1
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Castiglioni VG, Olmo-Uceda MJ, Martín S, Félix MA, González R, Elena SF. Experimental evolution of an RNA virus in Caenorhabditis elegans. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 123:105623. [PMID: 38901623 DOI: 10.1016/j.meegid.2024.105623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 06/02/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
The discovery of Orsay virus (OrV), the first virus infecting wild populations of Caenorhabditis elegans, has boosted studies of viral immunity pathways in this nematode. Considering the many advantages that C. elegans offers for fundamental research in host-pathogen interactions, this pathosystem has high potential to become a model system for experimental virus evolution studies. However, the evolutionary constraints - i.e, the balance between genetic variation, selection, drift and historical contingency- operating in this pathosystem have barely been explored. Here we describe for the first time an evolution experiment of two different OrV strains in C. elegans. Comparison of the two ancestral strains showed differences in infectivity and sequence, and highlighted the importance of consistently normalize viral inocula for meaningful comparisons among strains. After 10 serial passages of evolution, we report slight changes in infectivity and non-synonymous mutations fixed in the evolved viral populations. In addition, we observed numerous minor variants emerging in the viral population. These minor variants were not randomly distributed along the genome but concentrated in polymorphic genomic regions. Overall, our work established the grounds for future experimental virus evolution studies using Caenorhabditis nematodes.
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Affiliation(s)
- Victoria G Castiglioni
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - María J Olmo-Uceda
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Susana Martín
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain
| | - Marie-Anne Félix
- Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France
| | - Rubén González
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Institut de Biologie de l'École Normale Supérieure, CNRS, INSERM, 75005 Paris, France.
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, 46980 València, Spain; Santa Fe Institute, Sant Fe, NM 87501, USA.
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2
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Ruiz R, Montagud-Martínez R, Dorta-Gorrín A, Pablo-Marcos D, Gozalo M, Calvo-Montes J, Navas J, Rodrigo G. Rapid and Accurate Detection of the SARS-CoV-2 Omicron Variant with a CRISPR-Cas12a Reaction in the RT-qPCR Pot. ACS OMEGA 2024; 9:18046-18050. [PMID: 38680362 PMCID: PMC11044157 DOI: 10.1021/acsomega.3c09717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 05/01/2024]
Abstract
Gene sequencing in back of reverse transcription-quantitative polymerase chain reaction (RT-qPCR) is the current approach for discriminating infections produced by different severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants in the clinic. However, sequencing is often a time-consuming step, which hinders the deployment of a very fast response during a pandemic. Here, we propose to run a CRISPR-Cas12a reaction after completing the RT-qPCR and in the very same pot to detect with high specificity genetic marks characterizing variants of concern. A crRNA was appropriately designed to detect the S gene of the SARS-CoV-2 Omicron BA.1 variant. A significant response with >20-fold dynamic range was obtained for the Omicron BA.1 S gene, while the Delta S gene did not produce any detectable signal. The sensitivity of the method was analyzed with a series of diluted samples and different Cas12a nucleases. A correlation between the RT-qPCR CT values and the CRISPR-Cas12a reaction signals was observed. Variant discrimination with the CRISPR-Cas12a reaction was possible in some minutes with high accuracy from patient samples. In conclusion, CRISPR-Cas systems seem ready to be exploited in the clinic to boost personalized diagnoses and accelerate epidemiological surveillance in a cost-effective way.
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Affiliation(s)
- Raúl Ruiz
- Instituto
de Biología Integrativa de Sistemas (I2SysBio), CSIC—Universitat de València, 46980 Paterna, Spain
| | - Roser Montagud-Martínez
- Instituto
de Biología Integrativa de Sistemas (I2SysBio), CSIC—Universitat de València, 46980 Paterna, Spain
| | - Alexis Dorta-Gorrín
- Facultad
de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto
de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Daniel Pablo-Marcos
- Servicio
de Microbiología, Hospital Universitario
Marqués de Valdecilla, 39008 Santander, Spain
| | - Mónica Gozalo
- Instituto
de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
- Servicio
de Microbiología, Hospital Universitario
Marqués de Valdecilla, 39008 Santander, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Infecciosas
(CIBERINFEC), Instituto de Salud Carlos
III, 28029 Madrid, Spain
| | - Jorge Calvo-Montes
- Instituto
de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
- Servicio
de Microbiología, Hospital Universitario
Marqués de Valdecilla, 39008 Santander, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Infecciosas
(CIBERINFEC), Instituto de Salud Carlos
III, 28029 Madrid, Spain
| | - Jesús Navas
- Facultad
de Medicina, Universidad de Cantabria, 39011 Santander, Spain
- Instituto
de Investigación Sanitaria Marqués de Valdecilla (IDIVAL), 39011 Santander, Spain
| | - Guillermo Rodrigo
- Instituto
de Biología Integrativa de Sistemas (I2SysBio), CSIC—Universitat de València, 46980 Paterna, Spain
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3
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de Andrés-Torán R, Guidoum L, Zamfir AD, Mora MÁ, Moreno-Vázquez S, García-Arenal F. Tobacco Mild Green Mosaic Virus (TMGMV) Isolates from Different Plant Families Show No Evidence of Differential Adaptation to Their Host of Origin. Viruses 2023; 15:2384. [PMID: 38140625 PMCID: PMC10748040 DOI: 10.3390/v15122384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The relevance of tobamoviruses to crop production is increasing due to new emergences, which cannot be understood without knowledge of the tobamovirus host range and host specificity. Recent analyses of tobamovirus occurrence in different plant communities have shown unsuspectedly large host ranges. This was the case of the tobacco mild green mosaic virus (TMGMV), which previously was most associated with solanaceous hosts. We addressed two hypotheses concerning TMGMV host range evolution: (i) ecological fitting, rather than genome evolution, determines TMGMV host range, and (ii) isolates are adapted to the host of origin. We obtained TMGMV isolates from non-solanaceous hosts and we tested the capacity of genetically closely related TMGMV isolates from three host families to infect and multiply in 10 hosts of six families. All isolates systemically infected all hosts, with clear disease symptoms apparent only in solanaceous hosts. TMGMV multiplication depended on the assayed host but not on the isolate's host of origin, with all isolates accumulating to the highest levels in Nicotiana tabacum. Thus, results support that TMGMV isolates are adapted to hosts in the genus Nicotiana, consistent with a well-known old virus-host association. In addition, phenotypic plasticity allows Nicotiana-adapted TMGMV genotypes to infect a large range of hosts, as encountered according to plant community composition and transmission dynamics.
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Affiliation(s)
- Rafael de Andrés-Torán
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Laura Guidoum
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Adrian D. Zamfir
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Miguel Ángel Mora
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
| | - Santiago Moreno-Vázquez
- Departamento de Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2-4, 28040 Madrid, Spain;
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (CBGP UPM_INIA/CSIC), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain; (R.d.A.-T.); (L.G.); (A.D.Z.); (M.Á.M.)
- Departamento de Biotecnología-Biología Vegetal, E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avda. Puerta de Hierro 2-4, 28040 Madrid, Spain;
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4
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Lorenzo-Redondo R, de Sant’Anna Carvalho AM, Hultquist JF, Ozer EA. SARS-CoV-2 genomics and impact on clinical care for COVID-19. J Antimicrob Chemother 2023; 78:ii25-ii36. [PMID: 37995357 PMCID: PMC10667012 DOI: 10.1093/jac/dkad309] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 08/02/2023] [Indexed: 11/25/2023] Open
Abstract
The emergence and worldwide spread of SARS-CoV-2 during the COVID-19 pandemic necessitated the adaptation and rapid deployment of viral WGS and analysis techniques that had been previously applied on a more limited basis to other viral pathogens, such as HIV and influenza viruses. The need for WGS was driven in part by the low mutation rate of SARS-CoV-2, which necessitated measuring variation along the entire genome sequence to effectively differentiate lineages and characterize viral evolution. Several WGS approaches designed to maximize throughput and accuracy were quickly adopted by surveillance labs around the world. These broad-based SARS-CoV-2 genomic sequencing efforts revealed ongoing evolution of the virus, highlighted by the successive emergence of new viral variants throughout the course of the pandemic. These genomic insights were instrumental in characterizing the effects of viral mutations on transmissibility, immune escape and viral tropism, which in turn helped guide public health policy, the use of monoclonal antibody therapeutics and vaccine development strategies. As the use of direct-acting antivirals for the treatment of COVID-19 became more widespread, the potential for emergence of antiviral resistance has driven ongoing efforts to delineate resistance mutations and to monitor global sequence databases for their emergence. Given the critical role of viral genomics in the international effort to combat the COVID-19 pandemic, coordinated efforts should be made to expand global genomic surveillance capacity and infrastructure towards the anticipation and prevention of future pandemics.
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Affiliation(s)
- Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Alexandre Machado de Sant’Anna Carvalho
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Judd F Hultquist
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
| | - Egon A Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611, USA
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5
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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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6
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Rabitz H, Russell B, Ho TS. The Surprising Ease of Finding Optimal Solutions for Controlling Nonlinear Phenomena in Quantum and Classical Complex Systems. J Phys Chem A 2023; 127:4224-4236. [PMID: 37142303 DOI: 10.1021/acs.jpca.3c01896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
This Perspective addresses the often observed surprising ease of achieving optimal control of nonlinear phenomena in quantum and classical complex systems. The circumstances involved are wide-ranging, with scenarios including manipulation of atomic scale processes, maximization of chemical and material properties or synthesis yields, Nature's optimization of species' populations by natural selection, and directed evolution. Natural evolution will mainly be discussed in terms of laboratory experiments with microorganisms, and the field is also distinct from the other domains where a scientist specifies the goal(s) and oversees the control process. We use the word "control" in reference to all of the available variables, regardless of the circumstance. The empirical observations on the ease of achieving at least good, if not excellent, control in diverse domains of science raise the question of why this occurs despite the generally inherent complexity of the systems in each scenario. The key to addressing the question lies in examining the associated control landscape, which is defined as the optimization objective as a function of the control variables that can be as diverse as the phenomena under consideration. Controls may range from laser pulses, chemical reagents, chemical processing conditions, out to nucleic acids in the genome and more. This Perspective presents a conjecture, based on present findings, that the systematics of readily finding good outcomes from controlled phenomena may be unified through consideration of control landscapes with the same common set of three underlying assumptions─the existence of an optimal solution, the ability for local movement on the landscape, and the availability of sufficient control resources─whose validity needs assessment in each scenario. In practice, many cases permit using myopic gradient-like algorithms while other circumstances utilize algorithms having some elements of stochasticity or introduced noise, depending on whether the landscape is locally smooth or rough. The overarching observation is that only relatively short searches are required despite the common high dimensionality of the available controls in typical scenarios.
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Affiliation(s)
- Herschel Rabitz
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Benjamin Russell
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Tak-San Ho
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
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7
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Moreno‐Pérez MG, Bera S, McLeish M, Fraile A, García‐Arenal F. Reversion of a resistance-breaking mutation shows reversion costs and high virus diversity at necrotic local lesions. MOLECULAR PLANT PATHOLOGY 2023; 24:142-153. [PMID: 36435959 PMCID: PMC9831284 DOI: 10.1111/mpp.13281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/28/2022] [Accepted: 10/29/2022] [Indexed: 06/16/2023]
Abstract
An instance of host range evolution relevant to plant virus disease control is resistance breaking. Resistance breaking can be hindered by across-host fitness trade-offs generated by negative effects of resistance-breaking mutations on the virus fitness in susceptible hosts. Different mutations in pepper mild mottle virus (PMMoV) coat protein result in the breaking in pepper plants of the resistance determined by the L3 resistance allele. Of these, mutation M138N is widespread in PMMoV populations, despite associated fitness penalties in within-host multiplication and survival. The stability of mutation M138N was analysed by serial passaging in L3 resistant plants. Appearance on passaging of necrotic local lesions (NLL), indicating an effective L3 resistance, showed reversion to nonresistance-breaking phenotypes was common. Most revertant genotypes had the mutation N138K, which affects the properties of the virus particle, introducing a penalty of reversion. Hence, the costs of reversion may determine the evolution of resistance-breaking in addition to resistance-breaking costs. The genetic diversity of the virus population in NLL was much higher than in systemically infected tissues, and included mutations reported to break L3 resistance other than M138N. Infectivity assays on pepper genotypes with different L alleles showed high phenotypic diversity in respect to L alleles in NLL, including phenotypes not reported in nature. Thus, high diversity at NLL may potentiate the appearance of genotypes that enable the colonization of new host genotypes or species. Collectively, the results of this study contribute to better understanding the evolutionary dynamics of resistance breaking and host-range expansions.
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Affiliation(s)
- Manuel G. Moreno‐Pérez
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Sayanta Bera
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Michael McLeish
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
| | - Fernando García‐Arenal
- Centro de Biotecnología y Genómica de Plantas UPM‐INIA/CSICUniversidad Politécnica de MadridMadridSpain
- E.T.S.I. Agronómica, Alimentaria y de BiosistemasCampus de Montegancedo, UPMMadridSpain
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8
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Neher RA. Contributions of adaptation and purifying selection to SARS-CoV-2 evolution. Virus Evol 2022; 8:veac113. [PMID: 37593203 PMCID: PMC10431346 DOI: 10.1093/ve/veac113] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/30/2022] [Accepted: 12/05/2022] [Indexed: 08/19/2023] Open
Abstract
Continued evolution and adaptation of SARS-CoV-2 has led to more transmissible and immune-evasive variants with profound impacts on the course of the pandemic. Here I analyze the evolution of the virus over 2.5 years since its emergence and estimate the rates of evolution for synonymous and non-synonymous changes separately for evolution within clades-well-defined monophyletic groups with gradual evolution-and for the pandemic overall. The rate of synonymous mutation is found to be around 6 changes per year. Synonymous rates within variants vary little from variant to variant and are compatible with the overall rate of 7 changes per year (or [Formula: see text] per year and codon). In contrast, the rate at which variants accumulate amino acid changes (non-synonymous mutations) was initially around 12-16 changes per year, but in 2021 and 2022 it dropped to 6-9 changes per year. The overall rate of non-synonymous evolution, that is across variants, is estimated to be about 26 amino acid changes per year (or [Formula: see text] per year and codon). This strong acceleration of the overall rate compared to within clade evolution indicates that the evolutionary process that gave rise to the different variants is qualitatively different from that in typical transmission chains and likely dominated by adaptive evolution. I further quantify the spectrum of mutations and purifying selection in different SARS-CoV-2 proteins and show that the massive global sampling of SARS-CoV-2 is sufficient to estimate site-specific fitness costs across the entire genome. Many accessory proteins evolve under limited evolutionary constraints with little short-term purifying selection. About half of the mutations in other proteins are strongly deleterious.
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Affiliation(s)
- Richard A Neher
- Biozentrum, University of Basel, Spitalstrasse 41, Basel
4053, Switzerland
- Swiss Institute of Bioinformatics, Spitalstrasse 41, Basel
4053, Switzerland
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9
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Lansch‐Justen L, Cusseddu D, Schmitz MA, Bank C. The extinction time under mutational meltdown driven by high mutation rates. Ecol Evol 2022; 12:e9046. [PMID: 35813923 PMCID: PMC9257376 DOI: 10.1002/ece3.9046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/01/2022] [Accepted: 06/04/2022] [Indexed: 01/15/2023] Open
Abstract
Mutational meltdown describes an eco‐evolutionary process in which the accumulation of deleterious mutations causes a fitness decline that eventually leads to the extinction of a population. Possible applications of this concept include medical treatment of RNA virus infections based on mutagenic drugs that increase the mutation rate of the pathogen. To determine the usefulness and expected success of such an antiviral treatment, estimates of the expected time to mutational meltdown are necessary. Here, we compute the extinction time of a population under high mutation rates, using both analytical approaches and stochastic simulations. Extinction is the result of three consecutive processes: (a) initial accumulation of deleterious mutations due to the increased mutation pressure; (b) consecutive loss of the fittest haplotype due to Muller's ratchet; (c) rapid population decline toward extinction. We find accurate analytical results for the mean extinction time, which show that the deleterious mutation rate has the strongest effect on the extinction time. We confirm that intermediate‐sized deleterious selection coefficients minimize the extinction time. Finally, our simulations show that the variation in extinction time, given a set of parameters, is surprisingly small.
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Affiliation(s)
- Lucy Lansch‐Justen
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Institute of Evolution and Ecology University of Edinburgh Edinburgh UK
| | - Davide Cusseddu
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Grupo Física‐Matemática, Faculdade de Ciências Universidade de Lisboa Lisboa Portugal
| | | | - Claudia Bank
- Instituto Gulbenkian de Ciência Oeiras Portugal
- Institute of Ecology and Evolution University of Bern Bern Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
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10
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Kabi M, Filion GJ. Chromatin and viral integration in immunity: The challenge of silencing non-self genes. Trends Immunol 2022; 43:449-458. [PMID: 35490134 DOI: 10.1016/j.it.2022.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 11/24/2022]
Abstract
Several viruses hide in the genome of their host. To complete their replication cycle, they need to integrate in the form of a provirus and express their genes. In vertebrates, integrated viruses can be silenced by chromatin, implying that some specific mechanisms exist to detect non-self genes. The known mechanisms depend on sequence features of retroelements, but the fluctuations of virus expression suggest that other determinants also exist. Here we review the mechanisms allowing chromatin to silence integrated viruses and propose that DNA repair may help flag them as 'non-self' shortly after their genomic insertion.
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Affiliation(s)
- Manisha Kabi
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada
| | - Guillaume J Filion
- Department of Biological Sciences, University of Toronto Scarborough, Scarborough, ON, Canada.
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11
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Abstract
The success of many viruses depends upon cooperative interactions between viral genomes. However, whenever cooperation occurs, there is the potential for 'cheats' to exploit that cooperation. We suggest that: (1) the biology of viruses makes viral cooperation particularly susceptible to cheating; (2) cheats are common across a wide range of viruses, including viral entities that are already well studied, such as defective interfering genomes, and satellite viruses. Consequently, the evolutionary theory of cheating could help us understand and manipulate viral dynamics, while viruses also offer new opportunities to study the evolution of cheating.
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Affiliation(s)
- Asher Leeks
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK.
| | - Stuart A West
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
| | - Melanie Ghoul
- Department of Zoology, University of Oxford, Oxford, OX1 3PS, UK
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12
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Wang Y, Xue P, Cao M, Yu T, Lane ST, Zhao H. Directed Evolution: Methodologies and Applications. Chem Rev 2021; 121:12384-12444. [PMID: 34297541 DOI: 10.1021/acs.chemrev.1c00260] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Directed evolution aims to expedite the natural evolution process of biological molecules and systems in a test tube through iterative rounds of gene diversifications and library screening/selection. It has become one of the most powerful and widespread tools for engineering improved or novel functions in proteins, metabolic pathways, and even whole genomes. This review describes the commonly used gene diversification strategies, screening/selection methods, and recently developed continuous evolution strategies for directed evolution. Moreover, we highlight some representative applications of directed evolution in engineering nucleic acids, proteins, pathways, genetic circuits, viruses, and whole cells. Finally, we discuss the challenges and future perspectives in directed evolution.
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Affiliation(s)
- Yajie Wang
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Pu Xue
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mingfeng Cao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Tianhao Yu
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stephan T Lane
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Huimin Zhao
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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13
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Merleau NSC, Pénisson S, Gerrish PJ, Elena SF, Smerlak M. Why are viral genomes so fragile? The bottleneck hypothesis. PLoS Comput Biol 2021; 17:e1009128. [PMID: 34237053 PMCID: PMC8291636 DOI: 10.1371/journal.pcbi.1009128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/20/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
If they undergo new mutations at each replication cycle, why are RNA viral genomes so fragile, with most mutations being either strongly deleterious or lethal? Here we provide theoretical and numerical evidence for the hypothesis that genetic fragility is partly an evolutionary response to the multiple population bottlenecks experienced by viral populations at various stages of their life cycles. Modelling within-host viral populations as multi-type branching processes, we show that mutational fragility lowers the rate at which Muller’s ratchet clicks and increases the survival probability through multiple bottlenecks. In the context of a susceptible-exposed-infectious-recovered epidemiological model, we find that the attack rate of fragile viral strains can exceed that of more robust strains, particularly at low infectivities and high mutation rates. Our findings highlight the importance of demographic events such as transmission bottlenecks in shaping the genetic architecture of viral pathogens. Given that most mutations are deleterious, high mutation rates carry a significant evolutionary cost. To reduce this burden, an obvious evolutionary solution would be to reduce the fitness cost of mutations by becoming more robust; this solution is indeed selected in populations of constantly large size. Here, we show that when populations regularly experience bottlenecks, as viruses do upon transmission to a new host, a less obvious solution becomes more viable: namely, to increase the fitness cost of mutations so that unfit mutants are less likely to fix at each passage. This could explain why viruses—especially RNA viruses—do in fact have very fragile genomes.
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Affiliation(s)
| | - Sophie Pénisson
- Université Paris Est Créteil, CNRS, LAMA, Creteil, France
- Université Gustave Eiffel, LAMA, Marne-la-Vallée, France
| | - Philip J. Gerrish
- University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, València, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- * E-mail:
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14
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Aimone CD, Lavington E, Hoyer JS, Deppong DO, Mickelson-Young L, Jacobson A, Kennedy GG, Carbone I, Hanley-Bowdoin L, Duffy S. Population diversity of cassava mosaic begomoviruses increases over the course of serial vegetative propagation. J Gen Virol 2021; 102:001622. [PMID: 34310272 PMCID: PMC8491896 DOI: 10.1099/jgv.0.001622] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/05/2021] [Indexed: 01/06/2023] Open
Abstract
Cassava mosaic disease (CMD) represents a serious threat to cassava, a major root crop for more than 300 million Africans. CMD is caused by single-stranded DNA begomoviruses that evolve rapidly, making it challenging to develop durable disease resistance. In addition to the evolutionary forces of mutation, recombination and reassortment, factors such as climate, agriculture practices and the presence of DNA satellites may impact viral diversity. To gain insight into the factors that alter and shape viral diversity in planta, we used high-throughput sequencing to characterize the accumulation of nucleotide diversity after inoculation of infectious clones corresponding to African cassava mosaic virus (ACMV) and East African cassava mosaic Cameroon virus (EACMCV) in the susceptible cassava landrace Kibandameno. We found that vegetative propagation had a significant effect on viral nucleotide diversity, while temperature and a satellite DNA did not have measurable impacts in our study. EACMCV diversity increased linearly with the number of vegetative propagation passages, while ACMV diversity increased for a time and then decreased in later passages. We observed a substitution bias toward C→T and G→A for mutations in the viral genomes consistent with field isolates. Non-coding regions excluding the promoter regions of genes showed the highest levels of nucleotide diversity for each genome component. Changes in the 5' intergenic region of DNA-A resembled the sequence of the cognate DNA-B sequence. The majority of nucleotide changes in coding regions were non-synonymous, most with predicted deleterious effects on protein structure, indicative of relaxed selection pressure over six vegetative passages. Overall, these results underscore the importance of knowing how cropping practices affect viral evolution and disease progression.
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Affiliation(s)
- Catherine D. Aimone
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Erik Lavington
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
| | - David O. Deppong
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Leigh Mickelson-Young
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Alana Jacobson
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL 36849, USA
| | - George G. Kennedy
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC 27695, USA
| | - Ignazio Carbone
- Center for Integrated Fungal Research, Department of Entomology and Plant Pathology, North Carolina State University, Raleigh NC 27695, USA
| | - Linda Hanley-Bowdoin
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh NC 27695, USA
| | - Siobain Duffy
- Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA
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15
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Al-Zaher A, Domingo-Calap P, Sanjuán R. Experimental virus evolution in cancer cell monolayers, spheroids, and tissue explants. Virus Evol 2021; 7:veab045. [PMID: 34040797 PMCID: PMC8134955 DOI: 10.1093/ve/veab045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Viral laboratory evolution has been used for different applications, such as modeling viral emergence, drug-resistance prediction, and therapeutic virus optimization. However, these studies have been mainly performed in cell monolayers, a highly simplified environment, raising concerns about their applicability and relevance. To address this, we compared the evolution of a model virus in monolayers, spheroids, and tissue explants. We performed this analysis in the context of cancer virotherapy by performing serial transfers of an oncolytic vesicular stomatitis virus (VSV-Δ51) in 4T1 mouse mammary tumor cells. We found that VSV-Δ51 gained fitness in each of these three culture systems, and that adaptation to the more complex environments (spheroids or explants) correlated with increased fitness in monolayers. Most evolved lines improved their ability to suppress β-interferon secretion compared to the VSV-Δ51 founder, suggesting that the selective pressure exerted by antiviral innate immunity was important in the three systems. However, system-specific patterns were also found. First, viruses evolved in monolayers remained more oncoselective that those evolved in spheroids, since the latter showed concomitant adaptation to non-tumoral mouse cells. Second, deep sequencing indicated that viral populations evolved in monolayers or explants tended to be more genetically diverse than those evolved in spheroids. Finally, we found highly variable outcomes among independent evolutionary lines propagated in explants. We conclude that experimental evolution in monolayers tends to be more reproducible than in spheroids or explants, and better preserves oncoselectivity. Our results also suggest that monolayers capture at least some relevant selective pressures present in more complex systems.
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Affiliation(s)
- Ahmed Al-Zaher
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, València 46980, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, València 46980, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, C/ Catedrático Agustín Escardino 9, València 46980, Spain
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16
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Yañez O, Chávez-Galarza J, Tellgren-Roth C, Pinto MA, Neumann P, de Miranda JR. The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission. Sci Rep 2020; 10:5956. [PMID: 32249797 PMCID: PMC7136270 DOI: 10.1038/s41598-020-62673-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/17/2020] [Indexed: 11/23/2022] Open
Abstract
The main biological threat to the western honeybee (Apis mellifera) is the parasitic mite Varroa destructor, largely because it vectors lethal epidemics of honeybee viruses that, in the absence of this mite, are relatively innocuous. The severe pathology is a direct consequence of excessive virus titres caused by this novel transmission route. However, little is known about how the virus adapts genetically during transmission and whether this influences the pathology. Here, we show that upon injection into honeybee pupae, the deformed wing virus type-A (DWV-A) quasispecies undergoes a rapid, extensive expansion of its sequence space, followed by strong negative selection towards a uniform, common shape by the time the pupae have completed their development, with no difference between symptomatic and asymptomatic adults in either DWV titre or genetic composition. This suggests that the physiological and molecular environment during pupal development has a strong, conservative influence on shaping the DWV-A quasispecies in emerging adults. There was furthermore no evidence of any progressive adaptation of the DWV-A quasispecies to serial intra-abdominal injection, simulating mite transmission, despite the generation of ample variation immediately following each transmission, suggesting that the virus either had already adapted to transmission by injection, or was unaffected by it.
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Affiliation(s)
- Orlando Yañez
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, CH-3000, Switzerland
| | - Julio Chávez-Galarza
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
- Instituto Nacional de Innovación Agraria (INIA), Av. La Molina, 1981, Lima, Perú
| | | | - M Alice Pinto
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Campus de Sta. Apolónia, 5300-253, Bragança, Portugal
| | - Peter Neumann
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, CH-3000, Switzerland
| | - Joachim R de Miranda
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden.
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17
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Tamisier L, Szadkowski M, Nemouchi G, Lefebvre V, Szadkowski E, Duboscq R, Santoni S, Sarah G, Sauvage C, Palloix A, Moury B. Genome-wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding. MOLECULAR PLANT PATHOLOGY 2020; 21:3-16. [PMID: 31605444 PMCID: PMC6913244 DOI: 10.1111/mpp.12874] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping-by-sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome-wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
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Affiliation(s)
- Lucie Tamisier
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
- Present address:
Plant Pathology LaboratoryTERRA‐Gembloux Agro‐Bio TechUniversity of LiègePassage des Déportés, 25030GemblouxBelgium
| | - Marion Szadkowski
- GAFLINRA84140MontfavetFrance
- Pathologie VégétaleINRA84140MontfavetFrance
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18
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Altinli M, Lequime S, Courcelle M, François S, Justy F, Gosselin-Grenet AS, Ogliastro M, Weill M, Sicard M. Evolution and phylogeography of Culex pipiens densovirus. Virus Evol 2019; 5:vez053. [PMID: 31807318 PMCID: PMC6884738 DOI: 10.1093/ve/vez053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Viruses of the Parvoviridae family infect a wide range of animals including vertebrates and invertebrates. So far, our understanding of parvovirus diversity is biased towards medically or economically important viruses mainly infecting vertebrate hosts, while invertebrate infecting parvoviruses—namely densoviruses—have been largely neglected. Here, we investigated the prevalence and the evolution of the only mosquito-infecting ambidensovirus, Culex pipiens densovirus (CpDV), from laboratory mosquito lines and natural populations collected worldwide. CpDV diversity generally grouped in two clades, here named CpDV-1 and -2. The incongruence of the different gene trees for some samples suggested the possibility of recombination events between strains from different clades. We further investigated the role of selection on the evolution of CpDV genome and detected many individual sites under purifying selection both in non-structural and structural genes. However, some sites in structural genes were under diversifying selection, especially during the divergence of CpDV-1 and -2 clades. These substitutions between CpDV-1 and -2 clades were mostly located in the capsid protein encoding region and might cause changes in host specificity or pathogenicity of CpDV strains from the two clades. However, additional functional and experimental studies are necessary to fully understand the protein conformations and the resulting phenotype of these substitutions between clades of CpDV.
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Affiliation(s)
- Mine Altinli
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sebastian Lequime
- KU Leuven, Department of Microbiology, Immunology, and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Maxime Courcelle
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Sarah François
- DGIMI, INRA, Université de Montpellier, Montpellier, France.,Department of Zoology, University of Oxford, Oxford, UK
| | - Fabienne Justy
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | | | | | - Mylene Weill
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| | - Mathieu Sicard
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
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19
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Somovilla P, Manrubia S, Lázaro E. Evolutionary Dynamics in the RNA Bacteriophage Qβ Depends on the Pattern of Change in Selective Pressures. Pathogens 2019; 8:pathogens8020080. [PMID: 31216651 PMCID: PMC6631425 DOI: 10.3390/pathogens8020080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 12/14/2022] Open
Abstract
The rate of change in selective pressures is one of the main factors that determines the likelihood that populations can adapt to stress conditions. Generally, the reduction in the population size that accompanies abrupt environmental changes makes it difficult to generate and select adaptive mutations. However, in systems with high genetic diversity, as happens in RNA viruses, mutations with beneficial effects under new conditions can already be present in the population, facilitating adaptation. In this work, we have propagated an RNA bacteriophage (Qβ) at temperatures higher than the optimum, following different patterns of change. We have determined the fitness values and the consensus sequences of all lineages throughout the evolutionary process in order to establish correspondences between fitness variations and adaptive pathways. Our results show that populations subjected to a sudden temperature change gain fitness and fix mutations faster than those subjected to gradual changes, differing also in the particular selected mutations. The life-history of populations prior to the environmental change has great importance in the dynamics of adaptation. The conclusion is that in the bacteriophage Qβ, the standing genetic diversity together with the rate of temperature change determine both the rapidity of adaptation and the followed evolutionary pathways.
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Affiliation(s)
- Pilar Somovilla
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
| | - Susanna Manrubia
- Centro Nacional de Biotecnología (CSIC), 28049 Madrid, Spain.
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain.
| | - Ester Lázaro
- Centro de Astrobiología (CSIC-INTA), 28850 Torrejón de Ardoz, Madrid, Spain.
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20
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Abstract
Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution. RNA viruses, particularly genetically diverse members of the Picornavirales, are widespread and abundant in the ocean. Gene surveys suggest that there are spatial and temporal patterns in the composition of RNA virus assemblages, but data on their diversity and genetic variability in different oceanographic settings are limited. Here, we show that specific RNA virus genomes have widespread geographic distributions and that the dominant genotypes are under purifying selection. Genomes from three previously unknown picorna-like viruses (BC-1, -2, and -3) assembled from a coastal site in British Columbia, Canada, as well as marine RNA viruses JP-A, JP-B, and Heterosigma akashiwo RNA virus exhibited different biogeographical patterns. Thus, biotic factors such as host specificity and viral life cycle, and not just abiotic processes such as dispersal, affect marine RNA virus distribution. Sequence differences relative to reference genomes imply that virus quasispecies are under purifying selection, with synonymous single-nucleotide variations dominating in genomes from geographically distinct regions resulting in conservation of amino acid sequences. Conversely, sequences from coastal South Africa that mapped to marine RNA virus JP-A exhibited more nonsynonymous mutations, probably representing amino acid changes that accumulated over a longer separation. This biogeographical analysis of marine RNA viruses demonstrates that purifying selection is occurring across oceanographic provinces. These data add to the spectrum of known marine RNA virus genomes, show the importance of dispersal and purifying selection for these viruses, and indicate that closely related RNA viruses are pathogens of eukaryotic microbes across oceans. IMPORTANCE Very little is known about aquatic RNA virus populations and genome evolution. This is the first study that analyzes marine environmental RNA viral assemblages in an evolutionary and broad geographical context. This study contributes the largest marine RNA virus metagenomic data set to date, substantially increasing the sequencing space for RNA viruses and also providing a baseline for comparisons of marine RNA virus diversity. The new viruses discovered in this study are representative of the most abundant family of marine RNA viruses, the Marnaviridae, and expand our view of the diversity of this important group. Overall, our data and analyses provide a foundation for interpreting marine RNA virus diversity and evolution.
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21
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Ouedraogo RS, Pita JS, Somda IP, Traore O, Roossinck MJ. Impact of Cultivated Hosts on the Recombination of Cucumber Mosaic Virus. J Virol 2019; 93:e01770-18. [PMID: 30787159 PMCID: PMC6430555 DOI: 10.1128/jvi.01770-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Accepted: 01/16/2019] [Indexed: 01/30/2023] Open
Abstract
Cucumber mosaic virus (CMV) is one of the most successful viruses known, infecting over 1,200 species of plants. Like other single-stranded RNA viruses, CMV is known to have a high potential for population diversity due to error-prone replication and short generation times. Recombination is also a mechanism that allows viruses to adapt to new hosts. Host genes have been identified that impact the recombination of RNA viruses by using single-cell yeast systems. To determine the impact that the natural plant host has on virus recombination, we used a high-recombination-frequency strain of CMV, LS-CMV, which belongs to subgroup II, in three different cultivated hosts: Capsicum annuum cv. Marengo (pepper), Nicotiana tabacum cv. Xanthi nc (tobacco), and Cucurbita pepo cv. Black Beauty (zucchini). The recombination frequency was calculated by using an RNA 3 reporter carrying restriction enzyme sites created by introducing silent mutations. Our results show that the recombination frequency of LS-CMV is correlated with the infected host. The recombination events in pepper were 1.8-fold higher than those in tobacco and 5-fold higher than those in zucchini. Furthermore, we observed the generation of defective RNAs in inoculated pepper plants, but not in tobacco or zucchini. These results indicate that the host is involved in both intra- and intermolecular recombination events and that hosts like pepper could foster more rapid evolution of the virus. In addition, we report for the first time the production of defective RNAs in a CMV subgroup II isolate.IMPORTANCE Recombination is an important mechanism used by viruses for their diversification and to adapt to diverse hosts. Understanding the host role in the mechanisms of evolution is important for virus disease management and controlling the emergence of new strains. This study shows the impact that cultivated hosts are playing in the evolution of CMV. Furthermore, our results and previous studies show how some specific hosts could be an ideal environment for the emergence of new viral strains.
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Affiliation(s)
- Rimnoma S Ouedraogo
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
- Laboratoire de Virologie et de Biotechnologie Végétale (LVBV), Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
- Université Nazi Boni (UNB), Institut du Développement Rural (IDR), Unité Santé des Plantes du Laboratoire Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (Sy.N.A.I.E.), Bobo-Dioulasso, Burkina Faso
| | - Justin S Pita
- Université Félix Houphouët-Boigny, Laboratoire de Virologie Végétale, Pôle Scientifique et d'Innovation, Bingerville, Côte d'Ivoire
| | - Irenée P Somda
- Université Nazi Boni (UNB), Institut du Développement Rural (IDR), Unité Santé des Plantes du Laboratoire Systèmes Naturels, Agrosystèmes et Ingénierie de l'Environnement (Sy.N.A.I.E.), Bobo-Dioulasso, Burkina Faso
| | - Oumar Traore
- Laboratoire de Virologie et de Biotechnologie Végétale (LVBV), Institut de l'Environnement et de Recherches Agricoles (INERA), Ouagadougou, Burkina Faso
| | - Marilyn J Roossinck
- Department of Plant Pathology and Environmental Microbiology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, Pennsylvania, USA
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22
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Saxenhofer M, Schmidt S, Ulrich RG, Heckel G. Secondary contact between diverged host lineages entails ecological speciation in a European hantavirus. PLoS Biol 2019; 17:e3000142. [PMID: 30785873 PMCID: PMC6382107 DOI: 10.1371/journal.pbio.3000142] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 01/22/2019] [Indexed: 11/19/2022] Open
Abstract
The diversity of viruses probably exceeds biodiversity of eukaryotes, but little is known about the origin and emergence of novel virus species. Experimentation and disease outbreak investigations have allowed the characterization of rapid molecular virus adaptation. However, the processes leading to the establishment of functionally distinct virus taxa in nature remain obscure. Here, we demonstrate that incipient speciation in a natural host species has generated distinct ecological niches leading to adaptive isolation in an RNA virus. We found a very strong association between the distributions of two major phylogenetic clades in Tula orthohantavirus (TULV) and the rodent host lineages in a natural hybrid zone of the European common vole (Microtus arvalis). The spatial transition between the virus clades in replicated geographic clines is at least eight times narrower than between the hybridizing host lineages. This suggests a strong barrier for effective virus transmission despite frequent dispersal and gene flow among local host populations, and translates to a complete turnover of the adaptive background of TULV within a few hundred meters in the open, unobstructed landscape. Genetic differences between TULV clades are homogenously distributed in the genomes and mostly synonymous (93.1%), except for a cluster of nonsynonymous changes in the 5′ region of the viral envelope glycoprotein gene, potentially involved in host-driven isolation. Evolutionary relationships between TULV clades indicate an emergence of these viruses through rapid differential adaptation to the previously diverged host lineages that resulted in levels of ecological isolation exceeding the progress of speciation in their vertebrate hosts. Like host, like virus; analysis of a natural hybrid zone in the European common vole reveals speciation processes in Tula hantaviruses triggered by evolutionary divergence in the rodent host lineages. Natural biodiversity is driven by stochastic processes and evolutionary adaptation to ecological niches. In viruses, adaptation to specific hosts may cause diversification and eventually lead to the emergence of novel viruses. Here, we studied diversity in Tula orthohantavirus (TULV) in relation to evolutionary divergence in its natural rodent host, the European common vole (Microtus arvalis). In a geographical region in which two distinct evolutionary lineages in the common vole interact and interbreed (a hybrid zone), we found two substantially different TULV clades. Phylogenetic analyses revealed that the divergence among virus clades was likely triggered by a shift of an ancestral virus between the previously diverged host lineages in the hybrid zone. The strong association between virus clades and host lineages at a fine geographical scale results in effective separation of TULVs, despite incomplete reproductive isolation and frequent gene flow among local host populations. Virus genome sequences pointed to the amino-terminal part of the envelope protein as an important region for functional differentiation among these virus clades.
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Affiliation(s)
- Moritz Saxenhofer
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
| | - Sabrina Schmidt
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
| | - Rainer G. Ulrich
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Novel and Emerging Infectious Diseases, Greifswald-Insel Riems, Germany
- German Center for Infection Research (DZIF), partner site Hamburg-Luebeck-Borstel-Insel Riems, Germany
| | - Gerald Heckel
- Institute of Ecology and Evolution, University of Bern, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge, Bâtiment Génopode, Lausanne, Switzerland
- * E-mail:
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Bera S, Fraile A, García-Arenal F. Analysis of Fitness Trade-Offs in the Host Range Expansion of an RNA Virus, Tobacco Mild Green Mosaic Virus. J Virol 2018; 92:e01268-18. [PMID: 30257999 PMCID: PMC6258955 DOI: 10.1128/jvi.01268-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 09/13/2018] [Indexed: 12/14/2022] Open
Abstract
The acquisition of new hosts provides a virus with more opportunities for transmission and survival but may be limited by across-host fitness trade-offs. Major causes of across-host trade-offs are antagonistic pleiotropy, that is, host differential phenotypic effects of mutations, a Genotype x Environment interaction, and epistasis, a Genotype x Genotype interaction. Here, we analyze if there are trade-offs, and what are the causes, associated with the acquisition by tobacco mild green mosaic virus (TMGMV) of a new host. For this, the multiplication of sympatric field isolates of TMGMV from its wild reservoir host Nicotiana glauca and from pepper crops was quantified in the original and the heterologous hosts. TMGMV isolates from N. glauca were adapted to their host, but pepper isolates were not adapted to pepper, and the acquisition of this new host was associated with a fitness penalty in the original host. Analyses of the collection of field isolates and of mutant genotypes derived from biologically active cDNA clones showed a role of mutations in the coat protein and the 3' untranslated region in determining within-host virus fitness. Fitness depended on host-specific effects of these mutations, on the genetic background in which they occurred, and on higher-order interactions of the type Genotype x Genotype x Environment. These types of effects had been reported to generate across-host fitness trade-offs under experimental evolution. Our results show they may also operate in heterogeneous natural environments and could explain why pepper isolates were not adapted to pepper and their lower fitness in N. glaucaIMPORTANCE The acquisition of new hosts conditions virus epidemiology and emergence; hence it is important to understand the mechanisms behind host range expansion. Experimental evolution studies have identified antagonistic pleiotropy and epistasis as genetic mechanisms that limit host range expansion, but studies from virus field populations are few. Here, we compare the performance of isolates of tobacco mild green mosaic virus from its reservoir host, Nicotiana glauca, and its new host, pepper, showing that acquisition of a new host was not followed by adaptation to it but was associated with a fitness loss in the original host. Analysis of mutations determining host-specific virus multiplication identified antagonistic pleiotropy, epistasis, and host-specific epistasis as mechanisms generating across-host fitness trade-offs that may prevent adaptation to pepper and cause a loss of fitness in N. glauca Thus, mechanisms determining trade-offs, identified under experimental evolution, could also operate in the heterogeneous environment in which natural plant virus populations occur.
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Affiliation(s)
- Sayanta Bera
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas UPM-INIA and E.T.S.I. Agronómica, Alimentaria y de Biosistemas, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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24
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Cervera H, Lalić J, Elena SF. Efficient escape from local optima in a highly rugged fitness landscape by evolving RNA virus populations. Proc Biol Sci 2017; 283:rspb.2016.0984. [PMID: 27534955 DOI: 10.1098/rspb.2016.0984] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/26/2016] [Indexed: 12/25/2022] Open
Abstract
Predicting viral evolution has proven to be a particularly difficult task, mainly owing to our incomplete knowledge of some of the fundamental principles that drive it. Recently, valuable information has been provided about mutation and recombination rates, the role of genetic drift and the distribution of mutational, epistatic and pleiotropic fitness effects. However, information about the topography of virus' adaptive landscapes is still scarce, and to our knowledge no data has been reported so far on how its ruggedness may condition virus' evolvability. Here, we show that populations of an RNA virus move efficiently on a rugged landscape and scape from the basin of attraction of a local optimum. We have evolved a set of Tobacco etch virus genotypes located at increasing distances from a local adaptive optimum in a highly rugged fitness landscape, and we observed that few evolved lineages remained trapped in the local optimum, while many others explored distant regions of the landscape. Most of the diversification in fitness among the evolved lineages was explained by adaptation, while historical contingency and chance events contribution was less important. Our results demonstrate that the ruggedness of adaptive landscapes is not an impediment for RNA viruses to efficiently explore remote parts of it.
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Affiliation(s)
- Héctor Cervera
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Jasna Lalić
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 València, Spain The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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25
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Elena SF. Evolutionary transitions during RNA virus experimental evolution. Philos Trans R Soc Lond B Biol Sci 2017; 371:rstb.2015.0441. [PMID: 27431519 DOI: 10.1098/rstb.2015.0441] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/15/2016] [Indexed: 12/27/2022] Open
Abstract
In their search to understand the evolution of biological complexity, John Maynard Smith and Eörs Szathmáry put forward the notion of major evolutionary transitions as those in which elementary units get together to generate something new, larger and more complex. The origins of chromosomes, eukaryotic cells, multicellular organisms, colonies and, more recently, language and technological societies are examples that clearly illustrate this notion. However, a transition may be considered as anecdotal or as major depending on the specific level of biological organization under study. In this contribution, I will argue that transitions may also be occurring at a much smaller scale of biological organization: the viral world. Not only that, but also that we can observe in real time how these major transitions take place during experimental evolution. I will review the outcome of recent evolution experiments with viruses that illustrate four major evolutionary transitions: (i) the origin of a new virus that infects an otherwise inaccessible host and completely changes the way it interacts with the host regulatory and metabolic networks, (ii) the incorporation and loss of genes, (iii) the origin of segmented genomes from a non-segmented one, and (iv) the evolution of cooperative behaviour and cheating between different viruses or strains during co-infection of the same host.This article is part of the themed issue 'The major synthetic evolutionary transitions'.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022 València, Spain Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, Parc Científic de la Universitat de València, Catedrático Agustín Escardino 9, 46980 Paterna, Valencia, Spain Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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26
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Nerva L, Silvestri A, Ciuffo M, Palmano S, Varese GC, Turina M. Transmission of Penicillium aurantiogriseum partiti-like virus 1 to a new fungal host (Cryphonectria parasitica) confers higher resistance to salinity and reveals adaptive genomic changes. Environ Microbiol 2017; 19:4480-4492. [PMID: 28836717 DOI: 10.1111/1462-2920.13894] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 08/12/2017] [Indexed: 11/27/2022]
Abstract
We attempted to transfect six recently characterized virus species to protoplasts of Penicillium janczewskii and Chryphonectria parasitica. None of the recovered P. janczewskii colonies was positive for the transfected viruses, but Penicillium aurantiogriseum partiti-like virus 1 (PaPLV1) was detected in three distinct regenerated C. parasitica colonies. We screened the phenotype of the infected strains in up to 45 different conditions combining different media, salinity and temperatures: our results show that the infected strains grow slower than the virus- free in most of the tested conditions with the exception of halophilic stress in a specific nutrient combination media. We proceeded to characterize molecularly the population of distinct isolates of PaPLV1 infected C. parasitica through RNAseq: comparison to the viral population present in the original host - P. auratiogriseum - showed that two isolates accumulated non-synonymous mutations suggesting adaptation to the new host. RNAseq analyses identified a second genomic RNA segment and northern blot of RNA extracted from purified virus suspensions allowed establishing that PaPLV1 is at least bipartite in nature and that it forms isometric virions of circa 36-38 nm in diameter. In light of these new acquisitions, we discuss the taxonomic placement of PaPLV1 inside the Partitiviridae.
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Affiliation(s)
- Luca Nerva
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, Torino 10135, Italy.,Department of Life Sciences and Systems Biology, University of Turin, Mycotheca Universitatis Taurinensis (MUT), Viale Mattioli 25, Torino 10125, Italy
| | - Alessandro Silvestri
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, Torino 10135, Italy.,Department of Life Sciences and Systems Biology, University of Turin, Mycotheca Universitatis Taurinensis (MUT), Viale Mattioli 25, Torino 10125, Italy
| | - Marina Ciuffo
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Sabrina Palmano
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, Torino 10135, Italy
| | - Givanna Cristina Varese
- Department of Life Sciences and Systems Biology, University of Turin, Mycotheca Universitatis Taurinensis (MUT), Viale Mattioli 25, Torino 10125, Italy
| | - Massimo Turina
- Istituto per la Protezione Sostenibile delle Piante, CNR, Strada delle Cacce 73, Torino 10135, Italy
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27
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Sihelská N, Vozárová Z, Predajňa L, Šoltys K, Hudcovicová M, Mihálik D, Kraic J, Mrkvová M, Kúdela O, Glasa M. Experimental Infection of Different Tomato Genotypes with Tomato mosaic virus Led to a Low Viral Population Heterogeneity in the Capsid Protein Encoding Region. THE PLANT PATHOLOGY JOURNAL 2017; 33:508-513. [PMID: 29018314 PMCID: PMC5624493 DOI: 10.5423/ppj.nt.04.2017.0082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/12/2017] [Indexed: 06/07/2023]
Abstract
The complete genome sequence of a Slovak SL-1 isolate of Tomato mosaic virus (ToMV) was determined from the next generation sequencing (NGS) data, further confirming a limited sequence divergence in this tobamovirus species. Tomato genotypes Monalbo, Mobaci and Moperou, respectively carrying the susceptible tm-2 allele or the Tm-1 and Tm-2 resistant alleles, were tested for their susceptibility to ToMV SL-1. Although the three tomato genotypes accumulated ToMV SL-1 to similar amounts as judged by semi-quantitative DAS-ELISA, they showed variations in the rate of infection and symptomatology. Possible differences in the intra-isolate variability and polymorphism between viral populations propagating in these tomato genotypes were evaluated by analysis of the capsid protein (CP) encoding region. Irrespective of genotype infected, the intra-isolate haplotype structure showed the presence of the same highly dominant CP sequence and the low level of population diversity (0.08-0.19%). Our results suggest that ToMV CP encoding sequence is relatively stable in the viral population during its replication in vivo and provides further demonstration that RNA viruses may show high sequence stability, probably as a result of purifying selection.
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Affiliation(s)
- Nina Sihelská
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava,
Slovak Republic
| | - Zuzana Vozárová
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava,
Slovak Republic
| | - Lukáš Predajňa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava,
Slovak Republic
| | - Katarína Šoltys
- Comenius University Science Park, Comenius University in Bratislava, Ilkovičova 8, 841 04, Bratislava,
Slovak Republic
| | - Martina Hudcovicová
- National Agriculture and Food Centre-Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany,
Slovak Republic
| | - Daniel Mihálik
- National Agriculture and Food Centre-Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany,
Slovak Republic
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, 917 01 Trnava,
Slovak Republic
| | - Ján Kraic
- National Agriculture and Food Centre-Research Institute of Plant Production, Bratislavská cesta 122, 921 68 Piešťany,
Slovak Republic
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, 917 01 Trnava,
Slovak Republic
| | - Michaela Mrkvová
- Department of Biotechnologies, Faculty of Natural Sciences, University of SS. Cyril and Methodius, J. Herdu 2, 917 01 Trnava,
Slovak Republic
| | | | - Miroslav Glasa
- Institute of Virology, Biomedical Research Centre, Slovak Academy of Sciences, Dúbravská cesta 9, 84505 Bratislava,
Slovak Republic
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28
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Tamisier L, Rousseau E, Barraillé S, Nemouchi G, Szadkowski M, Mailleret L, Grognard F, Fabre F, Moury B, Palloix A. Quantitative trait loci in pepper control the effective population size of two RNA viruses at inoculation. J Gen Virol 2017; 98:1923-1931. [PMID: 28691663 DOI: 10.1099/jgv.0.000835] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Infection of plants by viruses is a complex process involving several steps: inoculation into plant cells, replication in inoculated cells and plant colonization. The success of the different steps depends, in part, on the viral effective population size (Ne), defined as the number of individuals passing their genes to the next generation. During infection, the virus population will undergo bottlenecks, leading to drastic reductions in Ne and, potentially, to the loss of the fittest variants. Therefore, it is crucial to better understand how plants affect Ne. We aimed to (i) identify the plant genetic factors controlling Ne during inoculation, (ii) understand the mechanisms used by the plant to control Ne and (iii) compare these genetic factors with the genes controlling plant resistance to viruses. Ne was measured in a doubled-haploid population of Capsicum annuum. Plants were inoculated with either a Potato virus Y (PVY) construct expressing the green fluorescent protein or a necrotic variant of Cucumber mosaic virus (CMV). Newas assessed by counting the number of primary infection foci on cotyledons for PVY or the number of necrotic local lesions on leaves for CMV. The number of foci and lesions was correlated (r=0.57) and showed a high heritability (h2=0.93 for PVY and h2=0.98 for CMV). The Ne of the two viruses was controlled by both common quantitative trait loci (QTLs) and virus-specific QTLs, indicating the contribution of general and specific mechanisms. The PVY-specific QTL colocalizes with a QTL that reduces PVY accumulation and the capacity to break down a major-effect resistance gene.
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Affiliation(s)
- Lucie Tamisier
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Elsa Rousseau
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France.,INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Sebastien Barraillé
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ghislaine Nemouchi
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Marion Szadkowski
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Ludovic Mailleret
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France.,INRA, Université Nice Sophia Antipolis, CNRS, UMR 1355-7254 Institut Sophia Agrobiotech, Sophia Antipolis, France
| | | | - Frederic Fabre
- INRA, UMR 1065 Santé et Agroécologie du Vignoble, BP 81, 33883 Villenave d'Ornon cedex, France
| | - Benoit Moury
- INRA, UR407 PV, Unité de Pathologie Végétale, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
| | - Alain Palloix
- INRA, UR1052 GAFL, Unité de Génétique et Amélioration des Fruits et Légumes, Domaine St Maurice - 67 Allée des Chênes, CS 60094, F-84143 Montfavet Cedex, France
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29
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Nadeem A, Wahl LM. Prophage as a genetic reservoir: Promoting diversity and driving innovation in the host community. Evolution 2017; 71:2080-2089. [PMID: 28590013 DOI: 10.1111/evo.13287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 05/07/2017] [Indexed: 12/16/2022]
Abstract
Sequencing of bacterial genomes has revealed an abundance of prophage sequences in many bacterial species. Since these sequences are accessible, through recombination, to infecting phages, bacteria carry an arsenal of genetic material that can be used by these viruses. We develop a mathematical model to isolate the effects of this phenomenon on the coevolution of temperate phage and bacteria. The model predicts that prophage sequences may play a key role in maintaining the phage population in situations that would otherwise favor host cell resistance. In addition, prophage recombination facilitates the existence of multiple phage types, thus promoting diverse co-existence in the phage-host ecosystem. Finally, because the host carries an archive of previous phage strategies, prophage recombination can drive waves of innovation in the host cell population.
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Affiliation(s)
- A Nadeem
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
| | - Lindi M Wahl
- Department of Applied Mathematics, The University of Western Ontario, London, Ontario, N6A 5B7, Canada
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30
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Morley VJ, Turner PE. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 2017; 71:872-883. [PMID: 28121018 PMCID: PMC5382103 DOI: 10.1111/evo.13193] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
Abstract
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520
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31
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Dennehy JJ. Evolutionary ecology of virus emergence. Ann N Y Acad Sci 2016; 1389:124-146. [PMID: 28036113 PMCID: PMC7167663 DOI: 10.1111/nyas.13304] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 10/24/2016] [Accepted: 11/09/2016] [Indexed: 12/22/2022]
Abstract
The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment.
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Affiliation(s)
- John J Dennehy
- Biology Department, Queens College of the City University of New York, Queens, New York and The Graduate Center of the City University of New York, New York, New York
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32
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Zwart MP, Elena SF. Matters of Size: Genetic Bottlenecks in Virus Infection and Their Potential Impact on Evolution. Annu Rev Virol 2016; 2:161-79. [PMID: 26958911 DOI: 10.1146/annurev-virology-100114-055135] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
For virus infections of multicellular hosts, narrow genetic bottlenecks during transmission and within-host spread appear to be widespread. These bottlenecks will affect the maintenance of genetic variation in a virus population and the prevalence of mixed-strain infections, thereby ultimately determining the strength with which different random forces act during evolution. Here we consider different approaches for estimating bottleneck sizes and weigh their merits. We then review quantitative estimates of bottleneck size during cellular infection, within-host spread, horizontal transmission, and finally vertical transmission. In most cases we find that bottlenecks do regularly occur, although in many cases they appear to be virion-concentration dependent. Finally, we consider the evolutionary implications of genetic bottlenecks during virus infection. Although on average strong bottlenecks will lead to declines in fitness, we consider a number of scenarios in which bottlenecks could also be advantageous for viruses.
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Affiliation(s)
- Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politècnica de València, 46022 València, Spain; .,Institute of Theoretical Physics, University of Cologne, 50937 Cologne, Germany;
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politècnica de València, 46022 València, Spain; .,The Santa Fe Institute, Santa Fe, New Mexico 87501
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33
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Moreno-Pérez MG, García-Luque I, Fraile A, García-Arenal F. Mutations That Determine Resistance Breaking in a Plant RNA Virus Have Pleiotropic Effects on Its Fitness That Depend on the Host Environment and on the Type, Single or Mixed, of Infection. J Virol 2016; 90:9128-37. [PMID: 27489266 PMCID: PMC5044817 DOI: 10.1128/jvi.00737-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 07/25/2016] [Indexed: 12/30/2022] Open
Abstract
UNLABELLED Overcoming host resistance in gene-for-gene host-virus interactions is an important instance of host range expansion, which can be hindered by across-host fitness trade-offs. Trade-offs are generated by negative effects of host range mutations on the virus fitness in the original host, i.e., by antagonistic pleiotropy. It has been reported that different mutations in Pepper mild mottle virus (PMMoV) coat protein result in overcoming L-gene resistance in pepper. To analyze if resistance-breaking mutations in PMMoV result in antagonistic pleiotropy, all reported mutations determining the overcoming of L(3) and L(4) alleles were introduced in biologically active cDNA clones. Then, the parental and mutant virus genotypes were assayed in susceptible pepper genotypes with an L(+), L(1), or L(2) allele, in single and in mixed infections. Resistance-breaking mutations had pleiotropic effects on the virus fitness that, according to the specific mutation, the host genotype, and the type of infection, single or mixed with other virus genotypes, were antagonistic or positive. Thus, resistance-breaking mutations can generate fitness trade-offs both across hosts and across types of infection, and the frequency of host range mutants will depend on the genetic structure of the host population and on the frequency of mixed infections by different virus genotypes. Also, resistance-breaking mutations variously affected virulence, which may further influence the evolution of host range expansion. IMPORTANCE A major cause of virus emergence is host range expansion, which may be hindered by across-host fitness trade-offs caused by negative pleiotropy of host range mutations. An important instance of host range expansion is overcoming host resistance in gene-for-gene plant-virus interactions. We analyze here if mutations in the coat protein of Pepper mild mottle virus determining L-gene resistance-breaking in pepper have associated fitness penalties in susceptible host genotypes. Results show that pleiotropic effects of resistance-breaking mutations on virus fitness depend on the specific mutation, the susceptible host genotype, and the type of infection, single or mixed, with other virus genotypes. Accordingly, resistance-breaking mutations can have negative, positive, or no pleiotropic effects on virus fitness. These results underscore the complexity of host range expansion evolution and, specifically, the difficulty of predicting the overcoming of resistance factors in crops.
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Affiliation(s)
- Manuel G Moreno-Pérez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | | | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA) and E.T.S.I. Agrónomos, Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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Mauck KE. Variation in virus effects on host plant phenotypes and insect vector behavior: what can it teach us about virus evolution? Curr Opin Virol 2016; 21:114-123. [PMID: 27644035 DOI: 10.1016/j.coviro.2016.09.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/18/2016] [Accepted: 09/01/2016] [Indexed: 01/17/2023]
Abstract
Virus infection can elicit changes in host plant cues that mediate vector orientation, feeding, and dispersal. Given the importance of plant cues for vector-mediated virus transmission, it is unlikely that selection is blind to these effects. Indeed, there are many examples of viruses altering plant cues in ways that should enhance transmission. However, there are also examples of viruses inducing transmission-limiting plant phenotypes. These apparently mal-adaptive effects occur when viruses experience host plant environments that also limit infectivity or within-host multiplication. The apparent link between virus effects and pathology argues for consideration of prior evolutionary relationships between viruses and host plants in order to understand how viruses might evolve to manipulate vector behavior via effects on host plant cues.
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Affiliation(s)
- Kerry E Mauck
- Department of Environmental Systems Science, ETH Zürich, Schmelzbergstrasse 9, 8092 Zürich, Switzerland.
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35
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Syller J, Grupa A. Antagonistic within-host interactions between plant viruses: molecular basis and impact on viral and host fitness. MOLECULAR PLANT PATHOLOGY 2016; 17:769-82. [PMID: 26416204 PMCID: PMC6638324 DOI: 10.1111/mpp.12322] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Double infections of related or unrelated viruses frequently occur in single plants, the viral agents being inoculated into the host plant simultaneously (co-infection) or sequentially (super-infection). Plants attacked by viruses activate sophisticated defence pathways which operate at different levels, often at significant fitness costs, resulting in yield reduction in crop plants. The occurrence and severity of the negative effects depend on the type of within-host interaction between the infecting viruses. Unrelated viruses generally interact with each other in a synergistic manner, whereas interactions between related viruses are mostly antagonistic. These can incur substantial fitness costs to one or both of the competitors. A relatively well-known antagonistic interaction is cross-protection, also referred to as super-infection exclusion. This type of interaction occurs when a previous infection with one virus prevents or interferes with subsequent infection by a homologous second virus. The current knowledge on why and how one virus variant excludes or restricts another is scant. Super-infection exclusion between viruses has predominantly been attributed to the induction of RNA silencing, which is a major antiviral defence mechanism in plants. There are, however, presumptions that various mechanisms are involved in this phenomenon. This review outlines the current state of knowledge concerning the molecular mechanisms behind antagonistic interactions between plant viruses. Harmful or beneficial effects of these interactions on viral and host plant fitness are also characterized. Moreover, the review briefly outlines the past and present attempts to utilize antagonistic interactions among viruses to protect crop plants against destructive diseases.
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Affiliation(s)
- Jerzy Syller
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
| | - Anna Grupa
- Plant Breeding and Acclimatization Institute-National Research Institute, Laboratory of Phytopathology, Centre Młochów, 05-831, Młochów, Poland
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Morley VJ, Mendiola SY, Turner PE. Rate of novel host invasion affects adaptability of evolving RNA virus lineages. Proc Biol Sci 2016; 282:20150801. [PMID: 26246544 DOI: 10.1098/rspb.2015.0801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Although differing rates of environmental turnover should be consequential for the dynamics of adaptive change, this idea has been rarely examined outside of theory. In particular, the importance of RNA viruses in disease emergence warrants experiments testing how differing rates of novel host invasion may impact the ability of viruses to adaptively shift onto a novel host. To test whether the rate of environmental turnover influences adaptation, we experimentally evolved 144 Sindbis virus lineages in replicated tissue-culture environments, which transitioned from being dominated by a permissive host cell type to a novel host cell type. The rate at which the novel host 'invaded' the environment varied by treatment. The fitness (growth rate) of evolved virus populations was measured on each host type, and molecular substitutions were mapped via whole genome consensus sequencing. Results showed that virus populations more consistently reached high fitness levels on the novel host when the novel host 'invaded' the environment more gradually, and gradual invasion resulted in less variable genomic outcomes. Moreover, virus populations that experienced a rapid shift onto the novel host converged upon different genotypes than populations that experienced a gradual shift onto the novel host, suggesting a strong effect of historical contingency.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
| | - Sandra Y Mendiola
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, PO Box 208106, 165 Prospect Street, New Haven, CT 06520-8106, USA
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He DC, Zhan J, Cheng ZB, Xie LH. Viruliferous rate of small brown planthopper is a good indicator of rice stripe disease epidemics. Sci Rep 2016; 6:21376. [PMID: 26898155 PMCID: PMC4761966 DOI: 10.1038/srep21376] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 01/21/2016] [Indexed: 02/05/2023] Open
Abstract
Rice stripe virus (RSV), its vector insect (small brown planthopper, SBPH) and climatic conditions in Jiangsu, China were monitored between 2002 and 2012 to determine key biotic and abiotic factors driving epidemics of the disease. Average disease severity, disease incidence and viruliferous rate of SBPH peaked in 2004 and then gradually decreased. Disease severity of RSV was positively correlated with viruliferous rate of the vector but not with the population density of the insect, suggesting that the proportion of vectors infected by the virus rather than the absolute number of vectors plays an important role in RSV epidemics and could be used for disease forecasting. The finding of a positive correlation of disease severity and viruliferous rate among years suggests that local infection is likely the main source of primary inoculum of RSV. Of the two main climatic factors, temperature plays a more important role than rainfall in RSV epidemics.
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Affiliation(s)
- Dun-Chun He
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiasui Zhan
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zhao-Bang Cheng
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Lian-Hui Xie
- Fujian Key Lab of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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38
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Nascimento-Brito S, Paulo Zukurov J, Maricato JT, Volpini AC, Salim ACM, Araújo FMG, Coimbra RS, Oliveira GC, Antoneli F, Janini LMR. HIV-1 Tropism Determines Different Mutation Profiles in Proviral DNA. PLoS One 2015; 10:e0139037. [PMID: 26413773 PMCID: PMC4587555 DOI: 10.1371/journal.pone.0139037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/07/2015] [Indexed: 01/19/2023] Open
Abstract
In order to establish new infections HIV-1 particles need to attach to receptors expressed on the cellular surface. HIV-1 particles interact with a cell membrane receptor known as CD4 and subsequently with another cell membrane molecule known as a co-receptor. Two major different co-receptors have been identified: C-C chemokine Receptor type 5 (CCR5) and C-X-C chemokine Receptor type 4 (CXCR4) Previous reports have demonstrated cellular modifications upon HIV-1 binding to its co-receptors including gene expression modulations. Here we investigated the effect of viral binding to either CCR5 or CXCR4 co-receptors on viral diversity after a single round of reverse transcription. CCR5 and CXCR4 pseudotyped viruses were used to infect non-stimulated and stimulated PBMCs and purified CD4 positive cells. We adopted the SOLiD methodology to sequence virtually the entire proviral DNA from all experimental infections. Infections with CCR5 and CXCR4 pseudotyped virus resulted in different patterns of genetic diversification. CCR5 virus infections produced extensive proviral diversity while in CXCR4 infections a more localized substitution process was observed. In addition, we present pioneering results of a recently developed method for the analysis of SOLiD generated sequencing data applicable to the study of viral quasi-species. Our findings demonstrate the feasibility of viral quasi-species evaluation by NGS methodologies. We presented for the first time strong evidence for a host cell driving mechanism acting on the HIV-1 genetic variability under the control of co-receptor stimulation. Additional investigations are needed to further clarify this question, which is relevant to viral diversification process and consequent disease progression.
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Affiliation(s)
- Sieberth Nascimento-Brito
- Departamento de Microbiologia e Imunologia Veterinária, Universidade Federal Rural do Rio de Janeiro (UFRRJ), Rio de Janeiro, Brazil
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | | | - Juliana T. Maricato
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
| | - Angela C. Volpini
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Anna Christina M. Salim
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Flávio M. G. Araújo
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Roney S. Coimbra
- Biosystems Informatics Group, CPqRR, FIOCRUZ, Belo Horizonte, Brazil
| | - Guilherme C. Oliveira
- Genomics and Computational Biology Group, Research Center René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, Brazil
| | - Fernando Antoneli
- Departamento de Informática em Saúde, EPM, UNIFESP, São Paulo, Brazil
- Laboratório de Biocomplexidade e Genômica Evolutiva, EPM, UNIFESP, São Paulo, Brazil
| | - Luiz Mário R. Janini
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina (EPM), Universidade Federal de São Paulo (UNIFESP), São Paulo, Brazil
- Departamento de Medicina, EPM, UNIFESP, São Paulo, Brazil
- * E-mail:
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Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF. Temporal dynamics of intrahost molecular evolution for a plant RNA virus. Mol Biol Evol 2015; 32:1132-47. [PMID: 25660377 DOI: 10.1093/molbev/msv028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.
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Affiliation(s)
- José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain The Santa Fe Institute, Santa Fe, NM
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40
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Freire JM, Santos NC, Veiga AS, Da Poian AT, Castanho MARB. Rethinking the capsid proteins of enveloped viruses: multifunctionality from genome packaging to genome transfection. FEBS J 2015; 282:2267-78. [DOI: 10.1111/febs.13274] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 03/05/2015] [Accepted: 03/17/2015] [Indexed: 11/29/2022]
Affiliation(s)
- João M. Freire
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Nuno C. Santos
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Ana Salomé Veiga
- Instituto de Medicina Molecular; Faculdade de Medicina; Universidade de Lisboa; Lisbon Portugal
| | - Andrea T. Da Poian
- Instituto de Bioquímica Médica Leopoldo de Meis; Universidade Federal do Rio de Janeiro; Rio de Janeiro Brazil
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41
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Elena SF, Pybus OG. Editorial: A home for virology, ecology, epidemiology, and evolutionary biology. Virus Evol 2015; 1:1-3. [PMID: 27774275 PMCID: PMC5014471 DOI: 10.1093/ve/vev001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, València, Spain, The Santa Fe Institute, Santa Fe, New Mexico, USA and Department of Zoology, University of Oxford, UK
| | - Oliver G Pybus
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, València, Spain, The Santa Fe Institute, Santa Fe, New Mexico, USA and Department of Zoology, University of Oxford, UK
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42
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Sanjuán R, Grdzelishvili VZ. Evolution of oncolytic viruses. Curr Opin Virol 2015; 13:1-5. [PMID: 25699475 DOI: 10.1016/j.coviro.2015.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 01/27/2015] [Accepted: 01/28/2015] [Indexed: 01/05/2023]
Abstract
Owing to their replicative capacity, oncolytic viruses (OVs) can evolve under the action of natural selection. Reversion to virulence and recombination with wild-type strains may compromise OV safety, therefore requiring evolutionary risk assessment studies. On the other hand, evolution can be directed in the laboratory to create more potent and safer OVs. Previous work in the experimental evolution field provides a background for OV directed evolution, and has identified interesting exploitable features. While genetic engineering has greatly advanced the field of oncolytic virotherapy, this approach is sometimes curtailed by the complexity and diversity of virus-host interactions. Directed evolution provides an alternative approach that may help to obtain new OVs without prejudice toward the underlying molecular mechanisms involved.
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Affiliation(s)
- Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva and Departament de Genètica, Universitat de València, Valencia, Spain.
| | - Valery Z Grdzelishvili
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC, USA
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Abstract
Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.
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Abstract
Selection-mutation dynamics is studied as adaptation and neutral drift on abstract fitness landscapes. Various models of fitness landscapes are introduced and analyzed with respect to the stationary mutant distributions adopted by populations upon them. The concept of quasispecies is introduced, and the error threshold phenomenon is analyzed. Complex fitness landscapes with large scatter of fitness values are shown to sustain error thresholds. The phenomenological theory of the quasispecies introduced in 1971 by Eigen is compared to approximation-free numerical computations. The concept of strong quasispecies understood as mutant distributions, which are especially stable against changes in mutations rates, is presented. The role of fitness neutral genotypes in quasispecies is discussed.
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Affiliation(s)
- Peter Schuster
- Institut für Theoretische Chemie der Universität Wien, Währingerstraße 17, 1090, Vienna, Austria.
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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Huang L, Li Z, Wu J, Xu Y, Yang X, Fan L, Fang R, Zhou X. Analysis of genetic variation and diversity of Rice stripe virus populations through high-throughput sequencing. FRONTIERS IN PLANT SCIENCE 2015; 6:176. [PMID: 25852724 PMCID: PMC4371650 DOI: 10.3389/fpls.2015.00176] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 03/05/2015] [Indexed: 05/09/2023]
Abstract
Plant RNA viruses often generate diverse populations in their host plants through error-prone replication and recombination. Recent studies on the genetic diversity of plant RNA viruses in various host plants have provided valuable information about RNA virus evolution and emergence of new diseases caused by RNA viruses. We analyzed and compared the genetic diversity of Rice stripe virus (RSV) populations in Oryza sativa (a natural host of RSV) and compared it with that of the RSV populations generated in an infection of Nicotiana benthamiana, an experimental host of RSV, using the high-throughput sequencing technology. From infected O. sativa and N. benthamiana plants, a total of 341 and 1675 site substitutions were identified in the RSV genome, respectively, and the average substitution ratio in these sites was 1.47 and 7.05 %, respectively, indicating that the RSV populations from infected N. benthamiana plant are more diverse than those from infected O. sativa plant. Our result gives a direct evidence that virus might allow higher genetic diversity for host adaptation.
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Affiliation(s)
- Lingzhe Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, HangzhouPeople’s Republic of China
| | - Zefeng Li
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, HangzhouPeople’s Republic of China
| | - Jianxiang Wu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, HangzhouPeople’s Republic of China
| | - Yi Xu
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, HangzhouPeople’s Republic of China
| | - Xiuling Yang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, HangzhouPeople’s Republic of China
| | - Longjiang Fan
- Institute of Crop Science and Institute of Bioinformatics, Zhejiang University, HangzhouPeople’s Republic of China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, BeijingPeople’s Republic of China
- *Correspondence: Xueping Zhou, State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China ; Rongxiang Fang, State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Xueping Zhou
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, HangzhouPeople’s Republic of China
- *Correspondence: Xueping Zhou, State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, People’s Republic of China ; Rongxiang Fang, State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
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Peña EJ, Ferriol I, Sambade A, Buschmann H, Niehl A, Elena SF, Rubio L, Heinlein M. Experimental virus evolution reveals a role of plant microtubule dynamics and TORTIFOLIA1/SPIRAL2 in RNA trafficking. PLoS One 2014; 9:e105364. [PMID: 25133612 PMCID: PMC4136834 DOI: 10.1371/journal.pone.0105364] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/17/2014] [Indexed: 01/12/2023] Open
Abstract
The cytoskeleton is a dynamic network composed of filamentous polymers and regulatory proteins that provide a flexible structural scaffold to the cell and plays a fundamental role in developmental processes. Mutations that alter the spatial orientation of the cortical microtubule (MT) array of plants are known to cause important changes in the pattern of cell wall synthesis and developmental phenotypes; however, the consequences of such alterations on other MT-network-associated functions in the cytoplasm are not known. In vivo observations suggested a role of cortical MTs in the formation and movement of Tobacco mosaic virus (TMV) RNA complexes along the endoplasmic reticulum (ER). Thus, to probe the significance of dynamic MT behavior in the coordination of MT-network-associated functions related to TMV infection and, thus, in the formation and transport of RNA complexes in the cytoplasm, we performed an evolution experiment with TMV in Arabidopsis thaliana tor1/spr2 and tor2 mutants with specific defects in MT dynamics and asked whether TMV is sensitive to these changes. We show that the altered cytoskeleton induced genetic changes in TMV that were correlated with efficient spread of infection in the mutant hosts. These observations demonstrate a role of dynamic MT rearrangements and of the MT-associated protein TORTIFOLIA1/SPIRAL2 in cellular functions related to virus spread and indicate that MT dynamics and MT-associated proteins represent constraints for virus evolution and adaptation. The results highlight the importance of the dynamic plasticity of the MT network in directing cytoplasmic functions in macromolecular assembly and trafficking and illustrate the value of experimental virus evolution for addressing the cellular functions of dynamic, long-range order systems in multicellular organisms.
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Affiliation(s)
- Eduardo José Peña
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Strasbourg, France
| | - Inmaculada Ferriol
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Adrián Sambade
- Department of Comparative Neurobiology, Institut Cavanilles de Biodiversitat i Biologia Evolutiva CIBERNED, Universidad de Valencia, Valencia, Spain
| | - Henrik Buschmann
- Institute for Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Niehl
- Department of Environmental Sciences, Plant Physiology, University of Basel, Basel, Switzerland
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
- * E-mail: (LR); (MH)
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Strasbourg, France
- Department of Environmental Sciences, Plant Physiology, University of Basel, Basel, Switzerland
- * E-mail: (LR); (MH)
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Garijo R, Hernández-Alonso P, Rivas C, Diallo JS, Sanjuán R. Experimental evolution of an oncolytic vesicular stomatitis virus with increased selectivity for p53-deficient cells. PLoS One 2014; 9:e102365. [PMID: 25010337 PMCID: PMC4092128 DOI: 10.1371/journal.pone.0102365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Accepted: 06/18/2014] [Indexed: 12/17/2022] Open
Abstract
Experimental evolution has been used for various biotechnological applications including protein and microbial cell engineering, but less commonly in the field of oncolytic virotherapy. Here, we sought to adapt a rapidly evolving RNA virus to cells deficient for the tumor suppressor gene p53, a hallmark of cancer cells. To achieve this goal, we established four independent evolution lines of the vesicular stomatitis virus (VSV) in p53-knockout mouse embryonic fibroblasts (p53-/- MEFs) under conditions favoring the action of natural selection. We found that some evolved viruses showed increased fitness and cytotoxicity in p53-/- cells but not in isogenic p53+/+ cells, indicating gene-specific adaptation. However, full-length sequencing revealed no obvious or previously described genetic changes associated with oncolytic activity. Half-maximal effective dose (EC50) assays in mouse p53-positive colon cancer (CT26) and p53-deficient breast cancer (4T1) cells indicated that the evolved viruses were more effective against 4T1 cells than the parental virus or a reference oncolytic VSV (MΔ51), but showed no increased efficacy against CT26 cells. In vivo assays using 4T1 syngeneic tumor models showed that one of the evolved lines significantly delayed tumor growth compared to mice treated with the parental virus or untreated controls, and was able to induce transient tumor suppression. Our results show that RNA viruses can be specifically adapted typical cancer features such as p53 inactivation, and illustrate the usefulness of experimental evolution for oncolytic virotherapy.
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Affiliation(s)
- Raquel Garijo
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Pablo Hernández-Alonso
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
| | - Carmen Rivas
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología, Madrid, Spain
- Centro de Investigación en Medicina Molecular (CIMUS) and Instituto de Investigaciones Sanitarias (IDIS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Jean-Simon Diallo
- Center for Innovative Cancer Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universidad de Valencia, Valencia, Spain
- Department of Genetics, Universidad de Valencia, Valencia, Spain
- * E-mail:
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A bioinformatics pipeline for the analyses of viral escape dynamics and host immune responses during an infection. BIOMED RESEARCH INTERNATIONAL 2014; 2014:264519. [PMID: 25013771 PMCID: PMC4072169 DOI: 10.1155/2014/264519] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/08/2014] [Indexed: 01/21/2023]
Abstract
Rapidly mutating viruses, such as hepatitis C virus (HCV) and HIV, have adopted evolutionary strategies that allow escape from the host immune response via genomic mutations. Recent advances in high-throughput sequencing are reshaping the field of immuno-virology of viral infections, as these allow fast and cheap generation of genomic data. However, due to the large volumes of data generated, a thorough understanding of the biological and immunological significance of such information is often difficult. This paper proposes a pipeline that allows visualization and statistical analysis of viral mutations that are associated with immune escape. Taking next generation sequencing data from longitudinal analysis of HCV viral genomes during a single HCV infection, along with antigen specific T-cell responses detected from the same subject, we demonstrate the applicability of these tools in the context of primary HCV infection. We provide a statistical and visual explanation of the relationship between cooccurring mutations on the viral genome and the parallel adaptive immune response against HCV.
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Huang LZ, Rao LX, Zhou XP, Wu JX. Genetic variability and evolution of rice stripe virus. J Zhejiang Univ Sci B 2014; 14:875-85. [PMID: 24101204 DOI: 10.1631/jzus.b1300014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rice stripe virus (RSV) is the type member of the genus Tenuivirus. RSV is known to have four segmented, single-stranded RNA molecules and causes rice stripe disease in the rice fields of China, Japan, and Korea. Based on the complete genomic sequences of the determined 6 RSV isolates (from Yunnan, Jiangsu, Zhejiang, and Liaoning Provinces, China) and 27 other RSV isolates (from Yunnan, Jiangsu, Anhui, Henan, and Shandong Provinces of China, also Japan and Korea) downloaded from GenBank, we provided a genotyping profile of RSV field isolates and described the population structure of RSV. All RSV isolates, except isolate CX, could be divided into two subtypes, one including 6 isolates from Yunnan Province, and the other including 26 isolates from different parts of China, Japan, and Korea, which were referred to as subtype II and subtype I, respectively. The amino acid distances between subtypes range from 0.053 to 0.085. RSV isolates in Yunnan Province were genetically differentiated from other parts of China, Japan, and Korea and showed infrequent gene flow. The RSV populations collected from other parts of China, Japan, and Korea were only composed of subtype I and showed very low genetic diversity. We speculated that isolate CX may be the result of recombination of isolates from two subtypes. Two potential recombination events were detected in RNA4 of isolate CX.
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Affiliation(s)
- Ling-zhe Huang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
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A phylogeographical study of the cauliflower mosaic virus population in mid-Eurasia Iran using complete genome analysis. Arch Virol 2013; 159:1329-40. [PMID: 24343265 DOI: 10.1007/s00705-013-1910-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2013] [Accepted: 10/26/2013] [Indexed: 10/25/2022]
Abstract
The full-length sequences of 34 Iranian cauliflower mosaic virus (CaMV) isolates were compared with others from public nucleotide sequence databases to provide a comprehensive overview of the genetic variability and patterns of genetic exchange in CaMV isolates from Iran. Based on the severity of symptoms and their ability to infect Brassica oleracea var. capitata, Iranian CaMV isolates were grouped into two distinct biotypes: latent/mild mottle (LI/MMo) and severe (S) infection. Recombination breakpoints were detected between the large intergenic region (LIR) and open reading frame (ORF) V (event 2); between ORF VII and ORF II (event 3), between ORF I and ORF III (event 4), and within ORF VI (event 1). Phylogenetic analysis indicated that Iranian CaMV isolates clustered into two subgroups belonging to group I (GI) that were distinct from North American and European isolates from group II (GII). Northeast Iranian isolates (subgroup B) and CaMV isolates from subgroup A closely corresponded to the S and LI/MMo biological groups, respectively. Genome-wide pairwise identity analysis of the CaMV isolates revealed three regions of pairwise identity representation: 92-94 % for GII and 94-96 % and 98-100 % for subgroups A and B. The within-population diversity was lower than the between-population diversity, suggesting the contribution of a founder effect on diversification of CaMV isolates. Amino acid sequences were conserved, with ω values ranging from 0.074 to 0.717 in different proteins. Thirteen amino acids in the deduced proteins of ORFs I, II, III, VI and VII were under positive selection (ω > 1), whereas purifying selection applied to the proteins encoded by ORFs IV and V. This study suggests that variation in the CaMV population can be explained by host-range differentiation and selection pressure. Moreover, recombination analysis revealed that a genomic exchange is responsible for the emergence of CaMV strains, providing valuable new information for understanding the diversity and evolution of caulimoviruses.
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