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Lievens EJP, Kühn S, Horas EL, Le Pennec G, Peter S, Petrosky AD, Künzel S, Feulner PGD, Becks L. High parasite diversity maintained after an alga-virus coevolutionary arms race. J Evol Biol 2024; 37:795-806. [PMID: 38699979 DOI: 10.1093/jeb/voae053] [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: 10/01/2023] [Revised: 02/27/2024] [Accepted: 05/02/2024] [Indexed: 05/05/2024]
Abstract
Arms race dynamics are a common outcome of host-parasite coevolution. While they can theoretically be maintained indefinitely, realistic arms races are expected to be finite. Once an arms race has ended, for example due to the evolution of a generalist-resistant host, the system may transition into coevolutionary dynamics that favour long-term diversity. In microbial experiments, host-parasite arms races often transition into a stable coexistence of generalist-resistant hosts, (semi-)susceptible hosts, and parasites. While long-term host diversity is implicit in these cases, parasite diversity is usually overlooked. In this study, we examined parasite diversity after the end of an experimental arms race between a unicellular alga (Chlorella variabilis) and its lytic virus (PBCV-1). First, we isolated virus genotypes from multiple time points from two replicate microcosms. A time-shift experiment confirmed that the virus isolates had escalating host ranges, i.e., that arms races had occurred. We then examined the phenotypic and genetic diversity of virus isolates from the post-arms race phase. Post-arms race virus isolates had diverse host ranges, survival probabilities, and growth rates; they also clustered into distinct genetic groups. Importantly, host range diversity was maintained throughout the post-arms race phase, and the frequency of host range phenotypes fluctuated over time. We hypothesize that this dynamic polymorphism was maintained by a combination of fluctuating selection and demographic stochasticity. Together with previous work in prokaryotic systems, our results link experimental observations of arms races to natural observations of long-term host and parasite diversity.
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Affiliation(s)
- Eva J P Lievens
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Samuel Kühn
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Elena L Horas
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Guénolé Le Pennec
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
| | - Sarah Peter
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Azade D Petrosky
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Sven Künzel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Philine G D Feulner
- Department of Fish Ecology and Evolution, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Kastanienbaum, Switzerland
- Department of Biology, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Department of Biology, University of Konstanz, Konstanz, Germany
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2
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Lewis JM, Williams J, Sagona AP. Making the leap from technique to treatment - genetic engineering is paving the way for more efficient phage therapy. Biochem Soc Trans 2024; 52:1373-1384. [PMID: 38716972 DOI: 10.1042/bst20231289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/27/2024]
Abstract
Bacteriophages (phages) are viruses specific to bacteria that target them with great efficiency and specificity. Phages were first studied for their antibacterial potential in the early twentieth century; however, their use was largely eclipsed by the popularity of antibiotics. Given the surge of antimicrobial-resistant strains worldwide, there has been a renaissance in harnessing phages as therapeutics once more. One of the key advantages of phages is their amenability to modification, allowing the generation of numerous derivatives optimised for specific functions depending on the modification. These enhanced derivatives could display higher infectivity, expanded host range or greater affinity to human tissues, where some bacterial species exert their pathogenesis. Despite this, there has been a noticeable discrepancy between the generation of derivatives in vitro and their clinical application in vivo. In most instances, phage therapy is only used on a compassionate-use basis, where all other treatment options have been exhausted. A lack of clinical trials and numerous regulatory hurdles hamper the progress of phage therapy and in turn, the engineered variants, in becoming widely used in the clinic. In this review, we outline the various types of modifications enacted upon phages and how these modifications contribute to their enhanced bactericidal function compared with wild-type phages. We also discuss the nascent progress of genetically modified phages in clinical trials along with the current issues these are confronted with, to validate it as a therapy in the clinic.
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Affiliation(s)
- Jessica M Lewis
- School of Life Sciences, University of Warwick, Coventry, U.K
| | - Joshua Williams
- School of Life Sciences, University of Warwick, Coventry, U.K
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3
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Singhal S, Balitactac AK, Nayagam AG, Pour Bahrami P, Nayeem S, Turner PE. Experimental Evolution Studies in Φ6 Cystovirus. Viruses 2024; 16:977. [PMID: 38932268 PMCID: PMC11209170 DOI: 10.3390/v16060977] [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: 04/27/2024] [Revised: 06/05/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Experimental evolution studies, in which biological populations are evolved in a specific environment over time, can address questions about the nature of spontaneous mutations, responses to selection, and the origins and maintenance of novel traits. Here, we review more than 30 years of experimental evolution studies using the bacteriophage (phage) Φ6 cystovirus. Similar to many lab-studied bacteriophages, Φ6 has a high mutation rate, large population size, fast generation time, and can be genetically engineered or cryogenically frozen, which facilitates its rapid evolution in the laboratory and the subsequent characterization of the effects of its mutations. Moreover, its segmented RNA genome, outer membrane, and capacity for multiple phages to coinfect a single host cell make Φ6 a good non-pathogenic model for investigating the evolution of RNA viruses that infect humans. We describe experiments that used Φ6 to address the fitness effects of spontaneous mutations, the consequences of evolution in the presence of coinfection, the evolution of host ranges, and mechanisms and consequences of the evolution of thermostability. We highlight open areas of inquiry where further experimentation on Φ6 could inform predictions for pathogenic viruses.
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Affiliation(s)
- Sonia Singhal
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Akiko K. Balitactac
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Aruna G. Nayagam
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Parnian Pour Bahrami
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Sara Nayeem
- Department of Biological Sciences, San José State University, San José, CA 95192, USA; (A.K.B.); (A.G.N.); (P.P.B.); (S.N.)
| | - Paul E. Turner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA;
- Program in Microbiology, Yale School of Medicine, New Haven, CT 06520, USA
- Center for Phage Biology and Therapy, Yale University, New Haven, CT 06511, USA
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4
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Doud MB, Gupta A, Li V, Medina SJ, De La Fuente CA, Meyer JR. Competition-driven eco-evolutionary feedback reshapes bacteriophage lambda's fitness landscape and enables speciation. Nat Commun 2024; 15:863. [PMID: 38286804 PMCID: PMC10825149 DOI: 10.1038/s41467-024-45008-5] [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: 08/21/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024] Open
Abstract
A major challenge in evolutionary biology is explaining how populations navigate rugged fitness landscapes without getting trapped on local optima. One idea illustrated by adaptive dynamics theory is that as populations adapt, their newly enhanced capacities to exploit resources alter fitness payoffs and restructure the landscape in ways that promote speciation by opening new adaptive pathways. While there have been indirect tests of this theory, to our knowledge none have measured how fitness landscapes deform during adaptation, or test whether these shifts promote diversification. Here, we achieve this by studying bacteriophage [Formula: see text], a virus that readily speciates into co-existing receptor specialists under controlled laboratory conditions. We use a high-throughput gene editing-phenotyping technology to measure [Formula: see text]'s fitness landscape in the presence of different evolved-[Formula: see text] competitors and find that the fitness effects of individual mutations, and their epistatic interactions, depend on the competitor. Using these empirical data, we simulate [Formula: see text]'s evolution on an unchanging landscape and one that recapitulates how the landscape deforms during evolution. [Formula: see text] heterogeneity only evolves in the shifting landscape regime. This study provides a test of adaptive dynamics, and, more broadly, shows how fitness landscapes dynamically change during adaptation, potentiating phenomena like speciation by opening new adaptive pathways.
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Affiliation(s)
- Michael B Doud
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California San Diego, San Diego, CA, USA
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Animesh Gupta
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Victor Li
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Sarah J Medina
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Caesar A De La Fuente
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA
| | - Justin R Meyer
- Department of Ecology, Behavior and Evolution, University of California San Diego, San Diego, CA, USA.
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5
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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6
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Strobel HM, Stuart EC, Meyer JR. A Trait-Based Approach to Predicting Viral Host-Range Evolvability. Annu Rev Virol 2022; 9:139-156. [PMID: 36173699 DOI: 10.1146/annurev-virology-091919-092003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Predicting the evolution of virus host range has proven to be extremely difficult, in part because of the sheer diversity of viruses, each with unique biology and ecological interactions. We have not solved this problem, but to make the problem more tractable, we narrowed our focus to three traits intrinsic to all viruses that may play a role in host-range evolvability: mutation rate, recombination rate, and phenotypic heterogeneity. Although each trait should increase evolvability, they cannot do so unbounded because fitness trade-offs limit the ability of all three traits to maximize evolvability. By examining these constraints, we can begin to identify groups of viruses with suites of traits that make them especially concerning, as well as ecological and environmental conditions that might push evolution toward accelerating host-range expansion.
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Affiliation(s)
- Hannah M Strobel
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Elizabeth C Stuart
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
| | - Justin R Meyer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA;
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7
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Shaw CL, Kennedy DA. Developing an empirical model for spillover and emergence: Orsay virus host range in Caenorhabditis. Proc Biol Sci 2022; 289:20221165. [PMID: 36126684 PMCID: PMC9489279 DOI: 10.1098/rspb.2022.1165] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/24/2022] [Indexed: 11/20/2022] Open
Abstract
A lack of tractable experimental systems in which to test hypotheses about the ecological and evolutionary drivers of disease spillover and emergence has limited our understanding of these processes. Here we introduce a promising system: Caenorhabditis hosts and Orsay virus, a positive-sense single-stranded RNA virus that naturally infects C. elegans. We assayed species across the Caenorhabditis tree and found Orsay virus susceptibility in 21 of 84 wild strains belonging to 14 of 44 species. Confirming patterns documented in other systems, we detected effects of host phylogeny on susceptibility. We then tested whether susceptible strains were capable of transmitting Orsay virus by transplanting exposed hosts and determining whether they transmitted infection to conspecifics during serial passage. We found no evidence of transmission in 10 strains (virus undetectable after passaging in all replicates), evidence of low-level transmission in 5 strains (virus lost between passage 1 and 5 in at least one replicate) and evidence of sustained transmission in 6 strains (including all three experimental C. elegans strains) in at least one replicate. Transmission was strongly associated with viral amplification in exposed populations. Variation in Orsay virus susceptibility and transmission among Caenorhabditis strains suggests that the system could be powerful for studying spillover and emergence.
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Affiliation(s)
- Clara L. Shaw
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - David A. Kennedy
- Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
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8
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A Review on SARS-CoV-2 Genome in the Aquatic Environment of Africa: Prevalence, Persistence and the Future Prospects. WATER 2022. [DOI: 10.3390/w14132020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The COVID-19 pandemic (Coronavirus disease 2019) remains problematic in all its manifestations on the global stage where countless events of human-to-human exposure have led to fatal cases; thus, the aftermath being an unprecedented public health concern, with inaccessible health care and the instability of economies and financial institutions. These pose massive obstacles that can insatiably devour existing human resources causing negative impacts, especially in developing countries. Tracking the origin, dissemination and mutating strains of the novel severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) on population-wide scales is a somewhat overwhelming task, with the urgent need to map the dissemination and magnitude of SARS-CoV-2 in near real-time. This review paper focuses on the poor sanitation of some waterbodies and wastewater management policies in low-income African countries, highlighting how these contribute to the COVID-19 pandemic on the continent. Since the outbreak of the novel coronavirus pandemic, there has been an upsurge in scientific literature and studies concerning SARS-CoV-2 with different opinions and findings. The current paper highlights the challenges and also summarizes the environmental aspects related to the monitoring and fate of the SARS-CoV-2 genomes in the aquatic milieu of Sub-Saharan Africa.
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9
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Montoya V, McLaughlin A, Mordecai GJ, Miller RL, Joy JB. Variable routes to genomic and host adaptation among coronaviruses. J Evol Biol 2021; 34:924-936. [PMID: 33751699 PMCID: PMC8242483 DOI: 10.1111/jeb.13771] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 01/19/2021] [Accepted: 01/25/2021] [Indexed: 12/19/2022]
Abstract
Natural selection operating on the genomes of viral pathogens in different host species strongly contributes to adaptation facilitating host colonization. Here, we analyse, quantify and compare viral adaptation in genomic sequence data derived from seven zoonotic events in the Coronaviridae family among primary, intermediate and human hosts. Rates of nonsynonymous (dN) and synonymous (dS) changes on specific amino acid positions were quantified for each open reading frame (ORF). Purifying selection accounted for 77% of all sites under selection. Diversifying selection was most frequently observed in viruses infecting the primary hosts of each virus and predominantly occurred in the orf1ab genomic region. Within all four intermediate hosts, diversifying selection on the spike gene was observed either solitarily or in combination with orf1ab and other genes. Consistent with previous evidence, pervasive diversifying selection on coronavirus spike genes corroborates the role this protein plays in host cellular entry, adaptation to new hosts and evasion of host cellular immune responses. Structural modelling of spike proteins identified a significantly higher proportion of sites for SARS‐CoV‐2 under positive selection in close proximity to sites of glycosylation relative to the other coronaviruses. Among human coronaviruses, there was a significant inverse correlation between the number of sites under positive selection and the estimated years since the virus was introduced into the human population. Abundant diversifying selection observed in SARS‐CoV‐2 suggests the virus remains in the adaptive phase of the host switch, typical of recent host switches. A mechanistic understanding of where, when and how genomic adaptation occurs in coronaviruses following a host shift is crucial for vaccine design, public health responses and predicting future pandemics.
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Affiliation(s)
- Vincent Montoya
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada
| | - Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Gideon J Mordecai
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Rachel L Miller
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDS, Vancouver, BC, Canada.,Bioinformatics Programme, University of British Columbia, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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10
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Abstract
The sudden outbreak of COVID-19 has once again shrouded people in the enormous threat of RNA virus. Extracellular vesicles (EVs), eukaryotic cells-derived small bi-layer vesicles mainly consisting of exosomes and microvesicles, share many properties with RNA viruses including structure, size, generation, and uptake. Emerging evidence has implicated the involvement of EVs in the pathogenesis of infectious diseases induced by RNA viruses. EVs can transfer viral receptors (e.g., ACE2 and CD9) to recipient cells to facilitate viral infection, directly transport infectious viral particles to adjacent cells for virus spreading, and mask viruses with a host structure to escape immune surveillance. Here, we examine the current status of EVs to summarize their roles in mediating RNA virus infection, together with a comprehensive discussion of the underlying mechanisms.
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11
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Variation Profile of the Orthotospovirus Genome. Pathogens 2020; 9:pathogens9070521. [PMID: 32610472 PMCID: PMC7400459 DOI: 10.3390/pathogens9070521] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022] Open
Abstract
Orthotospoviruses are plant-infecting members of the family Tospoviridae (order Bunyavirales), have a broad host range and are vectored by polyphagous thrips in a circulative-propagative manner. Because diverse hosts and vectors impose heterogeneous selection constraints on viral genomes, the evolutionary arms races between hosts and their pathogens might be manifested as selection for rapid changes in key genes. These observations suggest that orthotospoviruses contain key genetic components that rapidly mutate to mediate host adaptation and vector transmission. Using complete genome sequences, we profiled genomic variation in orthotospoviruses. Results show that the three genomic segments contain hypervariable areas at homologous locations across species. Remarkably, the highest nucleotide variation mapped to the intergenic region of RNA segments S and M, which fold into a hairpin. Secondary structure analyses showed that the hairpin is a dynamic structure with multiple functional shapes formed by stems and loops, contains sites under positive selection and covariable sites. Accumulation and tolerance of mutations in the intergenic region is a general feature of orthotospoviruses and might mediate adaptation to host plants and insect vectors.
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12
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Zhao L, Duffy S. Gauging genetic diversity of generalists: A test of genetic and ecological generalism with RNA virus experimental evolution. Virus Evol 2019; 5:vez019. [PMID: 31275611 PMCID: PMC6599687 DOI: 10.1093/ve/vez019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Generalist viruses, those with a comparatively larger host range, are considered more likely to emerge on new hosts. The potential to emerge in new hosts has been linked to viral genetic diversity, a measure of evolvability. However, there is no consensus on whether infecting a larger number of hosts leads to higher genetic diversity, or whether diversity is better maintained in a homogeneous environment, similar to the lifestyle of a specialist virus. Using experimental evolution with the RNA bacteriophage phi6, we directly tested whether genetic generalism (carrying an expanded host range mutation) or environmental generalism (growing on heterogeneous hosts) leads to viral populations with more genetic variation. Sixteen evolved viral lineages were deep sequenced to provide genetic evidence for population diversity. When evolved on a single host, specialist and generalist genotypes both maintained the same level of diversity (measured by the number of single nucleotide polymorphisms (SNPs) above 1%, P = 0.81). However, the generalist genotype evolved on a single host had higher SNP levels than generalist lineages under two heterogeneous host passaging schemes (P = 0.001, P < 0.001). RNA viruses’ response to selection in alternating hosts reduces standing genetic diversity compared to those evolving in a single host to which the virus is already well-adapted.
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Affiliation(s)
- Lele Zhao
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, 14 College Farm Road, New Brunswick, NJ, USA
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13
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Existing Host Range Mutations Constrain Further Emergence of RNA Viruses. J Virol 2019; 93:JVI.01385-18. [PMID: 30463962 DOI: 10.1128/jvi.01385-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 11/06/2018] [Indexed: 02/07/2023] Open
Abstract
RNA viruses are capable of rapid host shifting, typically due to a point mutation that confers expanded host range. As additional point mutations are necessary for further expansions, epistasis among host range mutations can potentially affect the mutational neighborhood and frequency of niche expansion. We mapped the mutational neighborhood of host range expansion using three genotypes of the double-stranded RNA (dsRNA) bacteriophage φ6 (wild type and two isogenic host range mutants) on the novel host Pseudomonas syringae pv. atrofaciens. Both Sanger sequencing of 50 P. syringae pv. atrofaciens mutant clones for each genotype and population Illumina sequencing revealed the same high-frequency mutations allowing infection of P. syringae pv. atrofaciens. Wild-type φ6 had at least nine different ways of mutating to enter the novel host, eight of which are in p3 (host attachment protein gene), and 13/50 clones had unchanged p3 genes. However, the two isogenic mutants had dramatically restricted neighborhoods: only one or two mutations, all in p3. Deep sequencing revealed that wild-type clones without mutations in p3 likely had changes in p12 (morphogenic protein), a region that was not polymorphic for the two isogenic host range mutants. Sanger sequencing confirmed that 10/13 of the wild-type φ6 clones had nonsynonymous mutations in p12, and 2 others had point mutations in p9 and p5. None of these genes had previously been associated with host range expansion in φ6. We demonstrate, for the first time, epistatic constraint in an RNA virus due to host range mutations themselves, which has implications for models of serial host range expansion.IMPORTANCE RNA viruses mutate rapidly and frequently expand their host ranges to infect novel hosts, leading to serial host shifts. Using an RNA bacteriophage model system (Pseudomonas phage φ6), we studied the impact of preexisting host range mutations on another host range expansion. Results from both clonal Sanger and Illumina sequencing show that extant host range mutations dramatically narrow the neighborhood of potential host range mutations compared to that of wild-type φ6. This research suggests that serial host-shifting viruses may follow a small number of molecular paths to enter additional novel hosts. We also identified new genes involved in φ6 host range expansion, expanding our knowledge of this important model system in experimental evolution.
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