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Lequime S. The sociality continuum of viruses: a commentary on Leeks et al. 2023. J Evol Biol 2023; 36:1568-1570. [PMID: 37975506 DOI: 10.1111/jeb.14247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Affiliation(s)
- Sebastian Lequime
- Cluster of Microbial Ecology, Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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2
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Lindenbach BD. Reinventing positive-strand RNA virus reverse genetics. Adv Virus Res 2022; 112:1-29. [PMID: 35840179 PMCID: PMC9273853 DOI: 10.1016/bs.aivir.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Reverse genetics is the prospective analysis of how genotype determines phenotype. In a typical experiment, a researcher alters a viral genome, then observes the phenotypic outcome. Among RNA viruses, this approach was first applied to positive-strand RNA viruses in the mid-1970s and over nearly 50 years has become a powerful and widely used approach for dissecting the mechanisms of viral replication and pathogenesis. During this time the global health importance of two virus groups, flaviviruses (genus Flavivirus, family Flaviviridae) and betacoronaviruses (genus Betacoronavirus, subfamily Orthocoronavirinae, family Coronaviridae), have dramatically increased, yet these viruses have genomes that are technically challenging to manipulate. As a result, several new techniques have been developed to overcome these challenges. Here I briefly review key historical aspects of positive-strand RNA virus reverse genetics, describe some recent reverse genetic innovations, particularly as applied to flaviviruses and coronaviruses, and discuss their benefits and limitations within the larger context of rigorous genetic analysis.
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3
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Domingo E, García-Crespo C, Perales C. Historical Perspective on the Discovery of the Quasispecies Concept. Annu Rev Virol 2021; 8:51-72. [PMID: 34586874 DOI: 10.1146/annurev-virology-091919-105900] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viral quasispecies are dynamic distributions of nonidentical but closely related mutant and recombinant viral genomes subjected to a continuous process of genetic variation, competition, and selection that may act as a unit of selection. The quasispecies concept owes its theoretical origins to a model for the origin of life as a collection of mutant RNA replicators. Independently, experimental evidence for the quasispecies concept was obtained from sampling of bacteriophage clones, which revealed that the viral populations consisted of many mutant genomes whose frequency varied with time of replication. Similar findings were made in animal and plant RNA viruses. Quasispecies became a theoretical framework to understand viral population dynamics and adaptability. The evidence came at a time when mutations were considered rare events in genetics, a perception that was to change dramatically in subsequent decades. Indeed, viral quasispecies was the conceptual forefront of a remarkable degree of biological diversity, now evident for cell populations and organisms, not only for viruses. Quasispecies dynamics unveiled complexities in the behavior of viral populations,with consequences for disease mechanisms and control strategies. This review addresses the origin of the quasispecies concept, its major implications on both viral evolution and antiviral strategies, and current and future prospects.
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Affiliation(s)
- Esteban Domingo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Carlos García-Crespo
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain;
| | - Celia Perales
- Department of Interactions with the Environment, Centro de Biología Molecular Severo Ochoa (CBMSO), Consejo Superior de Investigaciones Científicas (CSIC), 28049 Madrid, Spain; .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) del Instituto de Salud Carlos III, 28029 Madrid, Spain.,Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain
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4
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Al Khatib HA, Benslimane FM, Elbashir IE, Coyle PV, Al Maslamani MA, Al-Khal A, Al Thani AA, Yassine HM. Within-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities. Front Cell Infect Microbiol 2020; 10:575613. [PMID: 33123498 PMCID: PMC7572854 DOI: 10.3389/fcimb.2020.575613] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 08/25/2020] [Indexed: 01/08/2023] Open
Abstract
Background: The ongoing pandemic of SARS-COV-2 has already infected more than eight million people worldwide. The majority of COVID-19 patients either are asymptomatic or have mild symptoms. Yet, about 15% of the cases experience severe complications and require intensive care. Factors determining disease severity are not yet fully characterized. Aim: Here, we investigated the within-host virus diversity in COVID-19 patients with different clinical manifestations. Methods: We compared SARS-COV-2 genetic diversity in 19 mild and 27 severe cases. Viral RNA was extracted from nasopharyngeal samples and sequenced using the Illumina MiSeq platform. This was followed by deep-sequencing analyses of SARS-CoV-2 genomes at both consensus and sub-consensus sequence levels. Results: Consensus sequences of all viruses were very similar, showing more than 99.8% sequence identity regardless of the disease severity. However, the sub-consensus analysis revealed significant differences in within-host diversity between mild and severe cases. Patients with severe symptoms exhibited a significantly (p-value 0.001) higher number of variants in coding and non-coding regions compared to mild cases. Analysis also revealed higher prevalence of some variants among severe cases. Most importantly, severe cases exhibited significantly higher within-host diversity (mean = 13) compared to mild cases (mean = 6). Further, higher within-host diversity was observed in patients above the age of 60 compared to the younger age group. Conclusion: These observations provided evidence that within-host diversity might play a role in the development of severe disease outcomes in COVID-19 patients; however, further investigations are required to elucidate this association.
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Affiliation(s)
| | | | | | - Peter V. Coyle
- Virology Laboratory, Hamad Medical Corporation, Doha, Qatar
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5
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They are what you eat: Shaping of viral populations through nutrition and consequences for virulence. PLoS Pathog 2020; 16:e1008711. [PMID: 32790755 PMCID: PMC7425860 DOI: 10.1371/journal.ppat.1008711] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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6
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Inter- Versus Intra-Host Sequence Diversity of pH1N1 and Associated Clinical Outcomes. Microorganisms 2020; 8:microorganisms8010133. [PMID: 31963512 PMCID: PMC7022955 DOI: 10.3390/microorganisms8010133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 01/06/2020] [Accepted: 01/15/2020] [Indexed: 02/06/2023] Open
Abstract
The diversity of RNA viruses dictates their evolution in a particular host, community or environment. Here, we reported within- and between-host pH1N1virus diversity at consensus and sub-consensus levels over a three-year period (2015-2017) and its implications on disease severity. A total of 90 nasal samples positive for the pH1N1 virus were deep-sequenced and analyzed to detect low-frequency variants (LFVs) and haplotypes. Parallel evolution of LFVs was seen in the hemagglutinin (HA) gene across three scales: among patients (33%), across years (22%), and at global scale. Remarkably, investigating the emergence of LFVs at the consensus level demonstrated that within-host virus evolution recapitulates evolutionary dynamics seen at the global scale. Analysis of virus diversity at the HA haplotype level revealed the clustering of low-frequency haplotypes from early 2015 with dominant strains of 2016, indicating rapid haplotype evolution. Haplotype sharing was also noticed in all years, strongly suggesting haplotype transmission among patients infected during a specific influenza season. Finally, more than half of patients with severe symptoms harbored a larger number of haplotypes, mostly in patients under the age of five. Therefore, patient age, haplotype diversity, and the presence of certain LFVs should be considered when interpreting illness severity. In addition to its importance in understanding virus evolution, sub-consensus virus diversity together with whole genome sequencing is essential to explain variabilities in clinical outcomes that cannot be explained by either analysis alone.
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7
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Singanallur NB, Anderson DE, Sessions OM, Kamaraj US, Bowden TR, Horsington J, Cowled C, Wang LF, Vosloo W. Probe capture enrichment next-generation sequencing of complete foot-and-mouth disease virus genomes in clinical samples. J Virol Methods 2019; 272:113703. [PMID: 31336142 DOI: 10.1016/j.jviromet.2019.113703] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 07/04/2019] [Accepted: 07/17/2019] [Indexed: 01/02/2023]
Abstract
Next-generation sequencing (NGS) techniques offer an unprecedented "step-change" increase in the quantity and quality of sequence data rapidly generated from a sample and can be applied to obtain ultra-deep coverage of viral genomes. This is not possible with the routinely used Sanger sequencing method that gives the consensus reads, or by cloning approaches. In this study, a targeted-enrichment methodology for the simultaneous acquisition of complete foot-and-mouth disease virus (FMDV) genomes directly from clinical samples is presented. Biotinylated oligonucleotide probes (120 nt) were used to capture and enrich viral RNA following library preparation. To create a virus capture panel targeting serotype O and A simultaneously, 18 baits targeting the highly conserved regions of the 8.3 kb FMDV genome were synthesised, with 14 common to both serotypes, 2 specific to serotype O and 2 specific to serotype A. These baits were used to capture and enrich FMDV RNA (as cDNA) from samples collected during one pathogenesis and two vaccine efficacy trials, where pigs were infected with serotype O or A viruses. After enrichment, FMDV-specific sequencing reads increased by almost 3000-fold. The sequence data were used in variant call analysis to identify single nucleotide polymorphisms (SNPs). This methodology was robust in its ability to capture diverse sequences, was shown to be highly sensitive, and can be easily scaled for large-scale epidemiological studies.
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Affiliation(s)
| | - Danielle E Anderson
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - October M Sessions
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore; Department of Pharmacy, National University of Singapore, Singapore
| | - Uma S Kamaraj
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Timothy R Bowden
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Jacquelyn Horsington
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Christopher Cowled
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Wilna Vosloo
- Australian Animal Health Laboratory, CSIRO Health and Biosecurity, Geelong, Australia
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8
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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9
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Mohamed Ali S, Vega-Rúa A, Driouich JS, de Lamballerie X, Failloux AB, Nougairède A. Comparison of chikungunya viruses generated using infectious clone or the Infectious Subgenomic Amplicons (ISA) method in Aedes mosquitoes. PLoS One 2018; 13:e0199494. [PMID: 29953474 PMCID: PMC6023229 DOI: 10.1371/journal.pone.0199494] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 06/10/2018] [Indexed: 01/12/2023] Open
Abstract
Reverse genetics systems provide the opportunity to manipulate viral genomes and have been widely used to study RNA viruses and to develop new antiviral compounds and vaccine strategies. The recently described method called ISA (Infectious Subgenomic Amplicons) gives the possibility to rescue RNA viruses in days. We demonstrated in cell culture that the use of the ISA method led to a higher genetic diversity of viral populations than that observed using infectious clone technology. However, no replicative fitness difference was observed. In the present study, we used the chikungunya virus as a model to compare in Aedes aegypti and Aedes albopictus mosquitoes the genotypic and phenotypic characteristics of viruses produced either from an infectious clone or using the ISA method. We confirmed the results found in cellulo corroborating that the use of the ISA method was associated with higher genetic diversity of viral populations in mosquitoes but did not affect the vector competence validating its use for in vivo experiments.
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Affiliation(s)
- Souand Mohamed Ali
- Unité des Virus Émergents (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Anubis Vega-Rúa
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
| | - Anna-Bella Failloux
- Department of Virology, Arboviruses and Insect Vectors, Institut Pasteur, Paris, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ–IRD 190 –Inserm 1207 –IHU Méditerranée Infection), Marseille, France
- * E-mail:
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10
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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.
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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.
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11
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SuPReMe: a rapid reverse genetics method to generate clonal populations of recombinant RNA viruses. Emerg Microbes Infect 2018; 7:40. [PMID: 29559627 PMCID: PMC5861084 DOI: 10.1038/s41426-018-0040-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/10/2018] [Accepted: 01/14/2018] [Indexed: 11/26/2022]
Abstract
Reverse genetics systems enable the manipulation of viral genomes and are proving to be essential for studying RNA viruses. Methods for generating clonal virus populations are particularly useful for studying the impact of genomic modifications on viral properties. Here, by exploiting a chikungunya virus model, we compare viral populations and their replicative fitness when generated using either the rapid and user-friendly PCR-based ISA (Infectious Subgenomic Amplicons) method or classical infectious clone technology. As anticipated, the ISA method resulted in greater genetic diversity of the viral populations, but no significant difference in viral fitness in vitro was observed. On the basis of these results, a new ISA-derived reverse genetics procedure was developed. This method, designated ‘SuPReMe’ (Subgenomic Plasmids Recombination Method), in which digested plasmids containing subgenomic DNA fragments were directly transfected into permissive cells, retains the following major advantages of the ISA method: it is rapid, flexible and does not require the cloning of complete genomes. Moreover, SuPReMe has been shown to produce virus populations with genetic diversity and replicative fitness similar to those obtained using conventional infectious clone technology. SuPReMe, therefore, represents an effective and promising option for the rapid generation of clonal recombinant populations of single-stranded positive-sense RNA viruses.
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12
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Phylogeny of the infectious hematopoietic necrosis virus in European aquaculture. PLoS One 2017; 12:e0184490. [PMID: 28886189 PMCID: PMC5590938 DOI: 10.1371/journal.pone.0184490] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 08/24/2017] [Indexed: 11/19/2022] Open
Abstract
Infectious hematopoietic necrosis (IHN)-a highly lethal infectious salmonid disease-has caused substantial economic losses in the European production of rainbow trout (Oncorhynchus mykiss) since the late 1980s. The causal agent of IHN is the IHN virus (IHNV) introduced from overseas. However, until today, its phylogeographic spread in Europe remains poorly understood. We therefore sought to elucidate this unresolved topic by using the largest ever compiled dataset of European IHNV isolates (E isolates) (193 GenBank E isolates and 100 isolates from this study) for the complete glycoprotein (G) gene sequence. Our results clearly revealed that the active trout trade has left its traces in the E phylogeny. For example, the spread by trade of IHNV-infected trout was apparently the cause for the exposure of the E lineage to different local scenarios of selection and genetic drift, and therefore has led to the split of this lineage into various subordinated lineages. Accordingly, we also found evidence for E isolates being mixed Europe-wide by cross-border introduction events. Moreover, there were indications that this propagation of the E lineage within Europe corresponded with an extensive and rapid spread event, already during or shortly after its formation. Finally, in accordance with the high substitution rate of IHNV determined by previous studies, our dataset indicates that the mean period of occurrence of a single E haplotype is typically not longer than one calendar year.
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13
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Marston DA, Horton DL, Nunez J, Ellis RJ, Orton RJ, Johnson N, Banyard AC, McElhinney LM, Freuling CM, Fırat M, Ünal N, Müller T, de Lamballerie X, Fooks AR. Genetic analysis of a rabies virus host shift event reveals within-host viral dynamics in a new host. Virus Evol 2017; 3:vex038. [PMID: 29255631 PMCID: PMC5729694 DOI: 10.1093/ve/vex038] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Host shift events play an important role in epizootics as adaptation to new hosts can profoundly affect the spread of the disease and the measures needed to control it. During the late 1990s, an epizootic in Turkey resulted in a sustained maintenance of rabies virus (RABV) within the fox population. We used Bayesian inferences to investigate whole genome sequences from fox and dog brain tissues from Turkey to demonstrate that the epizootic occurred in 1997 (±1 year). Furthermore, these data indicated that the epizootic was most likely due to a host shift from locally infected domestic dogs, rather than an incursion of a novel fox or dog RABV. No evidence was observed for genetic adaptation to foxes at consensus sequence level and dN/dS analysis suggested purifying selection. Therefore, the deep sequence data were analysed to investigate the sub-viral population during a host shift event. Viral heterogeneity was measured in all RABV samples; viruses from the early period after the host shift exhibited greater sequence variation in comparison to those from the later stage, and to those not involved in the host shift event, possibly indicating a role in establishing transmission within a new host. The transient increase in variation observed in the new host species may represent virus replication within a new environment, perhaps due to increased replication within the CNS, resulting in a larger population of viruses, or due to the lack of host constraints present in the new host reservoir.
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Affiliation(s)
- Denise A Marston
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Daniel L Horton
- School of Veterinary Medicine, University of Surrey, Guildford, GU2 7AL UK
| | - Javier Nunez
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
- Centre for Virus Research, MRC-University of Glasgow, University of Glasgow, Glasgow, G61 1QH UK
| | - Nicholas Johnson
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Faculty of Health and Medical Science, University of Surrey, Guildford, GU2 7XH, UK
| | - Ashley C Banyard
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
| | - Lorraine M McElhinney
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
| | - Conrad M Freuling
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Müge Fırat
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Nil Ünal
- Etlik Veterinary Control Central Research Institute A.S.Kolayli Street. No.21-21/A, 06020, Etlik, Ankara, Turkey
| | - Thomas Müller
- Friedrich-Loeffler-Institute, (FLI), Institute of Molecular Virology and Cell Biology, Greifswald-Insel Riems, D-17493, Germany
| | - Xavier de Lamballerie
- UMR “Émergence des Pathologies Virales” (EPV: Aix-Marseille Univ—IRD 190—Inserm 1207 – EHESP – IHU Méditerranée Infection), Faculté de Médecine de Marseille, 27, Bd Jean Moulin,13005 Marseille, cedex 05 France
| | - Anthony R Fooks
- Wildlife Zoonoses & Vector-Borne Diseases Research Group, Animal and Plant Health Agency, New Haw, Addlestone, Surrey, KT15 3NB, UK
- Institute of Infection and Global Health, University of Liverpool, UK
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14
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Redondo RAF, de Vladar HP, Włodarski T, Bollback JP. Evolutionary interplay between structure, energy and epistasis in the coat protein of the ϕX174 phage family. J R Soc Interface 2017; 14:20160139. [PMID: 28053111 PMCID: PMC5310724 DOI: 10.1098/rsif.2016.0139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/29/2016] [Indexed: 01/01/2023] Open
Abstract
Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the ϕX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.
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Affiliation(s)
| | - Harold P de Vladar
- IST Austria, Am Campus 1, 3400 Klosterneuburg, Austria
- Center for the Conceptual Foundations of Science, Parmenides Foundation, 82049 Pullach, Germany
| | - Tomasz Włodarski
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
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15
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King DJ, Freimanis GL, Orton RJ, Waters RA, Haydon DT, King DP. Investigating intra-host and intra-herd sequence diversity of foot-and-mouth disease virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2016; 44:286-292. [PMID: 27421209 PMCID: PMC5036933 DOI: 10.1016/j.meegid.2016.07.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/06/2016] [Accepted: 07/11/2016] [Indexed: 11/23/2022]
Abstract
Due to the poor-fidelity of the enzymes involved in RNA genome replication, foot-and-mouth disease (FMD) virus samples comprise of unique polymorphic populations. In this study, deep sequencing was utilised to characterise the diversity of FMD virus (FMDV) populations in 6 infected cattle present on a single farm during the series of outbreaks in the UK in 2007. A novel RT-PCR method was developed to amplify a 7.6kb nucleotide fragment encompassing the polyprotein coding region of the FMDV genome. Illumina sequencing of each sample identified the fine polymorphic structures at each nucleotide position, from consensus level changes to variants present at a 0.24% frequency. These data were used to investigate population dynamics of FMDV at both herd and host levels, evaluate the impact of host on the viral swarm structure and to identify transmission links with viruses recovered from other farms in the same series of outbreaks. In 7 samples, from 6 different animals, a total of 5 consensus level variants were identified, in addition to 104 sub-consensus variants of which 22 were shared between 2 or more animals. Further analysis revealed differences in swarm structures from samples derived from the same animal suggesting the presence of distinct viral populations evolving independently at different lesion sites within the same infected animal.
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Affiliation(s)
- David J King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Graham L Freimanis
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Richard J Orton
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK; MRC-University of Glasgow, Centre for Virus Research, University of Glasgow, 464 Bearsden Road, G61 1QH, UK
| | - Ryan A Waters
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK
| | - Daniel T Haydon
- Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Donald P King
- The Pirbright Institute, Ash Road, Pirbright, Woking, Surrey GU24 0NF, UK.
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Tabachnick WJ. Climate Change and the Arboviruses: Lessons from the Evolution of the Dengue and Yellow Fever Viruses. Annu Rev Virol 2016; 3:125-145. [DOI: 10.1146/annurev-virology-110615-035630] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Walter J. Tabachnick
- Florida Medical Entomology Laboratory, Department of Entomology and Nematology, University of Florida, Vero Beach, Florida 32962;
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Hapuarachchi HC, Koo C, Kek R, Xu H, Lai YL, Liu L, Kok SY, Shi Y, Chuen RLT, Lee KS, Maurer-Stroh S, Ng LC. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission. Sci Rep 2016; 6:22592. [PMID: 26940650 PMCID: PMC4778070 DOI: 10.1038/srep22592] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
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Affiliation(s)
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Relus Kek
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Helen Xu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Lilac Liu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Suet Yheng Kok
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yuan Shi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Raphael Lee Tze Chuen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore 599489
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551.,National Public Health Laboratory (NPHL), Ministry of Health (MOH), 3 Biopolis Drive, #05-14 to 16, Synapse, Singapore 138623
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
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High-Frequency Variation of Purine Biosynthesis Genes Is a Mechanism of Success in Campylobacter jejuni. mBio 2015; 6:e00612-15. [PMID: 26419875 PMCID: PMC4611032 DOI: 10.1128/mbio.00612-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED Phenotypic variation is prevalent in the zoonotic pathogen Campylobacter jejuni, the leading agent of enterocolitis in the developed world. Heterogeneity enhances the survival and adaptive malleability of bacterial populations because variable phenotypes may allow some cells to be protected against future stress. Exposure to hyperosmotic stress previously revealed prevalent differences in growth between C. jejuni strain 81-176 colonies due to resistant or sensitive phenotypes, and these isolated colonies continued to produce progeny with differential phenotypes. In this study, whole-genome sequencing of isolated colonies identified allelic variants of two purine biosynthesis genes, purF and apt, encoding phosphoribosyltransferases that utilize a shared substrate. Genetic analyses determined that purF was essential for fitness, while apt was critical. Traditional and high-depth amplicon-sequencing analyses confirmed extensive intrapopulation genetic variation of purF and apt that resulted in viable strains bearing alleles with in-frame insertion duplications, deletions, or missense polymorphisms. Different purF and apt alleles were associated with various stress survival capabilities under several niche-relevant conditions and contributed to differential intracellular survival in an epithelial cell infection model. Amplicon sequencing revealed that intracellular survival selected for stress-fit purF and apt alleles, as did exposure to oxygen and hyperosmotic stress. Putative protein recognition direct repeat sequences were identified in purF and apt, and a DNA-protein affinity screen captured a predicted exonuclease that promoted the global spontaneous mutation rate. This work illustrates the adaptive properties of high-frequency genetic variation in two housekeeping genes, which influences C. jejuni survival under stress and promotes its success as a pathogen. IMPORTANCE C. jejuni is an important cause of bacterial diarrheal illness. Bacterial populations have many strategies for stress survival, but phenotypic variation due to genetic diversity has a powerful advantage: no matter how swift the change in environment, a fraction of the population already expresses the survival trait. Nonclonality is thus increasingly viewed as a mechanism of population success. Our previous work identified prominent resistant/sensitive colonial variation in C. jejuni bacteria in response to hyperosmotic stress; in the work presented here, we attribute that to high-frequency genetic variation in two purine biosynthesis genes, purF and apt. We demonstrated selective pressure for nonlethal mutant alleles of both genes, showed that single-cell variants had the capacity to give rise to diverse purF and apt populations, and determined that stress exposure selected for desirable alleles. Thus, a novel C. jejuni adaptive strategy was identified, which was, unusually, reliant on prevalent genetic variation in two housekeeping genes.
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Orton RJ, Wright CF, Morelli MJ, King DJ, Paton DJ, King DP, Haydon DT. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data. BMC Genomics 2015; 16:229. [PMID: 25886445 PMCID: PMC4425905 DOI: 10.1186/s12864-015-1456-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/09/2015] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND RNA viruses have high mutation rates and exist within their hosts as large, complex and heterogeneous populations, comprising a spectrum of related but non-identical genome sequences. Next generation sequencing is revolutionising the study of viral populations by enabling the ultra deep sequencing of their genomes, and the subsequent identification of the full spectrum of variants within the population. Identification of low frequency variants is important for our understanding of mutational dynamics, disease progression, immune pressure, and for the detection of drug resistant or pathogenic mutations. However, the current challenge is to accurately model the errors in the sequence data and distinguish real viral variants, particularly those that exist at low frequency, from errors introduced during sequencing and sample processing, which can both be substantial. RESULTS We have created a novel set of laboratory control samples that are derived from a plasmid containing a full-length viral genome with extremely limited diversity in the starting population. One sample was sequenced without PCR amplification whilst the other samples were subjected to increasing amounts of RT and PCR amplification prior to ultra-deep sequencing. This enabled the level of error introduced by the RT and PCR processes to be assessed and minimum frequency thresholds to be set for true viral variant identification. We developed a genome-scale computational model of the sample processing and NGS calling process to gain a detailed understanding of the errors at each step, which predicted that RT and PCR errors are more likely to occur at some genomic sites than others. The model can also be used to investigate whether the number of observed mutations at a given site of interest is greater than would be expected from processing errors alone in any NGS data set. After providing basic sample processing information and the site's coverage and quality scores, the model utilises the fitted RT-PCR error distributions to simulate the number of mutations that would be observed from processing errors alone. CONCLUSIONS These data sets and models provide an effective means of separating true viral mutations from those erroneously introduced during sample processing and sequencing.
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Affiliation(s)
- Richard J Orton
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
- Medical Research Council-University of Glasgow Centre for Virus Research, Institute of Infection, Inflammation and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
| | | | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Istituto Italiano di Tecnologia at the IFOM-IEO Campus, Via Adamello 16, Milano, 20139, Italy.
| | - David J King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - David J Paton
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Donald P King
- Pirbright Institute, Ash Road, Pirbright, GU24 0NF, UK.
| | - Daniel T Haydon
- Boyd Orr Centre for Population and Ecosystem Health, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, United Kingdom.
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20
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Nelson CW, Hughes AL. Within-host nucleotide diversity of virus populations: insights from next-generation sequencing. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2015; 30:1-7. [PMID: 25481279 PMCID: PMC4316684 DOI: 10.1016/j.meegid.2014.11.026] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 11/26/2014] [Accepted: 11/27/2014] [Indexed: 01/03/2023]
Abstract
Next-generation sequencing (NGS) technology offers new opportunities for understanding the evolution and dynamics of viral populations within individual hosts over the course of infection. We review simple methods for estimating synonymous and nonsynonymous nucleotide diversity in viral genes from NGS data without the need for inferring linkage. We discuss the potential usefulness of these data for addressing questions of both practical and theoretical interest, including fundamental questions regarding the effective population sizes of within-host viral populations and the modes of natural selection acting on them.
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Affiliation(s)
- Chase W Nelson
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Austin L Hughes
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA.
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21
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Gross R, Fouxon I, Lancet D, Markovitch O. Quasispecies in population of compositional assemblies. BMC Evol Biol 2014; 14:265. [PMID: 25547629 PMCID: PMC4357159 DOI: 10.1186/s12862-014-0265-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 12/11/2014] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics. RESULTS We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition. CONCLUSIONS Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.
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Affiliation(s)
- Renan Gross
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Itzhak Fouxon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Doron Lancet
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
| | - Omer Markovitch
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel.
- Interdisciplinary Computing and Complex Bio-Systems research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
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22
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Flavivirus reverse genetic systems, construction techniques and applications: a historical perspective. Antiviral Res 2014; 114:67-85. [PMID: 25512228 PMCID: PMC7173292 DOI: 10.1016/j.antiviral.2014.12.007] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/26/2014] [Accepted: 12/03/2014] [Indexed: 12/20/2022]
Abstract
The study of flaviviruses, which cause some of the most important emerging tropical and sub-tropical human arbovirus diseases, has greatly benefited from the use of reverse genetic systems since its first development for yellow fever virus in 1989. Reverse genetics technology has completely revolutionized the study of these viruses, making it possible to manipulate their genomes and evaluate the direct effects of these changes on their biology and pathogenesis. The most commonly used reverse genetics system is the infectious clone technology. Whilst flavivirus infectious clones provide a powerful tool, their construction as full-length cDNA molecules in bacterial vectors can be problematic, laborious and time consuming, because they are often unstable, contain unwanted induced substitutions and may be toxic for bacteria due to viral protein expression. The incredible technological advances that have been made during the past 30years, such as the use of PCR or new sequencing methods, have allowed the development of new approaches to improve preexisting systems or elaborate new strategies that overcome these problems. This review summarizes the evolution and major technical breakthroughs in the development of flavivirus reverse genetics technologies and their application to the further understanding and control of these viruses and their diseases.
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23
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Shadrin AA, Parkhomchuk DV. Drake’s rule as a consequence of approaching channel capacity. Naturwissenschaften 2014; 101:939-54. [PMID: 25228346 PMCID: PMC4209235 DOI: 10.1007/s00114-014-1235-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/26/2014] [Accepted: 08/28/2014] [Indexed: 12/03/2022]
Abstract
How mutations accumulate in genomes is the central question of molecular evolution theories. However, our understanding of this process is far from complete. Drake’s rule is a notoriously universal property of genomes from microbes to mammals—the number of (functional) mutations per-genome per-generation is approximately constant within a phylum, despite the orders of magnitude differences in genome sizes and diverse populations’ properties. So far, there is no concise explanation for this phenomenon. A formal model for the storage of genetic information suggests that a genome of any species operates near its maximum informational storage capacity, and the mutation rate per-genome per-generation is near its upper limit, providing a simple explanation for the rule with minimal assumptions.
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Affiliation(s)
- Alexey A. Shadrin
- Fachbereich Mathematik und Informatik, Freie Universität Berlin, Berlin, Germany
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Illingworth CJR, Fischer A, Mustonen V. Identifying selection in the within-host evolution of influenza using viral sequence data. PLoS Comput Biol 2014; 10:e1003755. [PMID: 25080215 PMCID: PMC4117419 DOI: 10.1371/journal.pcbi.1003755] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/13/2014] [Indexed: 02/07/2023] Open
Abstract
The within-host evolution of influenza is a vital component of its epidemiology. A question of particular interest is the role that selection plays in shaping the viral population over the course of a single infection. We here describe a method to measure selection acting upon the influenza virus within an individual host, based upon time-resolved genome sequence data from an infection. Analysing sequence data from a transmission study conducted in pigs, describing part of the haemagglutinin gene (HA1) of an influenza virus, we find signatures of non-neutrality in six of a total of sixteen infections. We find evidence for both positive and negative selection acting upon specific alleles, while in three cases, the data suggest the presence of time-dependent selection. In one infection we observe what is potentially a specific immune response against the virus; a non-synonymous mutation in an epitope region of the virus is found to be under initially positive, then strongly negative selection. Crucially, given the lack of homologous recombination in influenza, our method accounts for linkage disequilibrium between nucleotides at different positions in the haemagglutinin gene, allowing for the analysis of populations in which multiple mutations are present at any given time. Our approach offers a new insight into the dynamics of influenza infection, providing a detailed characterisation of the forces that underlie viral evolution. The evolution of the influenza virus is of great importance for human health. Through evolution, current influenza viruses develop the ability to infect people who have been vaccinated against earlier strains. New strains of influenza that infect birds and pigs could evolve to infect and spread between people, causing a global pandemic. The influenza virus lives within a human or animal host, so that viral evolution happens within, or in the spread between, individuals. As such, what happens to the virus during the course of an infection is a question of great interest. We here describe a statistical method that uses viral genome sequence data to measure how evolution affects the influenza virus within a single host. Studying data from infections transmitted between pigs, we find evidence for evolutionary adaptation in six of sixteen animals for which data were available. In one case, an immune response mounted by a pig against the virus is apparent. Our method provides a statistical framework for using sequence data to study viral evolution on very short timescales, enabling new research into within-host viral evolution.
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Affiliation(s)
| | - Andrej Fischer
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Ville Mustonen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
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25
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Pandit A, de Boer RJ. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants. Retrovirology 2014; 11:56. [PMID: 24996694 PMCID: PMC4227095 DOI: 10.1186/1742-4690-11-56] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/24/2014] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible because next generation sequencing delivers relatively short reads. RESULTS We here provide a proof of principle that whole HIV-1 genomes can be reliably reconstructed from short reads, and use this to study the selection of immune escape mutations at the level of whole genome haplotypes. Using realistically simulated HIV-1 populations, we demonstrate that reconstruction of complete genome haplotypes is feasible with high fidelity. We do not reconstruct all genetically distinct genomes, but each reconstructed haplotype represents one or more of the quasispecies in the HIV-1 population. We then reconstruct 30 whole genome haplotypes from published short sequence reads sampled longitudinally from a single HIV-1 infected patient. We confirm the reliability of the reconstruction by validating our predicted haplotype genes with single genome amplification sequences, and by comparing haplotype frequencies with observed epitope escape frequencies. CONCLUSIONS Phylogenetic analysis shows that the HIV-1 population undergoes selection driven evolution, with successive replacement of the viral population by novel dominant strains. We demonstrate that immune escape mutants evolve in a dependent manner with various mutations hitchhiking along with others. As a consequence of this clonal interference, selection coefficients have to be estimated for complete haplotypes and not for individual immune escapes.
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Affiliation(s)
- Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Rob J de Boer
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Abstract
The purpose of this introductory chapter is to provide the reader with a brief overview of the factors that drive disease emergence in order to set the scene for the more detailed chapters that follow. The chapter is divided into three parts. The first deals with the activities of humans that drive disease emergence. This ranges from historical factors such as animal domestication to the impact of new technologies such as air travel and agricultural intensification in response to population growth. The second section deals with virus properties that enable them to adapt to new hosts, particularly jumping between species. The final section deals with the activities of animals themselves that contribute to disease emergence.
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27
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Jackowiak P, Kuls K, Budzko L, Mania A, Figlerowicz M, Figlerowicz M. Phylogeny and molecular evolution of the hepatitis C virus. INFECTION GENETICS AND EVOLUTION 2013; 21:67-82. [PMID: 24200590 DOI: 10.1016/j.meegid.2013.10.021] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 10/24/2013] [Accepted: 10/26/2013] [Indexed: 12/14/2022]
Abstract
The hepatitis C virus (HCV) is a globally prevalent human pathogen that causes persistent liver infections in most infected individuals. HCV is classified into seven phylogenetically distinct genotypes, which have different geographical distributions and levels of genetic diversity. Some of these genotypes are endemic and highly divergent, whereas others disseminate rapidly on an epidemic scale but display lower variability. HCV phylogeny has an important impact on disease epidemiology and clinical practice because the viral genotype may determine the pathogenesis and severity of the resultant chronic liver disease. In addition, there is a clear association between the HCV genotype and its susceptibility to antiviral treatment. Similarly to other RNA viruses, in a single host, HCV exists as a combination of related but genetically different variants. The whole formation is the actual target of selection exerted by a host organism and antiviral therapeutics. The genetic structure of the viral population is largely shaped by mutations that are constantly introduced during an error-prone replication. However, it appears that genetic recombination may also contribute to this process. This heterogeneous collection of variants has a significant ability to evolve towards the fitness optimum. Interestingly, negative selection, which restricts diversity, emerges as an essential force that drives HCV evolution. It is becoming clear that HCV evolves to become stably adapted to the host environment. In this article we review the HCV phylogeny and molecular evolution in the context of host-virus interactions.
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Affiliation(s)
- Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Karolina Kuls
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Lucyna Budzko
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Anna Mania
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Magdalena Figlerowicz
- Department of Infectious Diseases and Child Neurology, Karol Marcinkowski University of Medical Sciences, Szpitalna 27/33, 60-572 Poznan, Poland
| | - Marek Figlerowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland; Institute of Computing Science, Poznan University of Technology, Piotrowo 3A, 60-965 Poznan, Poland.
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28
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Batty EM, Wong THN, Trebes A, Argoud K, Attar M, Buck D, Ip CLC, Golubchik T, Cule M, Bowden R, Manganis C, Klenerman P, Barnes E, Walker AS, Wyllie DH, Wilson DJ, Dingle KE, Peto TEA, Crook DW, Piazza P. A modified RNA-Seq approach for whole genome sequencing of RNA viruses from faecal and blood samples. PLoS One 2013; 8:e66129. [PMID: 23762474 PMCID: PMC3677912 DOI: 10.1371/journal.pone.0066129] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Accepted: 05/02/2013] [Indexed: 12/12/2022] Open
Abstract
To date, very large scale sequencing of many clinically important RNA viruses has been complicated by their high population molecular variation, which creates challenges for polymerase chain reaction and sequencing primer design. Many RNA viruses are also difficult or currently not possible to culture, severely limiting the amount and purity of available starting material. Here, we describe a simple, novel, high-throughput approach to Norovirus and Hepatitis C virus whole genome sequence determination based on RNA shotgun sequencing (also known as RNA-Seq). We demonstrate the effectiveness of this method by sequencing three Norovirus samples from faeces and two Hepatitis C virus samples from blood, on an Illumina MiSeq benchtop sequencer. More than 97% of reference genomes were recovered. Compared with Sanger sequencing, our method had no nucleotide differences in 14,019 nucleotides (nt) for Noroviruses (from a total of 2 Norovirus genomes obtained with Sanger sequencing), and 8 variants in 9,542 nt for Hepatitis C virus (1 variant per 1,193 nt). The three Norovirus samples had 2, 3, and 2 distinct positions called as heterozygous, while the two Hepatitis C virus samples had 117 and 131 positions called as heterozygous. To confirm that our sample and library preparation could be scaled to true high-throughput, we prepared and sequenced an additional 77 Norovirus samples in a single batch on an Illumina HiSeq 2000 sequencer, recovering >90% of the reference genome in all but one sample. No discrepancies were observed across 118,757 nt compared between Sanger and our custom RNA-Seq method in 16 samples. By generating viral genomic sequences that are not biased by primer-specific amplification or enrichment, this method offers the prospect of large-scale, affordable studies of RNA viruses which could be adapted to routine diagnostic laboratory workflows in the near future, with the potential to directly characterize within-host viral diversity.
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Affiliation(s)
| | - T. H. Nicholas Wong
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Amy Trebes
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Karène Argoud
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Moustafa Attar
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - David Buck
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Camilla L. C. Ip
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Tanya Golubchik
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Madeleine Cule
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Charis Manganis
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Eleanor Barnes
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - A. Sarah Walker
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David H. Wyllie
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Daniel J. Wilson
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Kate E. Dingle
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- Nuffield Department of Clinical Laboratory Sciences, Headley Way, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Tim E. A. Peto
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick W. Crook
- Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- Oxford NIHR Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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Haegeman A, Vrancken R, Neyts J, Koenen F. Intra-host variation structure of classical swine fever virus NS5B in relation to antiviral therapy. Antiviral Res 2013; 98:266-72. [PMID: 23511203 DOI: 10.1016/j.antiviral.2013.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 01/16/2013] [Accepted: 03/07/2013] [Indexed: 11/15/2022]
Abstract
Classical swine fever (CSF) is one of most important diseases of the Suidea with severe social economic consequences in case of outbreaks. Antivirals have been demonstrated, in recent publications, to be an interesting alternative method of fighting the disease. However, classical swine fever virus is an RNA virus which presents a challenge as intra-host variation and the error prone RNA dependent RNA polymerase (RdRp) could lead to the emergence/selection of resistant variants hampering further treatment. Therefore, it was the purpose of this study to investigate the intra-host variation of the RdRp gene, targeted by antivirals, in respect to antiviral treatment. Using the non-unique nucleotide changes, a limited intra-host variation was found in the wild type virus with 2 silent and 2 non-synonymous sites. This number shifted significantly when an antiviral resistant variant was analyzed. In total 22nt changes were found resulting in 14 amino acid changes whereby each genome copy contained at least 2 amino-acid changes in the RdRp. Interestingly, the frequency of the mutations situated in close proximity to a region involved in antiviral resistance in CSFV and bovine viral diarrhea virus (BVDV) was elevated compared to the other mutations. None of the identified mutations in the resistant variant and which could potentially result in antiviral resistance was present in the wild type virus as a non-unique mutation. In view of the spectrum of mutations identified in the resistance associated region and that none of the resistance associated mutations reported for another strain of classical swine fever for the same antiviral were observed in the study, it can be suggested that multiple mutations confer resistance to some degree. Although the followed classical approach allowed the analysis the RdRp as a whole, the contribution of unique mutations to the intra-host variation could not be completely resolved. There was a significant difference in de number of unique mutations found between: 1/wild type virus and the antiviral resistant variant and 2/between both and the number to be expected from the error rate of the RT-PCR process. This indicates that the some of the unique mutations contributed to the intra-host variation and that the antiviral pressure also shifted this pattern. This is important as one of the non-synonymous mutations found in the resistant variant and which was located in the antiviral resistance associated region, was present in the wild type virus as a unique mutation. The findings presented in this study not only show the importance of intra-host variation analysis but also warrants further research certainly in view of the potential inclusion of antivirals in a control/eradication strategy.
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Affiliation(s)
- Andy Haegeman
- Veterinary and Agrochemical Research Centre (VAR), Groeselenberg 99, 1180 Brussels, Belgium.
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30
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Orton RJ, Wright CF, Morelli MJ, Juleff N, Thébaud G, Knowles NJ, Valdazo-González B, Paton DJ, King DP, Haydon DT. Observing micro-evolutionary processes of viral populations at multiple scales. Philos Trans R Soc Lond B Biol Sci 2013; 368:20120203. [PMID: 23382425 PMCID: PMC3678327 DOI: 10.1098/rstb.2012.0203] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Advances in sequencing technology coupled with new integrative approaches to data analysis provide a potentially transformative opportunity to use pathogen genome data to advance our understanding of transmission. However, to maximize the insights such genetic data can provide, we need to understand more about how the microevolution of pathogens is observed at different scales of biological organization. Here, we examine the evolutionary processes in foot-and-mouth disease virus observed at different scales, ranging from the tissue, animal, herd and region. At each scale, we observe analogous processes of population expansion, mutation and selection resulting in the accumulation of mutations over increasing time scales. While the current data are limited, rates of nucleotide substitution appear to be faster over individual-to-individual transmission events compared with those observed at a within-individual scale suggesting that viral population bottlenecks between individuals facilitate the fixation of polymorphisms. Longer-term rates of nucleotide substitution were found to be equivalent in individual-to-individual transmission compared with herd-to-herd transmission indicating that viral diversification at the herd level is not retained at a regional scale.
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Affiliation(s)
- Richard J Orton
- College of Medical, Veterinary and Life Sciences, Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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31
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Maliogka VI, Salvador B, Carbonell A, Sáenz P, León DS, Oliveros JC, Delgadillo MO, García JA, Simón-Mateo C. Virus variants with differences in the P1 protein coexist in a Plum pox virus population and display particular host-dependent pathogenicity features. MOLECULAR PLANT PATHOLOGY 2012; 13:877-86. [PMID: 22458641 PMCID: PMC6638729 DOI: 10.1111/j.1364-3703.2012.00796.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Subisolates segregated from an M-type Plum pox virus (PPV) isolate, PPV-PS, differ widely in pathogenicity despite their high degree of sequence similarity. A single amino acid substitution, K109E, in the helper component proteinase (HCPro) protein of PPV caused a significant enhancement of symptom severity in herbaceous hosts, and notably modified virus infectivity in peach seedlings. The presence of this substitution in certain subisolates that induced mild symptoms in herbaceous hosts and did not infect peach seedlings suggested the existence of uncharacterized attenuating factors in these subisolates. In this study, we show that two amino acid changes in the P1 protein are specifically associated with the mild pathogenicity exhibited by some PS subisolates. Site-directed mutagenesis studies demonstrated that both substitutions, W29R and V139E, but especially W29R, resulted in lower levels of virus accumulation and symptom severity in a woody host, Prunus persica. Furthermore, when W29R and V139E mutations were expressed concomitantly, PPV infectivity was completely abolished in this host. In contrast, the V139E substitution, but not W29R, was found to be responsible for symptom attenuation in herbaceous hosts. Deep sequencing analysis demonstrated that the W29R and V139E heterogeneities already existed in the original PPV-PS isolate before its segregation in different subisolates by local lesion cloning. These results highlight the potential complexity of potyviral populations and the relevance of the P1 protein of potyviruses in pathogenesis and viral adaptation to the host.
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Affiliation(s)
- Varvara I Maliogka
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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32
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Barbosa VC, Donangelo R, Souza SR. Quasispecies dynamics with network constraints. J Theor Biol 2012; 312:114-9. [PMID: 22898555 DOI: 10.1016/j.jtbi.2012.07.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Revised: 07/20/2012] [Accepted: 07/31/2012] [Indexed: 02/05/2023]
Abstract
A quasispecies is a set of interrelated genotypes that have reached a stationary state while evolving according to the usual Darwinian principles of selection and mutation. Quasispecies studies invariably assume that it is possible for any genotype to mutate into any other, but recent finds indicate that this assumption is not necessarily true. Here we revisit the traditional quasispecies theory by adopting a network structure to constrain the occurrence of mutations. Such structure is governed by a random-graph model, whose single parameter (a probability p) controls both the graph's density and the dynamics of mutation. We contribute two further modifications to the theory, one to account for the fact that different loci in a genotype may be differently susceptible to the occurrence of mutations, the other to allow for a more plausible description of the transition from adaptation to degeneracy of the quasispecies as p is increased. We give analytical and simulation results for the usual case of binary genotypes, assuming the fitness landscape in which a genotype's fitness decays exponentially with its Hamming distance to the wild type. These results support the theory's assertions regarding the adaptation of the quasispecies to the fitness landscape and also its possible demise as a function of p.
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Affiliation(s)
- Valmir C Barbosa
- Programa de Engenharia de Sistemas e Computação, COPPE, Universidade Federal do Rio de Janeiro, Caixa Postal 68511, 21941-972 Rio de Janeiro, RJ, Brazil.
| | - Raul Donangelo
- Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, 21941-972 Rio de Janeiro, RJ, Brazil; Instituto de Física, Facultad de Ingeniería, Universidad de la República, Julio Herrera y Reissig 565, 11.300 Montevideo, Uruguay
| | - Sergio R Souza
- Instituto de Física, Universidade Federal do Rio de Janeiro, Caixa Postal 68528, 21941-972 Rio de Janeiro, RJ, Brazil; Instituto de Física, Universidade Federal do Rio Grande do Sul, Caixa Postal 15051, 91501-970 Porto Alegre, RS, Brazil
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33
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Bordería AV, Stapleford KA, Vignuzzi M. RNA virus population diversity: implications for inter-species transmission. Curr Opin Virol 2011; 1:643-8. [PMID: 22440922 DOI: 10.1016/j.coviro.2011.09.012] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Revised: 09/13/2011] [Accepted: 09/30/2011] [Indexed: 01/25/2023]
Abstract
RNA viruses are notorious for rapidly generating genetically diverse populations during a single replication cycle, and the implications of this mutant population, often referred to as quasispecies, can be vast. Previous studies have linked RNA virus genetic variability to changes in viral pathogenesis, the ability to adapt to a host during infection, and to the acquisition of mechanisms required to switch hosts entirely. However, these initial studies are just the beginning. With the development of next generation technologies, groups will be able to dig deeper into the sequence space that is generated during an RNA virus infection and more clearly understand the development, role, and consequences of viral genetic diversity.
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Affiliation(s)
- Antonio V Bordería
- Institut Pasteur, Viral Populations and Pathogenesis Group and CNRS 3015, 75724 Paris Cedex 15, France
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34
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Musso F. On the Relation Between the Eigen Model and the Asexual Wright–Fisher Model. Bull Math Biol 2011; 74:103-15. [DOI: 10.1007/s11538-011-9666-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2011] [Accepted: 05/13/2011] [Indexed: 01/06/2023]
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35
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MAPREC assay for quantitation of mutants in a recombinant flavivirus vaccine strain using near-infrared fluorescent dyes. J Virol Methods 2011; 175:14-9. [PMID: 21514323 DOI: 10.1016/j.jviromet.2011.04.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 03/28/2011] [Accepted: 04/07/2011] [Indexed: 12/14/2022]
Abstract
Mutant analysis by PCR and restriction enzyme cleavage (MAPREC) is a quantitative assay of revertants in batches of live viral vaccines. The assay is highly sensitive and reliable but requires radioactive isotopes, which complicates its use in quality control laboratories. To quantify mutants in the cDNA of the West Nile (WN)/Dengue 4 chimera that was proposed as a new candidate of live vaccine against West Nile disease, alternative MAPREC protocols using non-radioactive dyes were explored. To compare the utility of different fluorescent dyes for MAPREC, the G(2337)→C mutation that was revealed by microarray hybridization in WN/Dengue 4 chimera virus was used as a model. DNA fragments produced by restriction endonuclease digestion were visualized in polyacrylamide gels by visible-range fluorescent dyes including ethidium bromide (EtBr) and SYBR Green I as well as by near-infrared (NIR) dye SYTO 60 and NIR dyes 700 and 800. The MAPREC assay performed with SYTO 60 and SYBR Green I was more sensitive than with EtBr but less sensitive than with NIR dyes 700 or 800. The NIR dyes 700 and 800 exhibited a wide linear range that may enable the detection of 0.05% of mutants in viral stocks. The NIR-based MAPREC assay was validated by using World Health Organization (WHO) international references for poliovirus type 3 with known contents of mutants. Values of mutant content produced by the non-radioactive assay were similar to the values determined in a previous WHO international collaborative study. The modified MAPREC assay could be used as an alternative to the radioisotope-based standard protocol for quality control of live viral vaccines.
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36
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Wright CF, Morelli MJ, Thébaud G, Knowles NJ, Herzyk P, Paton DJ, Haydon DT, King DP. Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using next-generation genome sequencing. J Virol 2011; 85:2266-75. [PMID: 21159860 PMCID: PMC3067773 DOI: 10.1128/jvi.01396-10] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/29/2010] [Indexed: 01/03/2023] Open
Abstract
The diverse sequences of viral populations within individual hosts are the starting material for selection and subsequent evolution of RNA viruses such as foot-and-mouth disease virus (FMDV). Using next-generation sequencing (NGS) performed on a Genome Analyzer platform (Illumina), this study compared the viral populations within two bovine epithelial samples (foot lesions) from a single animal with the inoculum used to initiate experimental infection. Genomic sequences were determined in duplicate sequencing runs, and the consensus sequence of the inoculum determined by NGS was identical to that previously determined using the Sanger method. However, NGS revealed the fine polymorphic substructure of the viral population, from nucleotide variants present at just below 50% frequency to those present at fractions of 1%. Some of the higher-frequency polymorphisms identified encoded changes within codons associated with heparan sulfate binding and were present in both foot lesions, revealing intermediate stages in the evolution of a tissue culture-adapted virus replicating within a mammalian host. We identified 2,622, 1,434, and 1,703 polymorphisms in the inoculum and in the two foot lesions, respectively: most of the substitutions occurred in only a small fraction of the population and represented the progeny from recent cellular replication prior to onset of any selective pressures. We estimated the upper limit for the genome-wide mutation rate of the virus within a cell to be 7.8 × 10(-4) per nucleotide. The greater depth of detection achieved by NGS demonstrates that this method is a powerful and valuable tool for the dissection of FMDV populations within hosts.
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Affiliation(s)
- Caroline F. Wright
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Marco J. Morelli
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Gaël Thébaud
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Nick J. Knowles
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Pawel Herzyk
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - David J. Paton
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Daniel T. Haydon
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Donald P. King
- Institute for Animal Health, Ash Road, Pirbright, Woking, Surrey GU24 0NF, United Kingdom, MRC, University of Glasgow Centre for Virus Research, Institute of Biodiversity, Animal Health and Comparative Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom, Institut National de la Recherche Agronomique (INRA), UMR BGPI, Cirad TA A-54/K, Campus de Baillarguet, 34938 Montpellier Cedex 5, France, The Sir Henry Wellcome Functional Genomics Facility, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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Perales C, Lorenzo-Redondo R, López-Galíndez C, Martínez MA, Domingo E. Mutant spectra in virus behavior. Future Virol 2010. [DOI: 10.2217/fvl.10.61] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
RNA viruses replicate as complex mutant spectra, also termed ‘mutant clouds’, known as viral quasispecies. While this is a widely observed viral population structure, it is less known that a number of biologically relevant features of this important group of viral pathogens depend on (or are strongly influenced by) the complexity and composition of mutant spectra. Among them, fitness increase or decrease depending on intrapopulation complementation or interference, selection triggered by memory genomes, pathogenic potential of viruses, disease evolution and the response to antiviral treatments. Quasispecies represent the recognition of complex behavior in viruses, and it is an oversimplification to equate such a population structure with the classic polymorphism of population biology. Darwinian principles acting on genome collectivities that replicate with high error rates provide a unique population structure prone to flexible and largely unpredictable behavior.
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Affiliation(s)
- Celia Perales
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), C/ Nicolás Cabrera, 1 Universidad Autónoma de Madrid, Cantoblanco, Madrid 28049, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
| | - Ramón Lorenzo-Redondo
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
| | - Cecilio López-Galíndez
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Madrid 28220, Spain
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38
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Elena SF, Solé RV, Sardanyés J. Simple genomes, complex interactions: epistasis in RNA virus. CHAOS (WOODBURY, N.Y.) 2010; 20:026106. [PMID: 20590335 DOI: 10.1063/1.3449300] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Owed to their reduced size and low number of proteins encoded, RNA viruses and other subviral pathogens are often considered as being genetically too simple. However, this structural simplicity also creates the necessity for viral RNA sequences to encode for more than one protein and for proteins to carry out multiple functions, all together resulting in complex patterns of genetic interactions. In this work we will first review the experimental studies revealing that the architecture of viral genomes is dominated by antagonistic interactions among loci. Second, we will also review mathematical models and provide a description of computational tools for the study of RNA virus dynamics and evolution. As an application of these tools, we will finish this review article by analyzing a stochastic bit-string model of in silico virus replication. This model analyzes the interplay between epistasis and the mode of replication on determining the population load of deleterious mutations. The model suggests that, for a given mutation rate, the deleterious mutational load is always larger when epistasis is predominantly antagonistic than when synergism is the rule. However, the magnitude of this effect is larger if replication occurs geometrically than if it proceeds linearly.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Ingeniero Fausto Elio s/n, 46022 València, Spain.
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39
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Holmes EC. The RNA virus quasispecies: fact or fiction? J Mol Biol 2010; 400:271-3. [PMID: 20493194 DOI: 10.1016/j.jmb.2010.05.032] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Revised: 05/04/2010] [Accepted: 05/14/2010] [Indexed: 12/17/2022]
Affiliation(s)
- Edward C Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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40
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Díaz Arenas C, Lehman N. Quasispecies-like behavior observed in catalytic RNA populations evolving in a test tube. BMC Evol Biol 2010; 10:80. [PMID: 20331885 PMCID: PMC2850355 DOI: 10.1186/1471-2148-10-80] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2009] [Accepted: 03/23/2010] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND During the RNA World, molecular populations were probably very small and highly susceptible to the force of strong random drift. In conjunction with Muller's Ratchet, this would have imposed difficulties for the preservation of the genetic information and the survival of the populations. Mechanisms that allowed these nascent populations to overcome this problem must have been advantageous. RESULTS Using continuous in vitro evolution experimentation with an increased mutation rate imposed by MnCl2, it was found that clonal 100-molecule populations of ribozymes clearly exhibit certain characteristics of a quasispecies. This is the first time this has been seen with a catalytic RNA. Extensive genotypic sampling from two replicate lineages was gathered and phylogenetic networks were constructed to elucidate the structure of the evolving RNA populations. A common distribution was found in which a mutant sequence was present at high frequency, surrounded by a cloud of mutant with lower frequencies. This is a typical distribution of quasispecies. Most of the mutants in these clouds were connected by short Hamming distance values, indicating their close relatedness. CONCLUSIONS The quasispecies nature of mutant RNA clouds facilitates the recovery of genotypes under pressure of being removed from the population by random drift. The empirical populations therefore evolved a genotypic resiliency despite a high mutation rate by adopting the characteristics of quasispecies, implying that primordial RNA pools could have used this strategy to avoid extinction.
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Affiliation(s)
- Carolina Díaz Arenas
- Department of Chemistry, Portland State University, PO Box 751, Portland, Oregon, 97207, USA
| | - Niles Lehman
- Department of Chemistry, Portland State University, PO Box 751, Portland, Oregon, 97207, USA
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41
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Colombo AL, Janini M, Salomão R, Medeiros EAS, Wey SB, Pignatari ACC. Surveillance programs for detection and characterization of emergent pathogens and antimicrobial resistance: results from the Division of Infectious Diseases, UNIFESP. AN ACAD BRAS CIENC 2010; 81:571-87. [PMID: 19722025 DOI: 10.1590/s0001-37652009000300020] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 05/12/2009] [Indexed: 11/22/2022] Open
Abstract
Several epidemiological changes have occurred in the pattern of nosocomial and community acquired infectious diseases during the past 25 years. Social and demographic changes possibly related to this phenomenon include a rapid population growth, the increase in urban migration and movement across international borders by tourists and immigrants, alterations in the habitats of animals and arthropods that transmit disease, as well as the raise of patients with impaired host defense abilities. Continuous surveillance programs of emergent pathogens and antimicrobial resistance are warranted for detecting in real time new pathogens, as well as to characterize molecular mechanisms of resistance. In order to become more effective, surveillance programs of emergent pathogens should be organized as a multicenter laboratory network connected to the main public and private infection control centers. Microbiological data should be integrated to guide therapy, adapting therapy to local ecology and resistance patterns. This paper presents an overview of data generated by the Division of Infectious Diseases, Federal University of São Paulo, along with its participation in different surveillance programs of nosocomial and community acquired infectious diseases.
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Affiliation(s)
- Arnaldo L Colombo
- Divisão de Doenças Infecciosas, Departamento de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brasil.
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42
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González-Candelas F, López-Labrador FX. Clinical relevance of genetic heterogeneity in HCV. Future Virol 2010. [DOI: 10.2217/fvl.09.63] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Infection by HCV affects an estimated 170 million people worldwide and it represents one of the major causes of liver transplantation and a heavy burden to healthcare systems. As with many other RNA viruses, HCV is characterized by very high levels of genetic variation, which have been associated to differences in disease progression and efficiency of antiviral treatment. Studies show many contradictory results and little consensus on such associations. Nevertheless, some general guidelines translating research results to clinical practice have been postulated. Here, we review the main research results obtained on HCV variation so far and explore the reasons for their lack of congruence under a population genetics framework. Understanding the factors responsible for the variable dynamics of HCV diversity in human populations and variation within infected individuals is even more necessary in face of the soon-to-arrive new HCV therapies.
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Affiliation(s)
- Fernando González-Candelas
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Apartado Oficial 22085, 46071-Valencia, Spain
| | - F Xavier López-Labrador
- Genomics and Health Area, CSISP – Centre for Public Health Research, Public Health Department, Generalitat Valenciana, Av. Catalunya, 21, 46020 Valencia, Spain
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43
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Holmes EC. The Evolutionary Genetics of Emerging Viruses. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2009. [DOI: 10.1146/annurev.ecolsys.110308.120248] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, Pennsylvania State University, University Park, Pennsylvania 16802; and Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892
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44
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Fishman SL, Branch AD. The quasispecies nature and biological implications of the hepatitis C virus. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2009; 9:1158-67. [PMID: 19666142 PMCID: PMC2790008 DOI: 10.1016/j.meegid.2009.07.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 07/24/2009] [Accepted: 07/31/2009] [Indexed: 12/18/2022]
Abstract
Many RNA viruses exist as a cloud of closely related sequence variants called a quasispecies, rather than as a population of identical clones. In this article, we explain the quasispecies nature of RNA viral genomes, and briefly review the principles of quasispecies dynamics and the differences with classical population genetics. We then discuss the current methods for quasispecies analysis and conclude with the biological implications of this phenomenon, focusing on the hepatitis C virus.
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Affiliation(s)
- Sarah L Fishman
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
| | - Andrea D Branch
- Mount Sinai School of Medicine, Department of Medicine, Division of Liver Diseases. 1425 Madison Ave, Box 11-20 New York, NY 10029, +1 212 659 8371 Tel, +1 212 348 3571 Fax,
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45
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de Miranda JR, Genersch E. Deformed wing virus. J Invertebr Pathol 2009; 103 Suppl 1:S48-61. [PMID: 19909976 DOI: 10.1016/j.jip.2009.06.012] [Citation(s) in RCA: 309] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
Abstract
Deformed wing virus (DWV; Iflaviridae) is one of many viruses infecting honeybees and one of the most heavily investigated due to its close association with honeybee colony collapse induced by Varroadestructor. In the absence of V.destructor DWV infection does not result in visible symptoms or any apparent negative impact on host fitness. However, for reasons that are still not fully understood, the transmission of DWV by V.destructor to the developing pupae causes clinical symptoms, including pupal death and adult bees emerging with deformed wings, a bloated, shortened abdomen and discolouration. These bees are not viable and die soon after emergence. In this review we will summarize the historical and recent data on DWV and its relatives, covering the genetics, pathobiology, and transmission of this important viral honeybee pathogen, and discuss these within the wider theoretical concepts relating to the genetic variability and population structure of RNA viruses, the evolution of virulence and the development of disease symptoms.
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Affiliation(s)
- Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, 750-07 Uppsala, Sweden
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46
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Hughes MG, Rosen HR. Human liver transplantation as a model to study hepatitis C virus pathogenesis. Liver Transpl 2009; 15:1395-411. [PMID: 19877210 PMCID: PMC2954677 DOI: 10.1002/lt.21866] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hepatitis C is a leading etiology of liver cancer and a leading reason for liver transplantation. Although new therapies have improved the rates of sustained response, a large proportion of patients (approximately 50%) fail to respond to antiviral treatment, thus remaining at risk for disease progression. Although chimpanzees have been used to study hepatitis C virus biology and treatments, their cost is quite high, and their use is strictly regulated; indeed, the National Institutes of Health no longer supports the breeding of chimpanzees for study. The development of hepatitis C virus therapies has been hindered by the relative paucity of small animal models for studying hepatitis C virus pathogenesis. This review presents the strengths of human liver transplantation and highlights the advances derived from this model, including insights into viral kinetics and quasispecies, viral receptor binding and entry, and innate and adaptive immunity. Moreover, consideration is given to current and emerging antiviral therapeutic approaches based on translational research results.
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Affiliation(s)
- Michael G. Hughes
- Department of Surgery, Medical University of South Carolina, Charleston, SC
| | - Hugo R. Rosen
- Department of Medicine, Divisions of Gastroenterology & Hepatology and Liver Transplantation; University of Colorado Health Sciences Center & National Jewish Hospital, and Denver VA
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47
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Iqbal M, Xiao H, Baillie G, Warry A, Essen SC, Londt B, Brookes SM, Brown IH, McCauley JW. Within-host variation of avian influenza viruses. Philos Trans R Soc Lond B Biol Sci 2009; 364:2739-47. [PMID: 19687042 PMCID: PMC2865086 DOI: 10.1098/rstb.2009.0088] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The emergence and spread of H5N1 avian influenza viruses from Asia through to Europe and Africa pose a significant animal disease problem and have raised concerns that the virus may pose a pandemic threat to humans. The epizootological factors that have influenced the wide distribution of the virus are complex, and the variety of viruses currently circulating reflects these factors. Sequence analysis of the virus genes sheds light on the H5N1 virus evolution during its emergence and spread, but the degree of virus variation at the level of an individual infected bird has been described in only a few studies. Here, we describe some results of a study in which turkeys, ducks and chickens were infected with either one of two H5N1 or one of three H7N1 viruses, and the degree of sequence variation within an individual infected avian host was examined. We developed 'deep amplicon' sequence analysis for this work, and the methods and results provide a background framework for application to disease outbreaks in the field.
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Affiliation(s)
- Munir Iqbal
- Institute for Animal Health, Compton Laboratory, Compton, Newbury, Berkshire RG20 7NN, UK
| | - Hiaxia Xiao
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Greg Baillie
- Department of Veterinary Medicine, Cambridge Infectious Diseases Consortium, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
| | - Andrew Warry
- BBSRC Bioscience IT Services, West Common, Harpenden, Herts AL5 2JE, UK
| | - Steve C. Essen
- Avian Virology, Veterinary Laboratories Agency—Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Brandon Londt
- Avian Virology, Veterinary Laboratories Agency—Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Sharon M. Brookes
- Avian Virology, Veterinary Laboratories Agency—Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - Ian H. Brown
- Avian Virology, Veterinary Laboratories Agency—Weybridge, Addlestone, Surrey KT15 3NB, UK
| | - John W. McCauley
- Division of Virology, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK
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Vasilakis N, Deardorff ER, Kenney JL, Rossi SL, Hanley KA, Weaver SC. Mosquitoes put the brake on arbovirus evolution: experimental evolution reveals slower mutation accumulation in mosquito than vertebrate cells. PLoS Pathog 2009; 5:e1000467. [PMID: 19503824 PMCID: PMC2685980 DOI: 10.1371/journal.ppat.1000467] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 05/07/2009] [Indexed: 01/24/2023] Open
Abstract
Like other arthropod-borne viruses (arboviruses), mosquito-borne dengue virus (DENV) is maintained in an alternating cycle of replication in arthropod and vertebrate hosts. The trade-off hypothesis suggests that this alternation constrains DENV evolution because a fitness increase in one host usually diminishes fitness in the other. Moreover, the hypothesis predicts that releasing DENV from host alternation should facilitate adaptation. To test this prediction, DENV was serially passaged in either a single human cell line (Huh-7), a single mosquito cell line (C6/36), or in alternating passages between Huh-7 and C6/36 cells. After 10 passages, consensus mutations were identified and fitness was assayed by evaluating replication kinetics in both cell types as well as in a novel cell type (Vero) that was not utilized in any of the passage series. Viruses allowed to specialize in single host cell types exhibited fitness gains in the cell type in which they were passaged, but fitness losses in the bypassed cell type, and most alternating passages, exhibited fitness gains in both cell types. Interestingly, fitness gains were observed in the alternately passaged, cloned viruses, an observation that may be attributed to the acquisition of both host cell-specific and amphi-cell-specific adaptations or to recovery from the fitness losses due to the genetic bottleneck of biological cloning. Amino acid changes common to both passage series suggested convergent evolution to replication in cell culture via positive selection. However, intriguingly, mutations accumulated more rapidly in viruses passed in Huh-7 cells than in those passed in C6/36 cells or in alternation. These results support the hypothesis that releasing DENV from host alternation facilitates adaptation, but there is limited support for the hypothesis that such alternation necessitates a fitness trade-off. Moreover, these findings suggest that patterns of genetic evolution may differ between viruses replicating in mammalian and mosquito cells.
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Affiliation(s)
- Nikos Vasilakis
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Eleanor R. Deardorff
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Joan L. Kenney
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Shannan L. Rossi
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, New Mexico, United States of America
| | - Scott C. Weaver
- Center for Biodefense and Emerging Infectious Diseases and Department of Pathology, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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49
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Gisder S, Aumeier P, Genersch E. Deformed wing virus: replication and viral load in mites (Varroa destructor). J Gen Virol 2009; 90:463-467. [PMID: 19141457 DOI: 10.1099/vir.0.005579-0] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Deformed wing virus (DWV) normally causes covert infections but can have devastating effects on bees by inducing morphological deformity or even death when transmitted by the ectoparasitic mite Varroa destructor. In order to determine the role of V. destructor in the development of crippled wings, we analysed individual mites for the presence and replication of DWV. The results supported the correlation between viral replication in mites and morphologically deformed bees. Quantification of viral genome equivalents revealed that mites capable of inducing an overt DWV infection contained 10(10)-10(12) genome equivalents per mite. In contrast, mites which could not induce crippled wings contained a maximum of only 10(8) viral genome equivalents per mite. We conclude that the development of crippled wings not only depends on DWV transmission by V. destructor but also on viral replication in V. destructor and on the DWV titre in the parasitizing mites.
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Affiliation(s)
- Sebastian Gisder
- Institute for Bee Research, Friedrich-Engels-Str. 32, D-16540 Hohen Neuendorf, Germany
| | - Pia Aumeier
- Faculty for Biology and Biotechnology, Ruhr University Bochum, Bochum, Germany
| | - Elke Genersch
- Institute for Bee Research, Friedrich-Engels-Str. 32, D-16540 Hohen Neuendorf, Germany
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50
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Abstract
The fixation probability, the probability that the frequency of a particular allele in a population will ultimately reach unity, is one of the cornerstones of population genetics. In this review, we give a brief historical overview of mathematical approaches used to estimate the fixation probability of beneficial alleles. We then focus on more recent work that has relaxed some of the key assumptions in these early papers, providing estimates that have wider applicability to both natural and laboratory settings. In the final section, we address the possibility of future work that might bridge the gap between theoretical results to date and results that might realistically be applied to the experimental evolution of microbial populations. Our aim is to highlight the concrete, testable predictions that have arisen from the theoretical literature, with the intention of further motivating the invaluable interplay between theory and experiment.
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Affiliation(s)
- Z Patwa
- Applied Mathematics, University of Western Ontario, Middlesex College 255, London, Ontario, Canada
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