair
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; Biosecurity South Australia, Adelaide, South Australia, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases & Biosecurity, Charles Perkins Centre, School of Biological Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Tanja Strive
- Invasive Animals Cooperative Research Centre, University of Canberra, Bruce, ACT, Canberra, Australia; CSIRO Ecosystem Sciences, Canberra, ACT, Australia; CSIRO Biosecurity Flagship, Canberra, Australia.
| |
Collapse
|
39
|
Nunes MRT, Palacios G, Faria NR, Sousa EC, Pantoja JA, Rodrigues SG, Carvalho VL, Medeiros DBA, Savji N, Baele G, Suchard MA, Lemey P, Vasconcelos PFC, Lipkin WI. Air travel is associated with intracontinental spread of dengue virus serotypes 1-3 in Brazil. PLoS Negl Trop Dis 2014; 8:e2769. [PMID: 24743730 PMCID: PMC3990485 DOI: 10.1371/journal.pntd.0002769] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/18/2014] [Indexed: 01/01/2023] Open
Abstract
Dengue virus and its four serotypes (DENV-1 to DENV-4) infect 390 million people and are implicated in at least 25,000 deaths annually, with the largest disease burden in tropical and subtropical regions. We investigated the spatial dynamics of DENV-1, DENV-2 and DENV-3 in Brazil by applying a statistical framework to complete genome sequences. For all three serotypes, we estimated that the introduction of new lineages occurred within 7 to 10-year intervals. New lineages were most likely to be imported from the Caribbean region to the North and Northeast regions of Brazil, and then to disperse at a rate of approximately 0.5 km/day. Joint statistical analysis of evolutionary, epidemiological and ecological data indicates that aerial transportation of humans and/or vector mosquitoes, rather than Aedes aegypti infestation rates or geographical distances, determine dengue virus spread in Brazil.
Collapse
Affiliation(s)
- Marcio R. T. Nunes
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Gustavo Palacios
- Center for Genomic Sciences, United States Army Medical Research Institute for Infectious Diseases, Frederick, Maryland, United States of America
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | | | | | - Jamilla A. Pantoja
- Centro de Inovação Tecnológica, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Sueli G. Rodrigues
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Valéria L. Carvalho
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Daniele B. A. Medeiros
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Nazir Savji
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| | - Guy Baele
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Human Genetics, David Geffen School of Medicine, University of California – Los Angeles, Los Angeles, California, United States of America
- Department of Biostatistics, UCLA Fielding School of Public Health, University of California - Los Angeles, Los Angeles, California, United States of America
| | - Philippe Lemey
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Pedro F. C. Vasconcelos
- Departamento de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Brazil
- Universidade do Estado do Pará, Belém, Pará, Brazil
| | - W. Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health, Columbia University, New York, New York, United States of America
| |
Collapse
|
40
|
Changes in diversification patterns and signatures of selection during the evolution of murinae-associated hantaviruses. Viruses 2014; 6:1112-34. [PMID: 24618811 PMCID: PMC3970142 DOI: 10.3390/v6031112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 02/19/2014] [Accepted: 02/24/2014] [Indexed: 12/31/2022] Open
Abstract
In the last 50 years, hantaviruses have significantly affected public health worldwide, but the exact extent of the distribution of hantavirus diseases, species and lineages and the risk of their emergence into new geographic areas are still poorly known. In particular, the determinants of molecular evolution of hantaviruses circulating in different geographical areas or different host species are poorly documented. Yet, this understanding is essential for the establishment of more accurate scenarios of hantavirus emergence under different climatic and environmental constraints. In this study, we focused on Murinae-associated hantaviruses (mainly Seoul Dobrava and Hantaan virus) using sequences available in GenBank and conducted several complementary phylogenetic inferences. We sought for signatures of selection and changes in patterns and rates of diversification in order to characterize hantaviruses’ molecular evolution at different geographical scales (global and local). We then investigated whether these events were localized in particular geographic areas. Our phylogenetic analyses supported the assumption that RNA virus molecular variations were under strong evolutionary constraints and revealed changes in patterns of diversification during the evolutionary history of hantaviruses. These analyses provide new knowledge on the molecular evolution of hantaviruses at different scales of time and space.
Collapse
|
41
|
Wain-Hobson S. Pandemic influenza viruses: time to recognize our inability to predict the unpredictable and stop dangerous gain-of-function experiments. EMBO Mol Med 2013; 5:1637-41. [PMID: 24186378 PMCID: PMC3840482 DOI: 10.1002/emmm.201303475] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Simon Wain-Hobson
- Institut PasteurParis, France
- The Foundation for Vaccine ResearchWashington, DC, USA
| |
Collapse
|