1
|
O’Brien NLV, Holland B, Engelstädter J, Ortiz-Barrientos D. The distribution of fitness effects during adaptive walks using a simple genetic network. PLoS Genet 2024; 20:e1011289. [PMID: 38787919 PMCID: PMC11156440 DOI: 10.1371/journal.pgen.1011289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 06/06/2024] [Accepted: 05/04/2024] [Indexed: 05/26/2024] Open
Abstract
The tempo and mode of adaptation depends on the availability of beneficial alleles. Genetic interactions arising from gene networks can restrict this availability. However, the extent to which networks affect adaptation remains largely unknown. Current models of evolution consider additive genotype-phenotype relationships while often ignoring the contribution of gene interactions to phenotypic variance. In this study, we model a quantitative trait as the product of a simple gene regulatory network, the negative autoregulation motif. Using forward-time genetic simulations, we measure adaptive walks towards a phenotypic optimum in both additive and network models. A key expectation from adaptive walk theory is that the distribution of fitness effects of new beneficial mutations is exponential. We found that both models instead harbored distributions with fewer large-effect beneficial alleles than expected. The network model also had a complex and bimodal distribution of fitness effects among all mutations, with a considerable density at deleterious selection coefficients. This behavior is reminiscent of the cost of complexity, where correlations among traits constrain adaptation. Our results suggest that the interactions emerging from genetic networks can generate complex and multimodal distributions of fitness effects.
Collapse
Affiliation(s)
- Nicholas L. V. O’Brien
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Barbara Holland
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| | - Daniel Ortiz-Barrientos
- School of the Environment, The University of Queensland, Brisbane, Queensland, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, QLD, Australia
| |
Collapse
|
2
|
Terbot JW, Johri P, Liphardt SW, Soni V, Pfeifer SP, Cooper BS, Good JM, Jensen JD. Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples. PLoS Pathog 2023; 19:e1011265. [PMID: 37018331 PMCID: PMC10075409 DOI: 10.1371/journal.ppat.1011265] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2023] Open
Abstract
Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting in a global health crisis. In response, genomic surveillance efforts have proliferated in the hopes of tracking and anticipating the evolution of this virus, resulting in millions of patient isolates now being available in public databases. Yet, while there is a tremendous focus on identifying newly emerging adaptive viral variants, this quantification is far from trivial. Specifically, multiple co-occurring and interacting evolutionary processes are constantly in operation and must be jointly considered and modeled in order to perform accurate inference. We here outline critical individual components of such an evolutionary baseline model-mutation rates, recombination rates, the distribution of fitness effects, infection dynamics, and compartmentalization-and describe the current state of knowledge pertaining to the related parameters of each in SARS-CoV-2. We close with a series of recommendations for future clinical sampling, model construction, and statistical analysis.
Collapse
Affiliation(s)
- John W Terbot
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Parul Johri
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Schuyler W Liphardt
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Vivak Soni
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Susanne P Pfeifer
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| | - Brandon S Cooper
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey M Good
- University of Montana, Division of Biological Sciences, Missoula, Montana, United States of America
| | - Jeffrey D Jensen
- Arizona State University, School of Life Sciences, Center for Evolution & Medicine, Tempe, Arizona, United States of America
| |
Collapse
|
3
|
Shimagaki K, Barton JP. Bézier interpolation improves the inference of dynamical models from data. Phys Rev E 2023; 107:024116. [PMID: 36932614 PMCID: PMC10027371 DOI: 10.1103/physreve.107.024116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Many dynamical systems, from quantum many-body systems to evolving populations to financial markets, are described by stochastic processes. Parameters characterizing such processes can often be inferred using information integrated over stochastic paths. However, estimating time-integrated quantities from real data with limited time resolution is challenging. Here, we propose a framework for accurately estimating time-integrated quantities using Bézier interpolation. We applied our approach to two dynamical inference problems: Determining fitness parameters for evolving populations and inferring forces driving Ornstein-Uhlenbeck processes. We found that Bézier interpolation reduces the estimation bias for both dynamical inference problems. This improvement was especially noticeable for data sets with limited time resolution. Our method could be broadly applied to improve accuracy for other dynamical inference problems using finitely sampled data.
Collapse
Affiliation(s)
- Kai Shimagaki
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
| | - John P. Barton
- Department of Physics and Astronomy, University of California, Riverside, California 92521, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213, USA
| |
Collapse
|
4
|
Unpredictable repeatability in molecular evolution. Proc Natl Acad Sci U S A 2022; 119:e2209373119. [PMID: 36122210 PMCID: PMC9522380 DOI: 10.1073/pnas.2209373119] [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: 11/22/2022] Open
Abstract
The extent of parallel evolution at the genotypic level is quantitatively linked to the distribution of beneficial fitness effects (DBFE) of mutations. The standard view, based on light-tailed distributions (i.e., distributions with finite moments), is that the probability of parallel evolution in duplicate populations is inversely proportional to the number of available mutations and, moreover, that the DBFE is sufficient to determine the probability when the number of available mutations is large. Here, we show that when the DBFE is heavy-tailed, as found in several recent experiments, these expectations are defied. The probability of parallel evolution decays anomalously slowly in the number of mutations or even becomes independent of it, implying higher repeatability of evolution. At the same time, the probability of parallel evolution is non-self-averaging—that is, it does not converge to its mean value, even when a large number of mutations are involved. This behavior arises because the evolutionary process is dominated by only a few mutations of high weight. Consequently, the probability varies widely across systems with the same DBFE. Contrary to the standard view, the DBFE is no longer sufficient to determine the extent of parallel evolution, making it much less predictable. We illustrate these ideas theoretically and through analysis of empirical data on antibiotic-resistance evolution.
Collapse
|
5
|
Sharma M, Yadav A, Dubey KK, Tipple J, Das DB. Decentralized systems for the treatment of antimicrobial compounds released from hospital aquatic wastes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 840:156569. [PMID: 35690196 DOI: 10.1016/j.scitotenv.2022.156569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/04/2022] [Accepted: 06/05/2022] [Indexed: 06/15/2023]
Abstract
In many developing countries, untreated hospital effluents are discharged and treated simultaneously with municipal wastewater. However, if the hospital effluents are not treated separately, they pose concerning health risks due to the possible transport of the antimicrobial genes and microbes in the environment. Such effluent is considered as a point source for a number of potentially infectious microorganisms, waste antimicrobial compounds and other contaminants that could promote antimicrobial resistance development. The removal of these contaminants prior to discharge reduces the exposure of antimicrobials to the environment and this should lower the risk of superbug development. At an effluent discharge site, suitable pre-treatment of wastewater containing antimicrobials could maximise the ecological impact with potentially reduced risk to human health. In addressing these points, this paper reviews the applications of decentralized treatment systems toward reducing the concentration of antimicrobials in wastewater. The most commonly used techniques in decentralized wastewater treatment systems for onsite removal of antimicrobials were discussed and evidence suggests that hybrid techniques should be more useful for the efficient removal of antimicrobials. It is concluded that alongside the cooperation of administration departments, health industries, water treatment authorities and general public, decentralized treatment technology can efficiently enhance the removal of antimicrobial compounds, thereby decreasing the concentration of contaminants released to the environment that could pose risks to human and ecological health due to development of antimicrobial resistance in microbes.
Collapse
Affiliation(s)
- Manisha Sharma
- Bioprocess Engineering Laboratory, Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Ankush Yadav
- Bioprocess Engineering Laboratory, Department of Biotechnology, Central University of Haryana, Mahendergarh, Haryana 123031, India
| | - Kashyap Kumar Dubey
- Bioprocess Engineering Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India.
| | - Joshua Tipple
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, United Kingdom
| | - Diganta Bhusan Das
- Department of Chemical Engineering, Loughborough University, Loughborough LE11 3TU, United Kingdom.
| |
Collapse
|
6
|
Johri P, Aquadro CF, Beaumont M, Charlesworth B, Excoffier L, Eyre-Walker A, Keightley PD, Lynch M, McVean G, Payseur BA, Pfeifer SP, Stephan W, Jensen JD. Recommendations for improving statistical inference in population genomics. PLoS Biol 2022; 20:e3001669. [PMID: 35639797 PMCID: PMC9154105 DOI: 10.1371/journal.pbio.3001669] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.
Collapse
Affiliation(s)
- Parul Johri
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Charles F. Aquadro
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | - Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Berne, Berne, Switzerland
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Peter D. Keightley
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
| | - Bret A. Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Susanne P. Pfeifer
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | | | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| |
Collapse
|
7
|
Morales-Arce AY, Johri P, Jensen JD. Inferring the distribution of fitness effects in patient-sampled and experimental virus populations: two case studies. Heredity (Edinb) 2022; 128:79-87. [PMID: 34987185 PMCID: PMC8728706 DOI: 10.1038/s41437-021-00493-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 12/12/2021] [Accepted: 12/13/2021] [Indexed: 11/19/2022] Open
Abstract
We here propose an analysis pipeline for inferring the distribution of fitness effects (DFE) from either patient-sampled or experimentally-evolved viral populations, that explicitly accounts for non-Wright-Fisher and non-equilibrium population dynamics inherent to pathogens. We examine the performance of this approach via extensive power and performance analyses, and highlight two illustrative applications - one from an experimentally-passaged RNA virus, and the other from a clinically-sampled DNA virus. Finally, we discuss how such DFE inference may shed light on major research questions in virus evolution, ranging from a quantification of the population genetic processes governing genome size, to the role of Hill-Robertson interference in dictating adaptive outcomes, to the potential design of novel therapeutic approaches to eradicate within-patient viral populations via induced mutational meltdown.
Collapse
Affiliation(s)
- Ana Y. Morales-Arce
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Parul Johri
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| | - Jeffrey D. Jensen
- grid.215654.10000 0001 2151 2636Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ USA
| |
Collapse
|
8
|
Lange JD, Bastide H, Lack JB, Pool JE. A Population Genomic Assessment of Three Decades of Evolution in a Natural Drosophila Population. Mol Biol Evol 2021; 39:6491261. [PMID: 34971382 PMCID: PMC8826484 DOI: 10.1093/molbev/msab368] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Population genetics seeks to illuminate the forces shaping genetic variation, often based on a single snapshot of genomic variation. However, utilizing multiple sampling times to study changes in allele frequencies can help clarify the relative roles of neutral and non-neutral forces on short time scales. This study compares whole-genome sequence variation of recently collected natural population samples of Drosophila melanogaster against a collection made approximately 35 years prior from the same locality—encompassing roughly 500 generations of evolution. The allele frequency changes between these time points would suggest a relatively small local effective population size on the order of 10,000, significantly smaller than the global effective population size of the species. Some loci display stronger allele frequency changes than would be expected anywhere in the genome under neutrality—most notably the tandem paralogs Cyp6a17 and Cyp6a23, which are impacted by structural variation associated with resistance to pyrethroid insecticides. We find a genome-wide excess of outliers for high genetic differentiation between old and new samples, but a larger number of adaptation targets may have affected SNP-level differentiation versus window differentiation. We also find evidence for strengthening latitudinal allele frequency clines: northern-associated alleles have increased in frequency by an average of nearly 2.5% at SNPs previously identified as clinal outliers, but no such pattern is observed at random SNPs. This project underscores the scientific potential of using multiple sampling time points to investigate how evolution operates in natural populations, by quantifying how genetic variation has changed over ecologically relevant timescales.
Collapse
Affiliation(s)
- Jeremy D Lange
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Héloïse Bastide
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - Justin B Lack
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706
| |
Collapse
|
9
|
Charlesworth B, Jensen JD. Effects of Selection at Linked Sites on Patterns of Genetic Variability. ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS 2021; 52:177-197. [PMID: 37089401 PMCID: PMC10120885 DOI: 10.1146/annurev-ecolsys-010621-044528] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Patterns of variation and evolution at a given site in a genome can be strongly influenced by the effects of selection at genetically linked sites. In particular, the recombination rates of genomic regions correlate with their amount of within-population genetic variability, the degree to which the frequency distributions of DNA sequence variants differ from their neutral expectations, and the levels of adaptation of their functional components. We review the major population genetic processes that are thought to lead to these patterns, focusing on their effects on patterns of variability: selective sweeps, background selection, associative overdominance, and Hill–Robertson interference among deleterious mutations. We emphasize the difficulties in distinguishing among the footprints of these processes and disentangling them from the effects of purely demographic factors such as population size changes. We also discuss how interactions between selective and demographic processes can significantly affect patterns of variability within genomes.
Collapse
Affiliation(s)
- Brian Charlesworth
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona 85281, USA
| |
Collapse
|
10
|
Luqman H, Widmer A, Fior S, Wegmann D. Identifying loci under selection via explicit demographic models. Mol Ecol Resour 2021; 21:2719-2737. [PMID: 33964107 PMCID: PMC8596768 DOI: 10.1111/1755-0998.13415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 04/03/2021] [Accepted: 04/28/2021] [Indexed: 01/28/2023]
Abstract
Adaptive genetic variation is a function of both selective and neutral forces. To accurately identify adaptive loci, it is thus critical to account for demographic history. Theory suggests that signatures of selection can be inferred using the coalescent, following the premise that genealogies of selected loci deviate from neutral expectations. Here, we build on this theory to develop an analytical framework to identify loci under selection via explicit demographic models (LSD). Under this framework, signatures of selection are inferred through deviations in demographic parameters, rather than through summary statistics directly, and demographic history is accounted for explicitly. Leveraging the property of demographic models to incorporate directionality, we show that LSD can provide information on the environment in which selection acts on a population. This can prove useful in elucidating the selective processes underlying local adaptation, by characterizing genetic trade-offs and extending the concepts of antagonistic pleiotropy and conditional neutrality from ecological theory to practical application in genomic data. We implement LSD via approximate Bayesian computation and demonstrate, via simulations, that LSD (a) has high power to identify selected loci across a large range of demographic-selection regimes, (b) outperforms commonly applied genome-scan methods under complex demographies and (c) accurately infers the directionality of selection for identified candidates. Using the same simulations, we further characterize the behaviour of isolation-with-migration models conducive to the study of local adaptation under regimes of selection. Finally, we demonstrate an application of LSD by detecting loci and characterizing genetic trade-offs underlying flower colour in Antirrhinum majus.
Collapse
Affiliation(s)
- Hirzi Luqman
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Alex Widmer
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Simone Fior
- Institute of Integrative BiologyETH ZurichZürichSwitzerland
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| |
Collapse
|
11
|
Catania F, Ujvari B, Roche B, Capp JP, Thomas F. Bridging Tumorigenesis and Therapy Resistance With a Non-Darwinian and Non-Lamarckian Mechanism of Adaptive Evolution. Front Oncol 2021; 11:732081. [PMID: 34568068 PMCID: PMC8462274 DOI: 10.3389/fonc.2021.732081] [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: 06/28/2021] [Accepted: 08/25/2021] [Indexed: 12/13/2022] Open
Abstract
Although neo-Darwinian (and less often Lamarckian) dynamics are regularly invoked to interpret cancer's multifarious molecular profiles, they shine little light on how tumorigenesis unfolds and often fail to fully capture the frequency and breadth of resistance mechanisms. This uncertainty frames one of the most problematic gaps between science and practice in modern times. Here, we offer a theory of adaptive cancer evolution, which builds on a molecular mechanism that lies outside neo-Darwinian and Lamarckian schemes. This mechanism coherently integrates non-genetic and genetic changes, ecological and evolutionary time scales, and shifts the spotlight away from positive selection towards purifying selection, genetic drift, and the creative-disruptive power of environmental change. The surprisingly simple use-it or lose-it rationale of the proposed theory can help predict molecular dynamics during tumorigenesis. It also provides simple rules of thumb that should help improve therapeutic approaches in cancer.
Collapse
Affiliation(s)
- Francesco Catania
- Institute for Evolution and Biodiversity, University of Münster, Münster, Germany
| | - Beata Ujvari
- Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Deakin, VIC, Australia
| | - Benjamin Roche
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
| | - Jean-Pascal Capp
- Toulouse Biotechnology Institute, University of Toulouse, INSA, CNRS, INRAE, Toulouse, France
| | - Frédéric Thomas
- CREEC/CANECEV, MIVEGEC (CREES), Centre de Recherches Ecologiques et Evolutives sur le Cancer, University of Montpellier, CNRS, IRD, Montpellier, France
| |
Collapse
|
12
|
Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Nature 2021; 595:585-590. [PMID: 34163070 PMCID: PMC8396073 DOI: 10.1038/s41586-021-03648-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 05/17/2021] [Indexed: 02/02/2023]
Abstract
Progress in defining genomic fitness landscapes in cancer, especially those defined by copy number alterations (CNAs), has been impeded by lack of time-series single-cell sampling of polyclonal populations and temporal statistical models1-7. Here we generated 42,000 genomes from multi-year time-series single-cell whole-genome sequencing of breast epithelium and primary triple-negative breast cancer (TNBC) patient-derived xenografts (PDXs), revealing the nature of CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy. Using a new Wright-Fisher population genetics model8,9 to infer clonal fitness, we found that TP53 mutation alters the fitness landscape, reproducibly distributing fitness over a larger number of clones associated with distinct CNAs. Furthermore, in TNBC PDX models with mutated TP53, inferred fitness coefficients from CNA-based genotypes accurately forecast experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDXs resulted in cisplatin-resistant clones emerging from low-fitness phylogenetic lineages in the untreated setting. Conversely, high-fitness clones from treatment-naive controls were eradicated, signalling an inversion of the fitness landscape. Finally, upon release of drug, selection pressure dynamics were reversed, indicating a fitness cost of treatment resistance. Together, our findings define clonal fitness linked to both CNA and therapeutic resistance in polyclonal tumours.
Collapse
Affiliation(s)
- Sohrab Salehi
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mirela Andronescu
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kieran R Campbell
- Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Joseph & Wolf Lebovic Health Complex, Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Tehmina Masud
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Beixi Wang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Justina Biele
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - David Gee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hakwoo Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jerome Ting
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Hoa Tran
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Ciara O'Flanagan
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Fatemeh Dorri
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
- Department of Computer Science, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - So Ra Lee
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Brian Yu Chieh Cheng
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Takako Kono
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Jenifer Pham
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Daniel Lai
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexandre Bouchard-Côté
- Department of Statistics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Aparicio
- Department of Molecular Oncology, BC Cancer, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
13
|
Bailey SF, Alonso Morales LA, Kassen R. Effects of synonymous mutations beyond codon bias: The evidence for adaptive synonymous substitutions from microbial evolution experiments. Genome Biol Evol 2021; 13:6300525. [PMID: 34132772 PMCID: PMC8410137 DOI: 10.1093/gbe/evab141] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2021] [Indexed: 12/22/2022] Open
Abstract
Synonymous mutations are often assumed to be neutral with respect to fitness because they do not alter the encoded amino acid and so cannot be 'seen' by natural selection. Yet a growing body of evidence suggests that synonymous mutations can have fitness effects that drive adaptive evolution through their impacts on gene expression and protein folding. Here, we review what microbial experiments have taught us about the contribution of synonymous mutations to adaptation. A survey of site-directed mutagenesis experiments reveals the distributions of fitness effects for nonsynonymous and synonymous mutations are more similar, especially for beneficial mutations, than expected if all synonymous mutations were neutral, suggesting they should drive adaptive evolution more often than is typically observed. A review of experimental evolution studies where synonymous mutations have contributed to adaptation shows they can impact fitness through a range of mechanisms including the creation of illicit RNA polymerase binding sites impacting transcription and changes to mRNA folding stability that modulate translation. We suggest that clonal interference in evolving microbial populations may be the reason synonymous mutations play a smaller role in adaptive evolution than expected based on their observed fitness effects. We finish by discussing the impacts of falsely assuming synonymous mutations are neutral and discuss directions for future work exploring the role of synonymous mutations in adaptive evolution.
Collapse
Affiliation(s)
- Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, NY 13699, USA
| | | | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| |
Collapse
|
14
|
Abstract
RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance). IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution.
Collapse
|
15
|
Abstract
RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.
Collapse
Affiliation(s)
- Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
| |
Collapse
|
16
|
Alizon S. Treating symptomatic infections and the co-evolution of virulence and drug resistance. PEER COMMUNITY JOURNAL 2021; 1:e47. [PMID: 38707518 PMCID: PMC7615929 DOI: 10.24072/pcjournal.38] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
Antimicrobial therapeutic treatments are by definition applied after the onset of symptoms, which tend to correlate with infection severity. Using mathematical epidemiology models, I explore how this link affects the coevolutionary dynamics between the virulence of an infection, measured via host mortality rate, and its susceptibility to chemotherapy. I show that unless resistance pre-exists in the population, drug-resistant infections are initially more virulent than drug-sensitive ones. As the epidemic unfolds, virulence is more counter-selected in drug-sensitive than in drug-resistant infections. This difference decreases over time and, eventually, the exact shape of genetic trade-offs govern long-term evolutionary dynamics. Using adaptive dynamics, I show that two types of evolutionary stable strategies (ESS) may be reached in the context of this simple model and that, depending on the parameter values, an ESS may only be locally stable. In general, the more the treatment rate increases with virulence, the lower the ESS value. Overall, both on the short-term and long-term, having treatment rate depend on infection virulence tend to favour less virulent strains in drug-sensitive infections. These results highlight the importance of the feedbacks between epidemiology, public health policies and parasite evolution, and have implications for the monitoring of virulence evolution.
Collapse
Affiliation(s)
- Samuel Alizon
- Center for Interdisciplinary Research in Biology (CIRB), College de France, CNRS, INSERM, Université PSL, Paris, France
- MIVEGEC, CNRS, IRD, Université de Montpellier, France
| |
Collapse
|
17
|
Thi LAP, Panchangam SC, Do HT, Nguyen VH. Prospects and challenges of photocatalysis for degradation and mineralization of antiviral drugs. NANOSTRUCTURED PHOTOCATALYSTS 2021. [PMCID: PMC8237458 DOI: 10.1016/b978-0-12-823007-7.00012-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Among the outbreak of influenza and other pandemics such as SARS-CoV-2 recently over the globe, antiviral drugs were significantly concerned with controlling the disease and these pandemics. They have been developed for seven decades around more than 90 drugs categorized licensed to treat nine human infectious diseases. Based on their functional group, antiviral compounds will mitigate infectivity and symptoms and reduce the illness period by arresting the viral replication cycle at different stages. Antiviral drugs have been developed complexly and met many biothreat challenges due to their high biosafety level requirement. In recent years, the spreading of novel virus strains that are a threat to human life, the development in researching and manufacturing new types of antiviral drugs increases and the use by patients and clinicians have increased. Antiviral compounds have been reported only partly removed during wastewater treatment. They were available in wastewater treatment plant effluents and found in surface water from rivers and streams, underground water, and even in drinking water. Photocatalytic degradation of antiviral drugs was exploding to clear the environmental waters from the antiviral drugs. The principle of photocatalysis is based on the excitation of the catalyst material by irradiation of light. The catalyst produces free radicals under the action of photons, which will destroy the pollutants adsorbed on its surface. The photocatalytic degradation mechanism of antiviral drugs can be understood through decomposing in a heterogeneous photocatalytic system and which species are involved in the active decomposition of the drug and then photocatalytically degrading into intermediates or mineralization products. The intermediates and the reaction pathway of antiviral compound photocatalytic degradation are complicated. However, some of the degradation processes are complete, and inorganic compounds (CO2 and H2O) are their final products.
Collapse
|
18
|
Jensen JD, Stikeleather RA, Kowalik TF, Lynch M. Imposed mutational meltdown as an antiviral strategy. Evolution 2020; 74:2549-2559. [PMID: 33047822 PMCID: PMC7993354 DOI: 10.1111/evo.14107] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/30/2020] [Accepted: 10/10/2020] [Indexed: 12/25/2022]
Abstract
Following widespread infections of the most recent coronavirus known to infect humans, SARS‐CoV‐2, attention has turned to potential therapeutic options. With no drug or vaccine yet approved, one focal point of research is to evaluate the potential value of repurposing existing antiviral treatments, with the logical strategy being to identify at least a short‐term intervention to prevent within‐patient progression, while long‐term vaccine strategies unfold. Here, we offer an evolutionary/population‐genetic perspective on one approach that may overwhelm the capacity for pathogen defense (i.e., adaptation) – induced mutational meltdown – providing an overview of key concepts, review of previous theoretical and experimental work of relevance, and guidance for future research. Applied with appropriate care, including target specificity, induced mutational meltdown may provide a general, rapidly implemented approach for the within‐patient eradication of a wide range of pathogens or other undesirable microorganisms.
Collapse
Affiliation(s)
- Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Center for Evolution & Medicine, Arizona State University, Tempe, Arizona, 85281
| | - Ryan A Stikeleather
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, 01655
| | - Michael Lynch
- School of Life Sciences, Arizona State University, Tempe, Arizona, 85281.,Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, 85281
| |
Collapse
|
19
|
Lee J, Parvathareddy J, Yang D, Bansal S, O'Connell K, Golden JE, Jonsson CB. Emergence and Magnitude of ML336 Resistance in Venezuelan Equine Encephalitis Virus Depend on the Microenvironment. J Virol 2020; 94:e00317-20. [PMID: 32878897 PMCID: PMC7592223 DOI: 10.1128/jvi.00317-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/21/2020] [Indexed: 12/22/2022] Open
Abstract
Venezuelan equine encephalitis virus (VEEV) is a New World Alphavirus that can cause neurological disease and death in humans and equines following transmission from infected mosquitoes. Despite the continued epidemic threat of VEEV, and its potential use as a bioterrorism agent, there are no FDA-approved antivirals or vaccines for treatment or prevention. Previously, we reported the discovery of a small molecule, ML336, with potent antiviral activity against VEEV. To further explore the population-level resistance profiles of ML336, we developed a whole-genome next-generation sequencing (NGS) approach to examine single nucleotide polymorphisms (SNPs) from virus passaged in dose escalation studies in a nonhuman primate kidney epithelial and a human astrocyte cell line, Vero 76 and SVGA, respectively. We passaged VEEV TC-83 in these two cell lines over seven concentrations of ML336, starting at 50 nM. NGS revealed several prominent mutations in the nonstructural protein (nsP) 3 and nsP4 genes that emerged consistently in these two distinct in vitro environments-notably, a mutation at Q210 in nsP4. Several of these mutations were stable following passaging in the absence of ML336 in Vero 76 cells. Network analyses showed that the trajectory of resistance differed between Vero and SVGA. Moreover, the penetration of SNPs was lower in SVGA. In conclusion, we show that the microenvironment influenced the SNP profile of VEEV TC-83. Understanding the dynamics of resistance in VEEV against newly developed antiviral compounds will guide the design of optimal drug candidates and dosing regimens for minimizing the emergence of resistant viruses.IMPORTANCE RNA viruses, including Venezuelan equine encephalitis virus (VEEV), have high mutation rates that allow for rapid adaptation to selective pressures in their environment. Antiviral compounds exert one such pressure on virus populations during infections. Next-generation sequencing allows for examination of viruses at the population level, which enables tracking of low levels of single-nucleotide polymorphisms in the population over time. Therefore, the timing and extent of the emergence of resistance to antivirals can be tracked and assessed. We show here that in VEEV, the trajectory and penetration of antiviral resistance reflected the microenvironment in which the virus population replicates. In summary, we show the diversity of VEEV within a single population under antiviral pressure and two distinct cell types, and we show that population dynamics in these viruses can be examined to better understand how they evolve over time.
Collapse
Affiliation(s)
- Jasper Lee
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Dong Yang
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Shruti Bansal
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Kathryn O'Connell
- Laboratory Animal Care Unit, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jennifer E Golden
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Colleen B Jonsson
- Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, Tennessee, USA
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| |
Collapse
|
20
|
He Z, Dai X, Beaumont M, Yu F. Detecting and Quantifying Natural Selection at Two Linked Loci from Time Series Data of Allele Frequencies with Forward-in-Time Simulations. Genetics 2020; 216:521-541. [PMID: 32826299 PMCID: PMC7536848 DOI: 10.1534/genetics.120.303463] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 08/15/2020] [Indexed: 12/16/2022] Open
Abstract
Recent advances in DNA sequencing techniques have made it possible to monitor genomes in great detail over time. This improvement provides an opportunity for us to study natural selection based on time serial samples of genomes while accounting for genetic recombination effect and local linkage information. Such time series genomic data allow for more accurate estimation of population genetic parameters and hypothesis testing on the recent action of natural selection. In this work, we develop a novel Bayesian statistical framework for inferring natural selection at a pair of linked loci by capitalising on the temporal aspect of DNA data with the additional flexibility of modeling the sampled chromosomes that contain unknown alleles. Our approach is built on a hidden Markov model where the underlying process is a two-locus Wright-Fisher diffusion with selection, which enables us to explicitly model genetic recombination and local linkage. The posterior probability distribution for selection coefficients is computed by applying the particle marginal Metropolis-Hastings algorithm, which allows us to efficiently calculate the likelihood. We evaluate the performance of our Bayesian inference procedure through extensive simulations, showing that our approach can deliver accurate estimates of selection coefficients, and the addition of genetic recombination and local linkage brings about significant improvement in the inference of natural selection. We also illustrate the utility of our method on real data with an application to ancient DNA data associated with white spotting patterns in horses.
Collapse
Affiliation(s)
- Zhangyi He
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
| | - Xiaoyang Dai
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Mark Beaumont
- School of Biological Sciences, University of Bristol, BS8 1TQ, United Kingdom
| | - Feng Yu
- School of Mathematics, University of Bristol, BS8 1UG, United Kingdom
| |
Collapse
|
21
|
Lumby CK, Zhao L, Breuer J, Illingworth CJR. A large effective population size for established within-host influenza virus infection. eLife 2020; 9:e56915. [PMID: 32773034 PMCID: PMC7431133 DOI: 10.7554/elife.56915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 07/30/2020] [Indexed: 12/13/2022] Open
Abstract
Strains of the influenza virus form coherent global populations, yet exist at the level of single infections in individual hosts. The relationship between these scales is a critical topic for understanding viral evolution. Here we investigate the within-host relationship between selection and the stochastic effects of genetic drift, estimating an effective population size of infection Ne for influenza infection. Examining whole-genome sequence data describing a chronic case of influenza B in a severely immunocompromised child we infer an Ne of 2.5 × 107 (95% confidence range 1.0 × 107 to 9.0 × 107) suggesting that genetic drift is of minimal importance during an established influenza infection. Our result, supported by data from influenza A infection, suggests that positive selection during within-host infection is primarily limited by the typically short period of infection. Atypically long infections may have a disproportionate influence upon global patterns of viral evolution.
Collapse
Affiliation(s)
- Casper K Lumby
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Lei Zhao
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
| | - Judith Breuer
- Great Ormond Street HospitalLondonUnited Kingdom
- Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | - Christopher JR Illingworth
- Department of Genetics, University of CambridgeCambridgeUnited Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of CambridgeCambridgeUnited Kingdom
- Department of Computer Science, Institute of Biotechnology, University of HelsinkiHelsinkiFinland
| |
Collapse
|
22
|
Morales-Arce AY, Harris RB, Stone AC, Jensen JD. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 2020; 74:992-1001. [PMID: 32233086 DOI: 10.1111/evo.13954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
The within-host evolutionary dynamics of tuberculosis (TB) remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference represents a more appropriate evolutionary null model, against which the periodic effects of positive selection, associated with drug-resistance for example, may be better assessed.
Collapse
Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Rebecca B Harris
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| |
Collapse
|
23
|
Keshavarz M, Solaymani-Mohammadi F, Namdari H, Arjeini Y, Mousavi MJ, Rezaei F. Metabolic host response and therapeutic approaches to influenza infection. Cell Mol Biol Lett 2020; 25:15. [PMID: 32161622 PMCID: PMC7059726 DOI: 10.1186/s11658-020-00211-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 02/26/2020] [Indexed: 12/17/2022] Open
Abstract
Based on available metabolomic studies, influenza infection affects a variety of cellular metabolic pathways to ensure an optimal environment for its replication and production of viral particles. Following infection, glucose uptake and aerobic glycolysis increase in infected cells continually, which results in higher glucose consumption. The pentose phosphate shunt, as another glucose-consuming pathway, is enhanced by influenza infection to help produce more nucleotides, especially ATP. Regarding lipid species, following infection, levels of triglycerides, phospholipids, and several lipid derivatives undergo perturbations, some of which are associated with inflammatory responses. Also, mitochondrial fatty acid β-oxidation decreases significantly simultaneously with an increase in biosynthesis of fatty acids and membrane lipids. Moreover, essential amino acids are demonstrated to decline in infected tissues due to the production of large amounts of viral and cellular proteins. Immune responses against influenza infection, on the other hand, could significantly affect metabolic pathways. Mainly, interferon (IFN) production following viral infection affects cell function via alteration in amino acid synthesis, membrane composition, and lipid metabolism. Understanding metabolic alterations required for influenza virus replication has revealed novel therapeutic methods based on targeted inhibition of these cellular metabolic pathways.
Collapse
Affiliation(s)
- Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | | | - Haideh Namdari
- Iranian Tissue Bank and Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Yaser Arjeini
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Mousavi
- Department of Medical Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Immunology and Allergy, Faculty of Medicine, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Farhad Rezaei
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
- National Influenza Center, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
24
|
Nannou C, Ofrydopoulou A, Evgenidou E, Heath D, Heath E, Lambropoulou D. Antiviral drugs in aquatic environment and wastewater treatment plants: A review on occurrence, fate, removal and ecotoxicity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 699:134322. [PMID: 31678880 DOI: 10.1016/j.scitotenv.2019.134322] [Citation(s) in RCA: 104] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 09/04/2019] [Accepted: 09/05/2019] [Indexed: 05/23/2023]
Abstract
The environmental release of antiviral drugs is of considerable concern due to potential ecosystem alterations and the development of antiviral resistance. As a result, interest on their occurrence and fate in natural and engineered systems has grown substantially in recent years. The main scope of this review is to fill the void of information on the knowledge on the worldwide occurrence of antiviral drugs in wastewaters and natural waters and correlate their levels with their environmental fate. According to the conducted literature survey, few monitoring data exists for several European countries, such as Germany, France, and the UK. Lesser data are available for Asia, where approximately 80% of the studies focus on Japan. Several articles study the occurrence of mostly antiretroantivirals in sub-Saharan African countries, while there is a lack of data for other developing regions of the world, including the rest of Africa, South America, and the biggest part of Asia. An importantly smaller number of studies exists for North America, while no studies exist for Oceania. The against innfluenza drug oseltamivir along with its active carboxy metabolite is found to be the most studied antiviral drug. The distribution of antiviral drugs across all geographic regions varies from low ng L-1 to high μg L-1 levels, in some cases, even in surface waters. This overarching review reveals that monitoring of antiviral drugs is necessary, and some of those compounds may require toxicological attention, in the light of either spatial and temporal high concentration or potential antiviral resistance. Based on the information provided herein, the need for a better understanding of the water quality hazards posed by antiviral drugs existence in wastewater outputs and freshwater ecosystems is demosntrated. Finally, the future challenges concerning the occurrence, fate, and potential ecotoxicological risk to organisms posed by antiviral drug residues are discussed.
Collapse
Affiliation(s)
- Christina Nannou
- Department of Chemistry, Aristotle University of Thessaloniki. GR 54124, Thessaloniki, Greece
| | - Anna Ofrydopoulou
- Department of Chemistry, Aristotle University of Thessaloniki. GR 54124, Thessaloniki, Greece
| | - Eleni Evgenidou
- Department of Chemistry, Aristotle University of Thessaloniki. GR 54124, Thessaloniki, Greece
| | - David Heath
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Ester Heath
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia; Jožef Stefan International Postgraduate School, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Dimitra Lambropoulou
- Department of Chemistry, Aristotle University of Thessaloniki. GR 54124, Thessaloniki, Greece.
| |
Collapse
|
25
|
Lawson DJ, Davies NM, Haworth S, Ashraf B, Howe L, Crawford A, Hemani G, Davey Smith G, Timpson NJ. Is population structure in the genetic biobank era irrelevant, a challenge, or an opportunity? Hum Genet 2020; 139:23-41. [PMID: 31030318 PMCID: PMC6942007 DOI: 10.1007/s00439-019-02014-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Accepted: 04/12/2019] [Indexed: 12/11/2022]
Abstract
Replicable genetic association signals have consistently been found through genome-wide association studies in recent years. The recent dramatic expansion of study sizes improves power of estimation of effect sizes, genomic prediction, causal inference, and polygenic selection, but it simultaneously increases susceptibility of these methods to bias due to subtle population structure. Standard methods using genetic principal components to correct for structure might not always be appropriate and we use a simulation study to illustrate when correction might be ineffective for avoiding biases. New methods such as trans-ethnic modeling and chromosome painting allow for a richer understanding of the relationship between traits and population structure. We illustrate the arguments using real examples (stroke and educational attainment) and provide a more nuanced understanding of population structure, which is set to be revisited as a critical aspect of future analyses in genetic epidemiology. We also make simple recommendations for how problems can be avoided in the future. Our results have particular importance for the implementation of GWAS meta-analysis, for prediction of traits, and for causal inference.
Collapse
Affiliation(s)
- Daniel John Lawson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.
| | - Neil Martin Davies
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Simon Haworth
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Bilal Ashraf
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Laurence Howe
- Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, Gower Street, London, WC1E 6BT, UK
| | - Andrew Crawford
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Gibran Hemani
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Nicholas John Timpson
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| |
Collapse
|
26
|
Qian C, Yan X, Shi Y, Yin H, Chang Y, Chen J, Ingvarsson PK, Nevo E, Ma XF. Adaptive signals of flowering time pathways in wild barley from Israel over 28 generations. Heredity (Edinb) 2020; 124:62-76. [PMID: 31527784 PMCID: PMC6906298 DOI: 10.1038/s41437-019-0264-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/06/2023] Open
Abstract
Flowering time is one of the most critical traits for plants' life cycles, which is influenced by various environment changes, such as global warming. Previous studies have suggested that to guarantee reproductive success, plants have shifted flowering times to adapt to global warming. Although many studies focused on the molecular mechanisms of early flowering, little was supported by the repeated sampling at different time points through the changing climate. To fully dissect the temporal and spatial evolutionary genetics of flowering time, we investigated nucleotide variation in ten flowering time candidate genes and nine reference genes for the same ten wild-barley populations sampled 28 years apart (1980-2008). The overall genetic differentiation was significantly greater in the descendant populations (2008) compared with the ancestral populations (1980); however, local adaptation tests failed to detect any single-nucleotide polymorphism (SNP)/indel under spatial-diversifying selection at either time point. By contrast, the WFABC (Wright-Fisher ABC-based approach) that detected 54 SNPs/indels was under strong selection during the past 28 generations. Moreover, all these 54 alleles were segregated in the ancestral populations, but fixed in the descendent populations. Among the top ten SNPs/indels, seven were located in genes of FT1 (FLOWERING TIME LOCUS T 1), CO1 (CONSTANS-LIKE PROTEIN 1), and VRN-H2 (VERNALIZATION-H2), which have been documented to be associated with flowering time regulation in barley cultivars. This study might suggest that all ten populations have undergone parallel evolution over the past few decades in response to global warming, and even an overwhelming local adaptation and ecological differentiation.
Collapse
Affiliation(s)
- Chaoju Qian
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Xia Yan
- School of Life Sciences, Nantong University, Nantong, 226019, Jiangsu, China
| | - Yong Shi
- Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
| | - Hengxia Yin
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, Qinghai, China
| | - Yuxiao Chang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 450002, China
| | - Jun Chen
- College of Life Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Pär K Ingvarsson
- Department of Plant Biology, Swedish University of Agricultural Sciences, Uppsala BioCenter, SE-750 07, Uppsala, Sweden
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Haifa, 3498838, Israel.
| | - Xiao-Fei Ma
- Department of Ecology and Agriculture Research, Key Laboratory of Stress Physiology and Ecology in Cold and Arid Regions, Gansu Province, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
| |
Collapse
|
27
|
Živković D, John S, Verin M, Stephan W, Tellier A. Neutral genomic signatures of host-parasite coevolution. BMC Evol Biol 2019; 19:230. [PMID: 31856710 PMCID: PMC6924072 DOI: 10.1186/s12862-019-1556-3] [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: 04/10/2019] [Accepted: 12/09/2019] [Indexed: 12/21/2022] Open
Abstract
Background Coevolution is a selective process of reciprocal adaptation in hosts and parasites or in mutualistic symbionts. Classic population genetics theory predicts the signatures of selection at the interacting loci of both species, but not the neutral genome-wide polymorphism patterns. To bridge this gap, we build an eco-evolutionary model, where neutral genomic changes over time are driven by a single selected locus in hosts and parasites via a simple biallelic gene-for-gene or matching-allele interaction. This coevolutionary process may lead to cyclic changes in the sizes of the interacting populations. Results We investigate if and when these changes can be observed in the site frequency spectrum of neutral polymorphisms from host and parasite full genome data. We show that changes of the host population size are too smooth to be observable in its polymorphism pattern over the course of time. Conversely, the parasite population may undergo a series of strong bottlenecks occurring on a slower relative time scale, which may lead to observable changes in a time series sample. We also extend our results to cases with 1) several parasites per host accelerating relative time, and 2) multiple parasite generations per host generation slowing down rescaled time. Conclusions Our results show that time series sampling of host and parasite populations with full genome data are crucial to understand if and how coevolution occurs. This model provides therefore a framework to interpret and draw inference from genome-wide polymorphism data of interacting species.
Collapse
Affiliation(s)
- Daniel Živković
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| | - Sona John
- Section of Population Genetics, Technical University of Munich, Freising, Germany
| | - Mélissa Verin
- Section of Population Genetics, Technical University of Munich, Freising, Germany.,Department of Mathematics and Statistics, Queen's University, Kingston, Ontario, Canada
| | - Wolfgang Stephan
- Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Aurélien Tellier
- Section of Population Genetics, Technical University of Munich, Freising, Germany.
| |
Collapse
|
28
|
Bertels F, Leemann C, Metzner KJ, Regoes R. Parallel evolution of HIV-1 in a long-term experiment. Mol Biol Evol 2019; 36:2400-2414. [PMID: 31251344 PMCID: PMC6805227 DOI: 10.1093/molbev/msz155] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 06/22/2019] [Indexed: 12/15/2022] Open
Abstract
One of the most intriguing puzzles in biology is the degree to which evolution is repeatable. The repeatability of evolution, or parallel evolution, has been studied in a variety of model systems, but has rarely been investigated with clinically relevant viruses. To investigate parallel evolution of HIV-1, we passaged two replicate HIV-1 populations for almost 1 year in each of two human T-cell lines. For each of the four evolution lines, we determined the genetic composition of the viral population at nine time points by deep sequencing the entire genome. Mutations that were carried by the majority of the viral population accumulated continuously over 1 year in each evolution line. Many majority mutations appeared in more than one evolution line, that is, our experiments showed an extreme degree of parallel evolution. In one of the evolution lines, 62% of the majority mutations also occur in another line. The parallelism impairs our ability to reconstruct the evolutionary history by phylogenetic methods. We show that one can infer the correct phylogenetic topology by including minority mutations in our analysis. We also find that mutation diversity at the beginning of the experiment is predictive of the frequency of majority mutations at the end of the experiment.
Collapse
Affiliation(s)
- Frederic Bertels
- Department of Environmental Systems Sciences, ETH Zurich, Zurich.,Max-Planck-Institute for Evolutionary Biology, Department of Microbial Population Biology
| | - Christine Leemann
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich.,Insitute of Medical Virology, University of Zurich, Zurich
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich.,Insitute of Medical Virology, University of Zurich, Zurich
| | - Roland Regoes
- Department of Environmental Systems Sciences, ETH Zurich, Zurich
| |
Collapse
|
29
|
Jonsson CB, Cao X, Lee J, Gabbard JD, Chu YK, Fitzpatrick EA, Julander J, Chung DH, Stabenow J, Golden JE. Efficacy of a ML336 derivative against Venezuelan and eastern equine encephalitis viruses. Antiviral Res 2019; 167:25-34. [PMID: 30970271 DOI: 10.1016/j.antiviral.2019.04.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 03/30/2019] [Accepted: 04/03/2019] [Indexed: 02/08/2023]
Abstract
Currently, there are no licensed human vaccines or antivirals for treatment of or prevention from infection with encephalitic alphaviruses. Because epidemics are sporadic and unpredictable, and endemic disease is common but rarely diagnosed, it is difficult to identify all populations requiring vaccination; thus, an effective post-exposure treatment method is needed to interrupt ongoing outbreaks. To address this public health need, we have continued development of ML336 to deliver a molecule with prophylactic and therapeutic potential that could be relevant for use in natural epidemics or deliberate release scenario for Venezuelan equine encephalitis virus (VEEV). We report findings from in vitro assessments of four analogs of ML336, and in vivo screening of three of these new derivatives, BDGR-4, BDGR-69 and BDGR-70. The optimal dosing for maximal protection was observed at 12.5 mg/kg/day, twice daily for 8 days. BDGR-4 was tested further for prophylactic and therapeutic efficacy in mice challenged with VEEV Trinidad Donkey (TrD). Mice challenged with VEEV TrD showed 100% and 90% protection from lethal disease when treated at 24 and 48 h post-infection, respectively. We also measured 90% protection for BDGR-4 in mice challenged with Eastern equine encephalitis virus. In additional assessments of BDGR-4 in mice alone, we observed no appreciable toxicity as evaluated by clinical chemistry indicators up to a dose of 25 mg/kg/day over 4 days. In these same mice, we observed no induction of interferon. Lastly, the resistance of VEEV to BDGR-4 was evaluated by next-generation sequencing which revealed specific mutations in nsP4, the viral polymerase.
Collapse
Affiliation(s)
- Colleen B Jonsson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38103, USA.
| | - Xufeng Cao
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, 53705-2222, USA
| | - Jasper Lee
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38103, USA
| | - Jon D Gabbard
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, 40202, USA
| | - Yong-Kyu Chu
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, 40202, USA
| | - Elizabeth A Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, 858 Madison Avenue, Memphis, TN, 38103, USA
| | - Justin Julander
- Institute for Antiviral Research, Animal, Dairy, and Veterinary Sciences Department, 5600 Old Main Hill, Utah State University, Logan, UT, 84322-5600, USA
| | - Dong-Hoon Chung
- Center for Predictive Medicine for Biodefense and Emerging Infectious Diseases, University of Louisville, Louisville, KY, 40202, USA; Department of Microbiology and Immunology, University of Louisville, Louisville, KY, 40202, USA
| | - Jennifer Stabenow
- Regional Biocontainment Laboratory, University of Tennessee Health Science Center, 901 Madison Avenue, Memphis, TN, 38103, USA
| | - Jennifer E Golden
- Pharmaceutical Sciences Division, School of Pharmacy, University of Wisconsin, Madison, WI, 53705-2222, USA.
| |
Collapse
|
30
|
Ecological and Evolutionary Processes Shaping Viral Genetic Diversity. Viruses 2019; 11:v11030220. [PMID: 30841497 PMCID: PMC6466605 DOI: 10.3390/v11030220] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/22/2019] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
The contemporary genomic diversity of viruses is a result of the continuous and dynamic interaction of past ecological and evolutionary processes. Thus, genome sequences of viruses can be a valuable source of information about these processes. In this review, we first describe the relevant processes shaping viral genomic variation, with a focus on the role of host–virus coevolution and its potential to give rise to eco-evolutionary feedback loops. We further give a brief overview of available methodology designed to extract information about these processes from genomic data. Short generation times and small genomes make viruses ideal model systems to study the joint effect of complex coevolutionary and eco-evolutionary interactions on genetic evolution. This complexity, together with the diverse array of lifetime and reproductive strategies in viruses ask for extensions of existing inference methods, for example by integrating multiple information sources. Such integration can broaden the applicability of genetic inference methods and thus further improve our understanding of the role viruses play in biological communities.
Collapse
|
31
|
Inferring Demography and Selection in Organisms Characterized by Skewed Offspring Distributions. Genetics 2019; 211:1019-1028. [PMID: 30651284 DOI: 10.1534/genetics.118.301684] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/15/2019] [Indexed: 01/01/2023] Open
Abstract
The recent increase in time-series population genomic data from experimental, natural, and ancient populations has been accompanied by a promising growth in methodologies for inferring demographic and selective parameters from such data. However, these methods have largely presumed that the populations of interest are well-described by the Kingman coalescent. In reality, many groups of organisms, including viruses, marine organisms, and some plants, protists, and fungi, typified by high variance in progeny number, may be best characterized by multiple-merger coalescent models. Estimation of population genetic parameters under Wright-Fisher assumptions for these organisms may thus be prone to serious mis-inference. We propose a novel method for the joint inference of demography and selection under the Ψ-coalescent model, termed Multiple-Merger Coalescent Approximate Bayesian Computation, or MMC-ABC. We first demonstrate mis-inference under the Kingman, and then exhibit the superior performance of MMC-ABC under conditions of skewed offspring distributions. In order to highlight the utility of this approach, we reanalyzed previously published drug-selection lines of influenza A virus. We jointly inferred the extent of progeny-skew inherent to viral replication and identified putative drug-resistance mutations.
Collapse
|
32
|
Shim H. Feature Learning of Virus Genome Evolution With the Nucleotide Skip-Gram Neural Network. Evol Bioinform Online 2019; 15:1176934318821072. [PMID: 30692845 PMCID: PMC6335656 DOI: 10.1177/1176934318821072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/15/2018] [Indexed: 12/14/2022] Open
Abstract
Recent studies reveal that even the smallest genomes such as viruses evolve through complex and stochastic processes, and the assumption of independent alleles is not valid in most applications. Advances in sequencing technologies produce multiple time-point whole-genome data, which enable potential interactions between these alleles to be investigated empirically. To investigate these interactions, we represent alleles as distributed vectors that encode for relationships with other alleles in the course of evolution and apply artificial neural networks to time-sampled whole-genome datasets for feature learning. We build this platform using methods and algorithms derived from natural language processing (NLP), and we denote it as the nucleotide skip-gram neural network. We learn distributed vectors of alleles using the changes in allele frequency of echovirus 11 in the presence or absence of the disinfectant (ClO2) from the experimental evolution data. Results from the training using a new open-source software TensorFlow show that the learned distributed vectors can be clustered using principal component analysis and hierarchical clustering to reveal a list of non-synonymous mutations that arise on the structural protein VP1 in connection to the candidate mutation for ClO2 adaptation. Furthermore, this method can account for recombination rates by setting the extent of interactions as a biological hyper-parameter, and the results show that the most realistic scenario of mid-range interactions across the genome is most consistent with the previous studies.
Collapse
Affiliation(s)
- Hyunjin Shim
- Artificial Intelligence Laboratory, Stanford University, Stanford, CA, USA.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| |
Collapse
|
33
|
Mutations in Influenza A Virus Neuraminidase and Hemagglutinin Confer Resistance against a Broadly Neutralizing Hemagglutinin Stem Antibody. J Virol 2019; 93:JVI.01639-18. [PMID: 30381484 DOI: 10.1128/jvi.01639-18] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 10/22/2018] [Indexed: 11/20/2022] Open
Abstract
Influenza A virus (IAV), a major cause of human morbidity and mortality, continuously evolves in response to selective pressures. Stem-directed, broadly neutralizing antibodies (sBnAbs) targeting the influenza virus hemagglutinin (HA) are a promising therapeutic strategy, but neutralization escape mutants can develop. We used an integrated approach combining viral passaging, deep sequencing, and protein structural analyses to define escape mutations and mechanisms of neutralization escape in vitro for the F10 sBnAb. IAV was propagated with escalating concentrations of F10 over serial passages in cultured cells to select for escape mutations. Viral sequence analysis revealed three mutations in HA and one in neuraminidase (NA). Introduction of these specific mutations into IAV through reverse genetics confirmed their roles in resistance to F10. Structural analyses revealed that the selected HA mutations (S123G, N460S, and N203V) are away from the F10 epitope but may indirectly impact influenza virus receptor binding, endosomal fusion, or budding. The NA mutation E329K, which was previously identified to be associated with antibody escape, affects the active site of NA, highlighting the importance of the balance between HA and NA function for viral survival. Thus, whole-genome population sequencing enables the identification of viral resistance mutations responding to antibody-induced selective pressure.IMPORTANCE Influenza A virus is a public health threat for which currently available vaccines are not always effective. Broadly neutralizing antibodies that bind to the highly conserved stem region of the influenza virus hemagglutinin (HA) can neutralize many influenza virus strains. To understand how influenza virus can become resistant or escape such antibodies, we propagated influenza A virus in vitro with escalating concentrations of antibody and analyzed viral populations by whole-genome sequencing. We identified HA mutations near and distal to the antibody binding epitope that conferred resistance to antibody neutralization. Additionally, we identified a neuraminidase (NA) mutation that allowed the virus to grow in the presence of high concentrations of the antibody. Virus carrying dual mutations in HA and NA also grew under high antibody concentrations. We show that NA mutations mediate the escape of neutralization by antibodies against HA, highlighting the importance of a balance between HA and NA for optimal virus function.
Collapse
|
34
|
Zhao L, Abbasi AB, Illingworth CJR. Mutational load causes stochastic evolutionary outcomes in acute RNA viral infection. Virus Evol 2019; 5:vez008. [PMID: 31024738 PMCID: PMC6476161 DOI: 10.1093/ve/vez008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Mutational load is known to be of importance for the evolution of RNA viruses, the combination of a high mutation rate and large population size leading to an accumulation of deleterious mutations. However, while the effects of mutational load on global viral populations have been considered, its quantitative effects at the within-host scale of infection are less well understood. We here show that even on the rapid timescale of acute disease, mutational load has an effect on within-host viral adaptation, reducing the effective selection acting upon beneficial variants by ∼10 per cent. Furthermore, mutational load induces considerable stochasticity in the pattern of evolution, causing a more than five-fold uncertainty in the effective fitness of a transmitted beneficial variant. Our work aims to bridge the gap between classic models from population genetic theory and the biology of viral infection. In an advance on some previous models of mutational load, we replace the assumption of a constant variant fitness cost with an experimentally-derived distribution of fitness effects. Expanding previous frameworks for evolutionary simulation, we introduce the Wright-Fisher model with continuous mutation, which describes a continuum of possible modes of replication within a cell. Our results advance our understanding of adaptation in the context of strong selection and a high mutation rate. Despite viral populations having large absolute sizes, critical events in viral adaptation, including antigenic drift and the onset of drug resistance, arise through stochastic evolutionary processes.
Collapse
Affiliation(s)
- Lei Zhao
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Ali B Abbasi
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Christopher J R Illingworth
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
| |
Collapse
|
35
|
Zinger T, Gelbart M, Miller D, Pennings PS, Stern A. Inferring population genetics parameters of evolving viruses using time-series data. Virus Evol 2019; 5:vez011. [PMID: 31191979 PMCID: PMC6555871 DOI: 10.1093/ve/vez011] [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: 12/16/2022] Open
Abstract
With the advent of deep sequencing techniques, it is now possible to track the evolution of viruses with ever-increasing detail. Here, we present Flexible Inference from Time-Series (FITS)-a computational tool that allows inference of one of three parameters: the fitness of a specific mutation, the mutation rate or the population size from genomic time-series sequencing data. FITS was designed first and foremost for analysis of either short-term Evolve & Resequence (E&R) experiments or rapidly recombining populations of viruses. We thoroughly explore the performance of FITS on simulated data and highlight its ability to infer the fitness/mutation rate/population size. We further show that FITS can infer meaningful information even when the input parameters are inexact. In particular, FITS is able to successfully categorize a mutation as advantageous or deleterious. We next apply FITS to empirical data from an E&R experiment on poliovirus where parameters were determined experimentally and demonstrate high accuracy in inference.
Collapse
Affiliation(s)
- Tal Zinger
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Maoz Gelbart
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Danielle Miller
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| | - Pleuni S Pennings
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA, USA
| | - Adi Stern
- Department of Molecular Microbiology and Biotechnology, School of Molecular Cell Biology and Biotechnology, Haim Levanon Str., Tel-Aviv University, Tel-Aviv, Israel
| |
Collapse
|
36
|
Harris RB, Sackman A, Jensen JD. On the unfounded enthusiasm for soft selective sweeps II: Examining recent evidence from humans, flies, and viruses. PLoS Genet 2018; 14:e1007859. [PMID: 30592709 PMCID: PMC6336318 DOI: 10.1371/journal.pgen.1007859] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 01/17/2019] [Accepted: 11/28/2018] [Indexed: 12/13/2022] Open
Abstract
Since the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple beneficial mutations—so-called soft selective sweeps—researchers have sought to identify these patterns in natural population data. Indeed, over the past two years, large-scale data analyses have argued that soft sweeps are pervasive across organisms of very different effective population size and mutation rate—humans, Drosophila, and HIV. Yet, others have evaluated the relevance of these models to natural populations, as well as the identifiability of the models relative to other known population-level processes, arguing that soft sweeps are likely to be rare. Here, we look to reconcile these opposing results by carefully evaluating three recent studies and their underlying methodologies. Using population genetic theory, as well as extensive simulation, we find that all three examples are prone to extremely high false-positive rates, incorrectly identifying soft sweeps under both hard sweep and neutral models. Furthermore, we demonstrate that well-fit demographic histories combined with rare hard sweeps serve as the more parsimonious explanation. These findings represent a necessary response to the growing tendency of invoking parameter-heavy, assumption-laden models of pervasive positive selection, and neglecting best practices regarding the construction of proper demographic null models. A long-standing debate in evolutionary biology revolves around the role of selective vs. stochastic processes in driving molecular evolution and shaping genetic variation. With the advent of genomics, genome-wide polymorphism data have been utilized to characterize these processes, with a major interest in describing the fraction of genomic variation shaped by positive selection. These genomic scans were initially focused around a hard sweep model, in which selection acts upon rare, newly arising beneficial mutations. Recent years have seen the description of sweeps occurring from both standing and rapidly recurring beneficial mutations, collectively known as soft sweeps. However, common to both hard and soft sweeps is the difficulty in distinguishing these effects from neutral demographic patterns, and disentangling these processes has remained an important field of study within population genetics. Despite this, there is a recent and troubling tendency to neglect these demographic considerations, and to naively fit sweep models to genomic data. Recent realizations of such efforts have resulted in the claim that soft sweeps play a dominant role in shaping genomic variation and in driving adaptation across diverse branches of the tree of life. Here, we reanalyze these findings and demonstrate that a more careful consideration of neutral processes results in highly differing conclusions.
Collapse
Affiliation(s)
- Rebecca B. Harris
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Andrew Sackman
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
| | - Jeffrey D. Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ, United States of America
- * E-mail:
| |
Collapse
|
37
|
Majiya H, Adeyemi OO, Herod M, Stonehouse NJ, Millner P. Photodynamic inactivation of non-enveloped RNA viruses. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2018; 189:87-94. [DOI: 10.1016/j.jphotobiol.2018.10.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/24/2018] [Accepted: 10/07/2018] [Indexed: 10/28/2022]
|
38
|
Lumby CK, Nene NR, Illingworth CJR. A novel framework for inferring parameters of transmission from viral sequence data. PLoS Genet 2018; 14:e1007718. [PMID: 30325921 PMCID: PMC6203404 DOI: 10.1371/journal.pgen.1007718] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 10/26/2018] [Accepted: 09/26/2018] [Indexed: 11/18/2022] Open
Abstract
Transmission between hosts is a critical part of the viral lifecycle. Recent studies of viral transmission have used genome sequence data to evaluate the number of particles transmitted between hosts, and the role of selection as it operates during the transmission process. However, the interpretation of sequence data describing transmission events is a challenging task. We here present a novel and comprehensive framework for using short-read sequence data to understand viral transmission events, designed for influenza virus, but adaptable to other viral species. Our approach solves multiple shortcomings of previous methods for this purpose; for example, we consider transmission as an event involving whole viruses, rather than sets of independent alleles. We demonstrate how selection during transmission and noisy sequence data may each affect naive inferences of the population bottleneck, accounting for these in our framework so as to achieve a correct inference. We identify circumstances in which selection for increased viral transmission may or may not be identified from data. Applying our method to experimental data in which transmission occurs in the presence of strong selection, we show that our framework grants a more quantitative insight into transmission events than previous approaches, inferring the bottleneck in a manner that accounts for selection, both for within-host virulence, and for inherent viral transmissibility. Our work provides new opportunities for studying transmission processes in influenza, and by extension, in other infectious diseases.
Collapse
Affiliation(s)
- Casper K. Lumby
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Nuno R. Nene
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Christopher J. R. Illingworth
- Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
39
|
Sackman AM, McGee LW, Morrison AJ, Pierce J, Anisman J, Hamilton H, Sanderbeck S, Newman C, Rokyta DR. Mutation-Driven Parallel Evolution during Viral Adaptation. Mol Biol Evol 2018; 34:3243-3253. [PMID: 29029274 DOI: 10.1093/molbev/msx257] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Convergent evolution has been demonstrated across all levels of biological organization, from parallel nucleotide substitutions to convergent evolution of complex phenotypes, but whether instances of convergence are the result of selection repeatedly finding the same optimal solution to a recurring problem or are the product of mutational biases remains unsettled. We generated 20 replicate lineages allowed to fix a single mutation from each of four bacteriophage genotypes under identical selective regimes to test for parallel changes within and across genotypes at the levels of mutational effect distributions and gene, protein, amino acid, and nucleotide changes. All four genotypes shared a distribution of beneficial mutational effects best approximated by a distribution with a finite upper bound. Parallel adaptation was high at the protein, gene, amino acid, and nucleotide levels, both within and among phage genotypes, with the most common first-step mutation in each background fixing on an average in 7 of 20 replicates and half of the substitutions in two of the four genotypes occurring at shared sites. Remarkably, the mutation of largest beneficial effect that fixed for each genotype was never the most common, as would be expected if parallelism were driven by selection. In fact, the mutation of smallest benefit for each genotype fixed in a total of 7 of 80 lineages, equally as often as the mutation of largest benefit, leading us to conclude that adaptation was largely mutation-driven, such that mutational biases led to frequent parallel fixation of mutations of suboptimal effect.
Collapse
Affiliation(s)
- Andrew M Sackman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Lindsey W McGee
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Jessica Pierce
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Jeremy Anisman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Hunter Hamilton
- Department of Biological Science, Florida State University, Tallahassee, FL
| | | | - Cayla Newman
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
| |
Collapse
|
40
|
McCrone JT, Woods RJ, Martin ET, Malosh RE, Monto AS, Lauring AS. Stochastic processes constrain the within and between host evolution of influenza virus. eLife 2018; 7:e35962. [PMID: 29683424 PMCID: PMC5933925 DOI: 10.7554/elife.35962] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022] Open
Abstract
The evolutionary dynamics of influenza virus ultimately derive from processes that take place within and between infected individuals. Here we define influenza virus dynamics in human hosts through sequencing of 249 specimens from 200 individuals collected over 6290 person-seasons of observation. Because these viruses were collected from individuals in a prospective community-based cohort, they are broadly representative of natural infections with seasonal viruses. Consistent with a neutral model of evolution, sequence data from 49 serially sampled individuals illustrated the dynamic turnover of synonymous and nonsynonymous single nucleotide variants and provided little evidence for positive selection of antigenic variants. We also identified 43 genetically-validated transmission pairs in this cohort. Maximum likelihood optimization of multiple transmission models estimated an effective transmission bottleneck of 1-2 genomes. Our data suggest that positive selection is inefficient at the level of the individual host and that stochastic processes dominate the host-level evolution of influenza viruses.
Collapse
Affiliation(s)
- John T McCrone
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborUnited States
| | - Robert J Woods
- Division of Infectious Diseases, Department of Internal MedicineUniversity of MichiganAnn ArborUnited States
| | - Emily T Martin
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Ryan E Malosh
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Arnold S Monto
- Department of EpidemiologyUniversity of MichiganAnn ArborUnited States
| | - Adam S Lauring
- Department of Microbiology and ImmunologyUniversity of MichiganAnn ArborUnited States
- Division of Infectious Diseases, Department of Internal MedicineUniversity of MichiganAnn ArborUnited States
| |
Collapse
|
41
|
Kumar A, Meldgaard TS, Bertholet S. Novel Platforms for the Development of a Universal Influenza Vaccine. Front Immunol 2018; 9:600. [PMID: 29628926 PMCID: PMC5877485 DOI: 10.3389/fimmu.2018.00600] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/09/2018] [Indexed: 12/19/2022] Open
Abstract
Despite advancements in immunotherapeutic approaches, influenza continues to cause severe illness, particularly among immunocompromised individuals, young children, and elderly adults. Vaccination is the most effective way to reduce rates of morbidity and mortality caused by influenza viruses. Frequent genetic shift and drift among influenza-virus strains with the resultant disparity between circulating and vaccine virus strains limits the effectiveness of the available conventional influenza vaccines. One approach to overcome this limitation is to develop a universal influenza vaccine that could provide protection against all subtypes of influenza viruses. Moreover, the development of a novel or improved universal influenza vaccines may be greatly facilitated by new technologies including virus-like particles, T-cell-inducing peptides and recombinant proteins, synthetic viruses, broadly neutralizing antibodies, and nucleic acid-based vaccines. This review discusses recent scientific advances in the development of next-generation universal influenza vaccines.
Collapse
Affiliation(s)
- Arun Kumar
- GSK, Research and Development Center, Siena, Italy.,Linköping University, Linköping, Sweden
| | - Trine Sundebo Meldgaard
- GSK, Research and Development Center, Siena, Italy.,DTU Nanotech, Technical University of Denmark, Copenhagen, Denmark
| | - Sylvie Bertholet
- GSK, Research and Development Center, Siena, Italy.,GSK, Research and Development Center, Rockville, MD, United States
| |
Collapse
|
42
|
Abstract
Allele frequency time series data constitute a powerful resource for unraveling mechanisms of adaptation, because the temporal dimension captures important information about evolutionary forces. In particular, Evolve and Resequence (E&R), the whole-genome sequencing of replicated experimentally evolving populations, is becoming increasingly popular. Based on computer simulations several studies proposed experimental parameters to optimize the identification of the selection targets. No such recommendations are available for the underlying parameters selection strength and dominance. Here, we introduce a highly accurate method to estimate selection parameters from replicated time series data, which is fast enough to be applied on a genome scale. Using this new method, we evaluate how experimental parameters can be optimized to obtain the most reliable estimates for selection parameters. We show that the effective population size (Ne) and the number of replicates have the largest impact. Because the number of time points and sequencing coverage had only a minor effect, we suggest that time series analysis is feasible without major increase in sequencing costs. We anticipate that time series analysis will become routine in E&R studies.
Collapse
Affiliation(s)
- Thomas Taus
- Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Andreas Futschik
- Department of Applied Statistics, Johannes Kepler Universität Linz, Linz, Austria
| | | |
Collapse
|
43
|
Inferring Fitness Effects from Time-Resolved Sequence Data with a Delay-Deterministic Model. Genetics 2018; 209:255-264. [PMID: 29500183 PMCID: PMC5937181 DOI: 10.1534/genetics.118.300790] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 02/28/2018] [Indexed: 11/30/2022] Open
Abstract
A broad range of approaches have considered the challenge of inferring selection from time-resolved genome sequence data. Models describing deterministic changes in allele or haplotype frequency have been highlighted as providing accurate and computationally... A common challenge arising from the observation of an evolutionary system over time is to infer the magnitude of selection acting upon a specific genetic variant, or variants, within the population. The inference of selection may be confounded by the effects of genetic drift in a system, leading to the development of inference procedures to account for these effects. However, recent work has suggested that deterministic models of evolution may be effective in capturing the effects of selection even under complex models of demography, suggesting the more general application of deterministic approaches to inference. Responding to this literature, we here note a case in which a deterministic model of evolution may give highly misleading inferences, resulting from the nondeterministic properties of mutation in a finite population. We propose an alternative approach that acts to correct for this error, and which we denote the delay-deterministic model. Applying our model to a simple evolutionary system, we demonstrate its performance in quantifying the extent of selection acting within that system. We further consider the application of our model to sequence data from an evolutionary experiment. We outline scenarios in which our model may produce improved results for the inference of selection, noting that such situations can be easily identified via the use of a regular deterministic model.
Collapse
|
44
|
Tataru P, Simonsen M, Bataillon T, Hobolth A. Statistical Inference in the Wright-Fisher Model Using Allele Frequency Data. Syst Biol 2018; 66:e30-e46. [PMID: 28173553 PMCID: PMC5837693 DOI: 10.1093/sysbio/syw056] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 05/31/2016] [Accepted: 06/06/2016] [Indexed: 11/14/2022] Open
Abstract
The Wright–Fisher model provides an elegant mathematical framework for understanding allele frequency data. In particular, the model can be used to infer the demographic history of species and identify loci under selection. A crucial quantity for inference under the Wright–Fisher model is the distribution of allele frequencies (DAF). Despite the apparent simplicity of the model, the calculation of the DAF is challenging. We review and discuss strategies for approximating the DAF, and how these are used in methods that perform inference from allele frequency data. Various evolutionary forces can be incorporated in the Wright–Fisher model, and we consider these in turn. We begin our review with the basic bi-allelic Wright–Fisher model where random genetic drift is the only evolutionary force. We then consider mutation, migration, and selection. In particular, we compare diffusion-based and moment-based methods in terms of accuracy, computational efficiency, and analytical tractability. We conclude with a brief overview of the multi-allelic process with a general mutation model.
Collapse
Affiliation(s)
- Paula Tataru
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Maria Simonsen
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Asger Hobolth
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| |
Collapse
|
45
|
Obolski U, Ram Y, Hadany L. Key issues review: evolution on rugged adaptive landscapes. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:012602. [PMID: 29051394 DOI: 10.1088/1361-6633/aa94d4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Adaptive landscapes represent a mapping between genotype and fitness. Rugged adaptive landscapes contain two or more adaptive peaks: allele combinations with higher fitness than any of their neighbors in the genetic space. How do populations evolve on such rugged landscapes? Evolutionary biologists have struggled with this question since it was first introduced in the 1930s by Sewall Wright. Discoveries in the fields of genetics and biochemistry inspired various mathematical models of adaptive landscapes. The development of landscape models led to numerous theoretical studies analyzing evolution on rugged landscapes under different biological conditions. The large body of theoretical work suggests that adaptive landscapes are major determinants of the progress and outcome of evolutionary processes. Recent technological advances in molecular biology and microbiology allow experimenters to measure adaptive values of large sets of allele combinations and construct empirical adaptive landscapes for the first time. Such empirical landscapes have already been generated in bacteria, yeast, viruses, and fungi, and are contributing to new insights about evolution on adaptive landscapes. In this Key Issues Review we will: (i) introduce the concept of adaptive landscapes; (ii) review the major theoretical studies of evolution on rugged landscapes; (iii) review some of the recently obtained empirical adaptive landscapes; (iv) discuss recent mathematical and statistical analyses motivated by empirical adaptive landscapes, as well as provide the reader with instructions and source code to implement simulations of evolution on adaptive landscapes; and (v) discuss possible future directions for this exciting field.
Collapse
|
46
|
Ormond L, Liu P, Matuszewski S, Renzette N, Bank C, Zeldovich K, Bolon DN, Kowalik TF, Finberg RW, Jensen JD, Wang JP. The Combined Effect of Oseltamivir and Favipiravir on Influenza A Virus Evolution. Genome Biol Evol 2017; 9:1913-1924. [PMID: 28854600 PMCID: PMC5570085 DOI: 10.1093/gbe/evx138] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2017] [Indexed: 01/14/2023] Open
Abstract
Influenza virus inflicts a heavy death toll annually and resistance to existing antiviral drugs has generated interest in the development of agents with novel mechanisms of action. Favipiravir is an antiviral drug that acts by increasing the genome-wide mutation rate of influenza A virus (IAV). Potential synergistic benefits of combining oseltamivir and favipiravir have been demonstrated in animal models of influenza, but the population-level effects of combining the drugs are unknown. In order to elucidate the underlying evolutionary processes at play, we performed genome-wide sequencing of IAV experimental populations subjected to serial passaging in vitro under a combined protocol of oseltamivir and favipiravir. We describe the interplay between mutation, selection, and genetic drift that ultimately culminates in population extinction. In particular, selective sweeps around oseltamivir resistance mutations reduce genome-wide variation while deleterious mutations hitchhike to fixation given the increased mutational load generated by favipiravir. This latter effect reduces viral fitness and accelerates extinction compared with IAV populations treated with favipiravir alone, but risks spreading both established and newly emerging mutations, including possible drug resistance mutations, if transmission occurs before the viral populations are eradicated.
Collapse
Affiliation(s)
- Louise Ormond
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Ping Liu
- Department of Medicine, University of Massachusetts Medical School
| | - Sebastian Matuszewski
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Nicholas Renzette
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Department of Microbiology and Physiological Systems, University of Massachusetts Medical School
| | - Claudia Bank
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - Konstantin Zeldovich
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School
| | - Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School
| | - Timothy F Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School
| | - Robert W Finberg
- Department of Medicine, University of Massachusetts Medical School
| | - Jeffrey D Jensen
- École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.,Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland.,School of Life Sciences, Center for Evolution & Medicine, Arizona State University
| | - Jennifer P Wang
- Department of Medicine, University of Massachusetts Medical School
| |
Collapse
|
47
|
Rousseau E, Moury B, Mailleret L, Senoussi R, Palloix A, Simon V, Valière S, Grognard F, Fabre F. Estimating virus effective population size and selection without neutral markers. PLoS Pathog 2017; 13:e1006702. [PMID: 29155894 PMCID: PMC5720836 DOI: 10.1371/journal.ppat.1006702] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 12/07/2017] [Accepted: 10/19/2017] [Indexed: 12/04/2022] Open
Abstract
By combining high-throughput sequencing (HTS) with experimental evolution, we can observe the within-host dynamics of pathogen variants of biomedical or ecological interest. We studied the evolutionary dynamics of five variants of Potato virus Y (PVY) in 15 doubled-haploid lines of pepper. All plants were inoculated with the same mixture of virus variants and variant frequencies were determined by HTS in eight plants of each pepper line at each of six sampling dates. We developed a method for estimating the intensities of selection and genetic drift in a multi-allelic Wright-Fisher model, applicable whether these forces are strong or weak, and in the absence of neutral markers. This method requires variant frequency determination at several time points, in independent hosts. The parameters are the selection coefficients for each PVY variant and four effective population sizes Ne at different time-points of the experiment. Numerical simulations of asexual haploid Wright-Fisher populations subjected to contrasting genetic drift (Ne ∈ [10, 2000]) and selection (|s| ∈ [0, 0.15]) regimes were used to validate the method proposed. The experiment in closely related pepper host genotypes revealed that viruses experienced a considerable diversity of selection and genetic drift regimes. The resulting variant dynamics were accurately described by Wright-Fisher models. The fitness ranks of the variants were almost identical between host genotypes. By contrast, the dynamics of Ne were highly variable, although a bottleneck was often identified during the systemic movement of the virus. We demonstrated that, for a fixed initial PVY population, virus effective population size is a heritable trait in plants. These findings pave the way for the breeding of plant varieties exposing viruses to stronger genetic drift, thereby slowing virus adaptation. A growing number of experimental evolution studies are using an “evolve-and-resequence” approach to observe the within-host dynamics of pathogen variants of biomedical or ecological interest. The resulting data are particularly appropriate for studying the effects of evolutionary forces, such as selection and genetic drift, on the emergence of new pathogen variants. However, it remains challenging to unravel the effects of selection and genetic drift in the absence of neutral markers, a situation frequently encountered for microbes, such as viruses, due to their small constrained genomes. Using such an approach on a plant virus, we observed that the same set of virus variants displayed highly diverse dynamics in closely related plant genotypes. We developed and validated a method that does not require neutral markers, for estimating selection coefficients and effective population sizes from these experimental evolution data. We found that the viruses experienced considerable diversity in genetic drift regimes, depending on host genotype. Importantly, genetic drift experienced by virus populations was shown to be a heritable plant trait. These findings pave the way for the breeding of plant varieties exposing viruses to strong genetic drift, thereby slowing virus adaptation.
Collapse
Affiliation(s)
- Elsa Rousseau
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
- Pathologie Végétale, INRA, 84140 Montfavet, France
- * E-mail: (ER); (FF)
| | - Benoît Moury
- Pathologie Végétale, INRA, 84140 Montfavet, France
| | - Ludovic Mailleret
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
- Université Côte d’Azur, INRA, CNRS, ISA, Sophia Antipolis, France
| | | | | | - Vincent Simon
- Pathologie Végétale, INRA, 84140 Montfavet, France
- UMR BFP, INRA, Villenave d’Ornon, France
| | - Sophie Valière
- GeT-PlaGe, INRA, Genotoul, Castanet-tolosan, France
- UAR DEPT GA, INRA, Castanet-Tolosan, France
| | - Frédéric Grognard
- Université Côte d’Azur, Inria, INRA, CNRS, UPMC Univ Paris 06, Biocore team, Sophia Antipolis, France
| | - Frédéric Fabre
- UMR SAVE, INRA, Villenave d’Ornon, France
- * E-mail: (ER); (FF)
| |
Collapse
|
48
|
Illingworth CJR, Roy S, Beale MA, Tutill H, Williams R, Breuer J. On the effective depth of viral sequence data. Virus Evol 2017; 3:vex030. [PMID: 29250429 PMCID: PMC5724399 DOI: 10.1093/ve/vex030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Genome sequence data are of great value in describing evolutionary processes in viral populations. However, in such studies, the extent to which data accurately describes the viral population is a matter of importance. Multiple factors may influence the accuracy of a dataset, including the quantity and nature of the sample collected, and the subsequent steps in viral processing. To investigate this phenomenon, we sequenced replica datasets spanning a range of viruses, and in which the point at which samples were split was different in each case, from a dataset in which independent samples were collected from a single patient to another in which all processing steps up to sequencing were applied to a single sample before splitting the sample and sequencing each replicate. We conclude that neither a high read depth nor a high template number in a sample guarantee the precision of a dataset. Measures of consistency calculated from within a single biological sample may also be insufficient; distortion of the composition of a population by the experimental procedure or genuine within-host diversity between samples may each affect the results. Where it is possible, data from replicate samples should be collected to validate the consistency of short-read sequence data.
Collapse
Affiliation(s)
- Christopher J R Illingworth
- Department of Genetics, University of Cambridge, Cambridge, UK.,Department of Applied Maths and Theoretical Physics, Centre for Mathematical Sciences, University of Cambridge, Cambridge, UK
| | - Sunando Roy
- Division of Infection and Immunity, University College London, London, UK
| | | | - Helena Tutill
- Division of Infection and Immunity, University College London, London, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| |
Collapse
|
49
|
Arenas M, Araujo NM, Branco C, Castelhano N, Castro-Nallar E, Pérez-Losada M. Mutation and recombination in pathogen evolution: Relevance, methods and controversies. INFECTION GENETICS AND EVOLUTION 2017; 63:295-306. [PMID: 28951202 DOI: 10.1016/j.meegid.2017.09.029] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 02/06/2023]
Abstract
Mutation and recombination drive the evolution of most pathogens by generating the genetic variants upon which selection operates. Those variants can, for example, confer resistance to host immune systems and drug therapies or lead to epidemic outbreaks. Given their importance, diverse evolutionary studies have investigated the abundance and consequences of mutation and recombination in pathogen populations. However, some controversies persist regarding the contribution of each evolutionary force to the development of particular phenotypic observations (e.g., drug resistance). In this study, we revise the importance of mutation and recombination in the evolution of pathogens at both intra-host and inter-host levels. We also describe state-of-the-art analytical methodologies to detect and quantify these two evolutionary forces, including biases that are often ignored in evolutionary studies. Finally, we present some of our former studies involving pathogenic taxa where mutation and recombination played crucial roles in the recovery of pathogenic fitness, the generation of interspecific genetic diversity, or the design of centralized vaccines. This review also illustrates several common controversies and pitfalls in the analysis and in the evaluation and interpretation of mutation and recombination outcomes.
Collapse
Affiliation(s)
- Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain; Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Natalia M Araujo
- Laboratory of Molecular Virology, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil.
| | - Catarina Branco
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Nadine Castelhano
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, Porto, Portugal; Institute of Molecular Pathology and Immunology of the University of Porto (IPATIMUP), Porto, Portugal.
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago, Chile.
| | - Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, Washington, DC, United States; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal.
| |
Collapse
|
50
|
Time-Sampled Population Sequencing Reveals the Interplay of Selection and Genetic Drift in Experimental Evolution of Potato Virus Y. J Virol 2017; 91:JVI.00690-17. [PMID: 28592544 PMCID: PMC5533922 DOI: 10.1128/jvi.00690-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 05/28/2017] [Indexed: 11/20/2022] Open
Abstract
RNA viruses are one of the fastest-evolving biological entities. Within their hosts, they exist as genetically diverse populations (i.e., viral mutant swarms), which are sculpted by different evolutionary mechanisms, such as mutation, natural selection, and genetic drift, and also the interactions between genetic variants within the mutant swarms. To elucidate the mechanisms that modulate the population diversity of an important plant-pathogenic virus, we performed evolution experiments with Potato virus Y (PVY) in potato genotypes that differ in their defense response against the virus. Using deep sequencing of small RNAs, we followed the temporal dynamics of standing and newly generated variations in the evolving viral lineages. A time-sampled approach allowed us to (i) reconstruct theoretical haplotypes in the starting population by using clustering of single nucleotide polymorphisms' trajectories and (ii) use quantitative population genetics approaches to estimate the contribution of selection and genetic drift, and their interplay, to the evolution of the virus. We detected imprints of strong selective sweeps and narrow genetic bottlenecks, followed by the shift in frequency of selected haplotypes. Comparison of patterns of viral evolution in differently susceptible host genotypes indicated possible diversifying evolution of PVY in the less-susceptible host (efficient in the accumulation of salicylic acid).IMPORTANCE High diversity of within-host populations of RNA viruses is an important aspect of their biology, since they represent a reservoir of genetic variants, which can enable quick adaptation of viruses to a changing environment. This study focuses on an important plant virus, Potato virus Y, and describes, at high resolution, temporal changes in the structure of viral populations within different potato genotypes. A novel and easy-to-implement computational approach was established to cluster single nucleotide polymorphisms into viral haplotypes from very short sequencing reads. During the experiment, a shift in the frequency of selected viral haplotypes was observed after a narrow genetic bottleneck, indicating an important role of the genetic drift in the evolution of the virus. On the other hand, a possible case of diversifying selection of the virus was observed in less susceptible host genotypes.
Collapse
|