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Wagner A. Genotype sampling for deep-learning assisted experimental mapping of a combinatorially complete fitness landscape. Bioinformatics 2024; 40:btae317. [PMID: 38745436 PMCID: PMC11132821 DOI: 10.1093/bioinformatics/btae317] [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: 01/22/2024] [Revised: 03/21/2024] [Accepted: 05/14/2024] [Indexed: 05/16/2024] Open
Abstract
MOTIVATION Experimental characterization of fitness landscapes, which map genotypes onto fitness, is important for both evolutionary biology and protein engineering. It faces a fundamental obstacle in the astronomical number of genotypes whose fitness needs to be measured for any one protein. Deep learning may help to predict the fitness of many genotypes from a smaller neural network training sample of genotypes with experimentally measured fitness. Here I use a recently published experimentally mapped fitness landscape of more than 260 000 protein genotypes to ask how such sampling is best performed. RESULTS I show that multilayer perceptrons, recurrent neural networks, convolutional networks, and transformers, can explain more than 90% of fitness variance in the data. In addition, 90% of this performance is reached with a training sample comprising merely ≈103 sequences. Generalization to unseen test data is best when training data is sampled randomly and uniformly, or sampled to minimize the number of synonymous sequences. In contrast, sampling to maximize sequence diversity or codon usage bias reduces performance substantially. These observations hold for more than one network architecture. Simple sampling strategies may perform best when training deep learning neural networks to map fitness landscapes from experimental data. AVAILABILITY AND IMPLEMENTATION The fitness landscape data analyzed here is publicly available as described previously (Papkou et al. 2023). All code used to analyze this landscape is publicly available at https://github.com/andreas-wagner-uzh/fitness_landscape_sampling.
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Affiliation(s)
- Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode,1015 Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, 87501 NM, United States
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2
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Nkurikiyimfura O, Waheed A, Fang H, Yuan X, Chen L, Wang YP, Lu G, Zhan J, Yang L. Fitness difference between two synonymous mutations of Phytophthora infestans ATP6 gene. BMC Ecol Evol 2024; 24:36. [PMID: 38494489 PMCID: PMC10946160 DOI: 10.1186/s12862-024-02223-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/11/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND Sequence variation produced by mutation provides the ultimate source of natural selection for species adaptation. Unlike nonsynonymous mutation, synonymous mutations are generally considered to be selectively neutral but accumulating evidence suggests they also contribute to species adaptation by regulating the flow of genetic information and the development of functional traits. In this study, we analysed sequence characteristics of ATP6, a housekeeping gene from 139 Phytophthora infestans isolates, and compared the fitness components including metabolic rate, temperature sensitivity, aggressiveness, and fungicide tolerance among synonymous mutations. RESULTS We found that the housekeeping gene exhibited low genetic variation and was represented by two major synonymous mutants at similar frequency (0.496 and 0.468, respectively). The two synonymous mutants were generated by a single nucleotide substitution but differed significantly in fitness as well as temperature-mediated spatial distribution and expression. The synonymous mutant ending in AT was more common in cold regions and was more expressed at lower experimental temperature than the synonymous mutant ending in GC and vice versa. CONCLUSION Our results are consistent with the argument that synonymous mutations can modulate the adaptive evolution of species including pathogens and have important implications for sustainable disease management, especially under climate change.
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Affiliation(s)
- Oswald Nkurikiyimfura
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Abdul Waheed
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Hanmei Fang
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Xiaoxian Yuan
- Institute of Plant Virology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Lixia Chen
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Yan-Ping Wang
- College of Chemistry and Life Sciences, Sichuan Provincial Key Laboratory for Development and Utilization of Characteristic Horticultural Biological Resources, Chengdu Normal University, Chengdu, Sichuan, 611130, China
| | - Guodong Lu
- Department of Plant Pathology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, 75007, Sweden.
| | - Lina Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
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3
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Hurabielle C, LaFlam TN, Gearing M, Ye CJ. Functional genomics in inborn errors of immunity. Immunol Rev 2024; 322:53-70. [PMID: 38329267 PMCID: PMC10950534 DOI: 10.1111/imr.13309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Inborn errors of immunity (IEI) comprise a diverse spectrum of 485 disorders as recognized by the International Union of Immunological Societies Committee on Inborn Error of Immunity in 2022. While IEI are monogenic by definition, they illuminate various pathways involved in the pathogenesis of polygenic immune dysregulation as in autoimmune or autoinflammatory syndromes, or in more common infectious diseases that may not have a significant genetic basis. Rapid improvement in genomic technologies has been the main driver of the accelerated rate of discovery of IEI and has led to the development of innovative treatment strategies. In this review, we will explore various facets of IEI, delving into the distinctions between PIDD and PIRD. We will examine how Mendelian inheritance patterns contribute to these disorders and discuss advancements in functional genomics that aid in characterizing new IEI. Additionally, we will explore how emerging genomic tools help to characterize new IEI as well as how they are paving the way for innovative treatment approaches for managing and potentially curing these complex immune conditions.
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Affiliation(s)
- Charlotte Hurabielle
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Taylor N LaFlam
- Division of Pediatric Rheumatology, Department of Pediatrics, UCSF, San Francisco, California, USA
| | - Melissa Gearing
- Division of Rheumatology, Department of Medicine, UCSF, San Francisco, California, USA
| | - Chun Jimmie Ye
- Institute for Human Genetics, UCSF, San Francisco, California, USA
- Institute of Computational Health Sciences, UCSF, San Francisco, California, USA
- Gladstone Genomic Immunology Institute, San Francisco, California, USA
- Parker Institute for Cancer Immunotherapy, UCSF, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California, USA
- Department of Microbiology and Immunology, UCSF, San Francisco, California, USA
- Department of Bioengineering and Therapeutic Sciences, UCSF, San Francisco, California, USA
- Arc Institute, Palo Alto, California, USA
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4
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Giacoletto CJ, Rotter JI, Grody WW, Schiller MR. Synonymous Variants of Uncertain Silence. Int J Mol Sci 2023; 24:10556. [PMID: 37445732 DOI: 10.3390/ijms241310556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/12/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
Synonymous variants, traditionally regarded as silent mutations due to their lack of impact on protein sequence, structure and function, have been the subject of increasing scrutiny. This commentary explores the emerging evidence challenging the notion of synonymous variants as functionally inert. Analysis of the activity of 70 synonymous variants in the HIV Tat transcription factor revealed that 50% of the variants exhibited significant deviations from wild-type activity. Our analysis supports previous work and raises important questions about the broader impact of non-silent synonymous variants in human genes. Considering the potential functional implications, the authors propose classifying such variants as "synonymous variants of uncertain silence" (sVUS), highlighting the need for cautious interpretation and further investigations in clinical and genetic testing settings.
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Affiliation(s)
- Christopher J Giacoletto
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
- Heligenics Inc., 10530 Discovery Drive, Las Vegas, NV 89135, USA
- School of Life Sciences, University of Nevada Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
| | - Jerome I Rotter
- Heligenics Inc., 10530 Discovery Drive, Las Vegas, NV 89135, USA
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Wayne W Grody
- Department of Pathology and Laboratory Medicine, University of California Los Angeles School of Medicine, 10833 Le Conte Ave., 705, Los Angeles, CA 90095, USA
- Department of Pediatrics, University of California Los Angeles School of Medicine, 10833 Le Conte Ave., Los Angeles, CA 90095, USA
- Department of Human Genetics, University of California Los Angeles School of Medicine, 10833 Le Conte Ave., Los Angeles, CA 90095, USA
| | - Martin R Schiller
- Nevada Institute of Personalized Medicine, University of Nevada Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
- Heligenics Inc., 10530 Discovery Drive, Las Vegas, NV 89135, USA
- School of Life Sciences, University of Nevada Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154, USA
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5
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Lin BC, Katneni U, Jankowska KI, Meyer D, Kimchi-Sarfaty C. In silico methods for predicting functional synonymous variants. Genome Biol 2023; 24:126. [PMID: 37217943 PMCID: PMC10204308 DOI: 10.1186/s13059-023-02966-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/10/2023] [Indexed: 05/24/2023] Open
Abstract
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous SNVs are previously considered to be "silent," but mounting evidence has revealed that these variants can cause RNA and protein changes and are implicated in over 85 human diseases and cancers. Recent improvements in computational platforms have led to the development of numerous machine-learning tools, which can be used to advance synonymous SNV research. In this review, we discuss tools that should be used to investigate synonymous variants. We provide supportive examples from seminal studies that demonstrate how these tools have driven new discoveries of functional synonymous SNVs.
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Affiliation(s)
- Brian C Lin
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Upendra Katneni
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Katarzyna I Jankowska
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Douglas Meyer
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA
| | - Chava Kimchi-Sarfaty
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics CMC, Office of Therapeutic Products, Center for Biologics Evaluation and Research, US FDA, Silver Spring, MD, USA.
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6
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Caspi I, Meir M, Ben Nun N, Abu Rass R, Yakhini U, Stern A, Ram Y. Mutation rate, selection, and epistasis inferred from RNA virus haplotypes via neural posterior estimation. Virus Evol 2023; 9:vead033. [PMID: 37305706 PMCID: PMC10256221 DOI: 10.1093/ve/vead033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/30/2023] [Accepted: 05/16/2023] [Indexed: 06/13/2023] Open
Abstract
RNA viruses are particularly notorious for their high levels of genetic diversity, which is generated through the forces of mutation and natural selection. However, disentangling these two forces is a considerable challenge, and this may lead to widely divergent estimates of viral mutation rates, as well as difficulties in inferring the fitness effects of mutations. Here, we develop, test, and apply an approach aimed at inferring the mutation rate and key parameters that govern natural selection, from haplotype sequences covering full-length genomes of an evolving virus population. Our approach employs neural posterior estimation, a computational technique that applies simulation-based inference with neural networks to jointly infer multiple model parameters. We first tested our approach on synthetic data simulated using different mutation rates and selection parameters while accounting for sequencing errors. Reassuringly, the inferred parameter estimates were accurate and unbiased. We then applied our approach to haplotype sequencing data from a serial passaging experiment with the MS2 bacteriophage, a virus that parasites Escherichia coli. We estimated that the mutation rate of this phage is around 0.2 mutations per genome per replication cycle (95% highest density interval: 0.051-0.56). We validated this finding with two different approaches based on single-locus models that gave similar estimates but with much broader posterior distributions. Furthermore, we found evidence for reciprocal sign epistasis between four strongly beneficial mutations that all reside in an RNA stem loop that controls the expression of the viral lysis protein, responsible for lysing host cells and viral egress. We surmise that there is a fine balance between over- and underexpression of lysis that leads to this pattern of epistasis. To recap, we have developed an approach for joint inference of the mutation rate and selection parameters from full haplotype data with sequencing errors and used it to reveal features governing MS2 evolution.
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Affiliation(s)
- Itamar Caspi
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Moran Meir
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | - Nadav Ben Nun
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | | | - Uri Yakhini
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
- Edmond J. Safra Center for Bioinformatics, Tel Aviv University, P.O. Box 39040, Tel Aviv 6997801, Israel
| | | | - Yoav Ram
- *Corresponding author: E-mail: ;
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7
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Guo J, He Y, Wang X, Merits A, Wang M, Jia R, Zhu D, Liu M, Zhao X, Yang Q, Wu Y, Zhang S, Huang J, Mao S, Ou X, Gao Q, Sun D, Tian B, Cheng A, Chen S. Attenuation of Avian Flavivirus by Rewiring the Leucine and Serine Codons of Its E-NS1 Protein toward Stop Mutation To Redirect Virus Evolution. Microbiol Spectr 2023; 11:e0292122. [PMID: 36625643 PMCID: PMC9927255 DOI: 10.1128/spectrum.02921-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Recently, a new strategy for attenuating RNA viruses by redirecting their evolution in sequence space was confirmed for Enterovirus and Influenza viruses. Using avian flavivirus as a model, the 69 serine and 53 leucine codons on the E-NS1 genes were modified to change evolutionary direction of the viral sequence space. This means that all codons encoding serine or leucine residues were substituted with codons that are only one base different from the three stop codons, resulting in the initial position of the virus genome in sequence space being closer to the detrimental areas to achieve attenuation by reducing viral adaptability. The growth curve and plaque size of CQW1-one-to-stop (CQW1-OTS) were similar to those of CQW1-wild type (CQW1-WT) in vitro, but attenuated proliferation was detected when treated with a mutagenic reagent (ribavirin). However, comparably high CQW1-OTS and CQW1-WT lethality rates were detected in 9-day-old duck embryos and 5-day-old ducklings, suggesting that this strategy works but with limitations. With that in mind, homologous hosts in nonsensitive age (25-day-old ducks) and heterologous hosts (3-week-old Kunming mice) were employed to investigate if CQW1-OTS was attenuated under host selection pressure. Minimal attenuation of CQW1-OTS in elder ducks and apparent attenuation in mice were reported, providing reduced viral titers, mild clinical signs, and lower specific infectivity. Collectively, we experimentally demonstrate that the attenuation strategy of redirecting virus evolution in sequence space works for flavivirus. Redirection of the virus is attenuated only under some outside pressure, such as heterologous hosts or antiviral drugs treatment, limiting its usage in flaviviruses. IMPORTANCE Flaviviruses are medically important arboviruses that threaten public health, but no approved treatments are currently available. Vaccines prevent flavivirus infection. We employed duck Tembusu virus (TMUV), a mosquito-borne flavivirus, to evaluate virus redirection. TMUV is native to birds and could infect mice by intracerebral injection, making it an experimental animal model to study flavivirus characteristics in vivo. The 69 serine and 53 leucine codons on the E-NS1 proteins of CQW1 were synonymously substituted to change evolutionary direction of the virus in sequence space. In vitro mutagen reagent treatment suppressed CQW1-OTS viral multiplication, but in vivo attenuation depended on host selective pressure. CQW1-OTS viral attenuation was observed in older ducks but not sensitive ducklings; considerable attenuation was also observed in heterogenous host (mice), which provides more selective pressure on viruses. Collectively, these data indicated that there are very important preconditions for application of evaluating whether this strategy shows application prospects in novel flavivirus vaccine development.
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Affiliation(s)
- Jiaqi Guo
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu He
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaoli Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Andres Merits
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Mingshu Wang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Renyong Jia
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dekang Zhu
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mafeng Liu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinxin Zhao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiao Yang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ying Wu
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shaqiu Zhang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Juan Huang
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Sai Mao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xumin Ou
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qun Gao
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Di Sun
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bin Tian
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Anchun Cheng
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shun Chen
- Institute of Preventive Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Research Center of Avian Disease, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu, Sichuan, China
- Key Laboratory of Animal Disease and Human Health of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, China
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8
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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9
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Makau DN, Lycett S, Michalska-Smith M, Paploski IAD, Cheeran MCJ, Craft ME, Kao RR, Schroeder DC, Doeschl-Wilson A, VanderWaal K. Ecological and evolutionary dynamics of multi-strain RNA viruses. Nat Ecol Evol 2022; 6:1414-1422. [PMID: 36138206 DOI: 10.1038/s41559-022-01860-6] [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: 12/21/2021] [Accepted: 07/28/2022] [Indexed: 11/09/2022]
Abstract
Potential interactions among co-circulating viral strains in host populations are often overlooked in the study of virus transmission. However, these interactions probably shape transmission dynamics by influencing host immune responses or altering the relative fitness among co-circulating strains. In this Review, we describe multi-strain dynamics from ecological and evolutionary perspectives, outline scales in which multi-strain dynamics occur and summarize important immunological, phylogenetic and mathematical modelling approaches used to quantify interactions among strains. We also discuss how host-pathogen interactions influence the co-circulation of pathogens. Finally, we highlight outstanding questions and knowledge gaps in the current theory and study of ecological and evolutionary dynamics of multi-strain viruses.
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Affiliation(s)
- Dennis N Makau
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | | | | | - Igor A D Paploski
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Maxim C-J Cheeran
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
| | - Meggan E Craft
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, MN, USA
| | - Rowland R Kao
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Declan C Schroeder
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA
- School of Biological Sciences, University of Reading, Reading, UK
| | | | - Kimberly VanderWaal
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, MN, USA.
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10
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Chandra S, Gupta K, Khare S, Kohli P, Asok A, Mohan SV, Gowda H, Varadarajan R. The High Mutational Sensitivity of ccdA Antitoxin Is Linked to Codon Optimality. Mol Biol Evol 2022; 39:6693774. [PMID: 36069948 PMCID: PMC9555053 DOI: 10.1093/molbev/msac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Deep mutational scanning studies suggest that synonymous mutations are typically silent and that most exposed, nonactive-site residues are tolerant to mutations. Here, we show that the ccdA antitoxin component of the Escherichia coli ccdAB toxin-antitoxin system is unusually sensitive to mutations when studied in the operonic context. A large fraction (∼80%) of single-codon mutations, including many synonymous mutations in the ccdA gene shows inactive phenotype, but they retain native-like binding affinity towards cognate toxin, CcdB. Therefore, the observed phenotypic effects are largely not due to alterations in protein structure/stability, consistent with a large region of CcdA being intrinsically disordered. E. coli codon preference and strength of ribosome-binding associated with translation of downstream ccdB gene are found to be major contributors of the observed ccdA mutant phenotypes. In select cases, proteomics studies reveal altered ratios of CcdA:CcdB protein levels in vivo, suggesting that the ccdA mutations likely alter relative translation efficiencies of the two genes in the operon. We extend these results by studying single-site synonymous mutations that lead to loss of function phenotypes in the relBE operon upon introduction of rarer codons. Thus, in their operonic context, genes are likely to be more sensitive to both synonymous and nonsynonymous point mutations than inferred previously.
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Affiliation(s)
| | | | - Shruti Khare
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Pehu Kohli
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Aparna Asok
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | | | - Harsha Gowda
- Institute of Bioinformatics, Bangalore 560100, India
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11
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Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Lee SS. Continent-wide evolutionary trends of emerging SARS-CoV-2 variants: dynamic profiles from Alpha to Omicron. GeroScience 2022; 44:2371-2392. [PMID: 35831773 PMCID: PMC9281186 DOI: 10.1007/s11357-022-00619-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 06/27/2022] [Indexed: 01/06/2023] Open
Abstract
The ongoing SARS-CoV-2 evolution process has generated several variants due to its continuous mutations, making pandemics more critical. The present study illustrates SARS-CoV-2 evolution and its emerging mutations in five directions. First, the significant mutations in the genome and S-glycoprotein were analyzed in different variants. Three linear models were developed with the regression line to depict the mutational load for S-glycoprotein, total genome excluding S-glycoprotein, and whole genome. Second, the continent-wide evolution of SARS-CoV-2 and its variants with their clades and divergence were evaluated. It showed the region-wise evolution of the SARS-CoV-2 variants and their clustering event. The major clades for each variant were identified. One example is clade 21K, a major clade of the Omicron variant. Third, lineage dynamics and comparison between SARS-CoV-2 lineages across different countries are also illustrated, demonstrating dominant variants in various countries over time. Fourth, gene-wise mutation patterns and genetic variability of SARS-CoV-2 variants across various countries are illustrated. High mutation patterns were found in the ORF10, ORF6, S, and low mutation pattern E genes. Finally, emerging AA point mutations (T478K, L452R, N501Y, S477N, E484A, Q498R, and Y505H), their frequencies, and country-wise occurrence were identified, and the highest event of two mutations (T478K and L452R) was observed.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal 700126 India
| | - Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore, 756020 Odisha India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
| | - Kuldeep Dhama
- Division of Pathology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122 Uttar Pradesh India
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252 Gangwon-do Republic of Korea
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12
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Retel C, Kowallik V, Becks L, Feulner PGD. Strong Selection and High Mutation Supply Characterize Experimental Chlorovirus Evolution. Virus Evol 2022; 8:veac003. [PMID: 35169490 PMCID: PMC8838748 DOI: 10.1093/ve/veac003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/24/2022] Open
Abstract
Characterizing how viruses evolve expands our understanding of the underlying fundamental processes, such as mutation, selection and drift. One group of viruses whose evolution has not yet been extensively studied is the Phycodnaviridae, a globally abundant family of aquatic large double-stranded (ds) DNA viruses. Here we studied the evolutionary change of Paramecium bursaria chlorella virus 1 during experimental coevolution with its algal host. We used pooled genome sequencing of six independently evolved populations to characterize genomic change over five time points. Across six experimental replicates involving either strong or weak demographic fluctuations, we found single nucleotide polymorphisms (SNPs) at sixty-seven sites. The occurrence of genetic variants was highly repeatable, with just two of the SNPs found in only a single experimental replicate. Three genes A122/123R, A140/145R and A540L showed an excess of variable sites, providing new information about potential targets of selection during Chlorella–Chlorovirus coevolution. Our data indicated that the studied populations were not mutation-limited and experienced strong positive selection. Our investigation highlighted relevant processes governing the evolution of aquatic large dsDNA viruses, which ultimately contributes to a better understanding of the functioning of natural aquatic ecosystems.
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Affiliation(s)
- Cas Retel
- Department of Fish Ecology and Evolution, Center for Ecology, Evolution and Bio-geochemistry, EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Seestrasse 79, Kastanienbaum 6047, Switzerland
- Division of Aquatic Ecology, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
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13
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Curlin JZ, Schmitt K, Remling-Mulder L, Moriarty R, Baczenas JJ, Goff K, O’Connor S, Stenglein M, Marx PA, Akkina R. In vivo infection dynamics and human adaptive changes of SIVsm-derived viral siblings SIVmac239, SIV B670 and SIVhu in humanized mice as a paralog of HIV-2 genesis. FRONTIERS IN VIROLOGY (LAUSANNE, SWITZERLAND) 2021; 1:813606. [PMID: 37168442 PMCID: PMC10168645 DOI: 10.3389/fviro.2021.813606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Simian immunodeficiency virus native to sooty mangabeys (SIVsm) is believed to have given rise to HIV-2 through cross-species transmission and evolution in the human. SIVmac239 and SIVB670, pathogenic to macaques, and SIVhu, isolated from an accidental human infection, also have origins in SIVsm. With their common ancestral lineage as that of HIV-2 from the progenitor SIVsm, but with different passage history in different hosts, they provide a unique opportunity to evaluate cross-species transmission to a new host and their adaptation/evolution both in terms of potential genetic and phenotypic changes. Using humanized mice with a transplanted human system, we evaluated in vivo replication kinetics, CD4+ T cell dynamics and genetic adaptive changes during serial passage with a goal to understand their evolution under human selective immune pressure. All the three viruses readily infected hu-mice causing chronic viremia. While SIVmac and SIVB670 caused CD4+ T cell depletion during sequential passaging, SIVhu with a deletion in nef gene was found to be less pathogenic. Deep sequencing of the genomes of these viruses isolated at different times revealed numerous adaptive mutations of significance that increased in frequency during sequential passages. The ability of these viruses to infect and replicate in humanized mice provides a new small animal model to study SIVs in vivo in addition to more expensive macaques. Since SIVmac and related viruses have been indispensable in many areas of HIV pathogenesis, therapeutics and cure research, availability of this small animal hu-mouse model that is susceptible to both SIV and HIV viruses is likely to open novel avenues of investigation for comparative studies using the same host.
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Affiliation(s)
- James Z. Curlin
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
- Antiviral Discovery, Evaluation and Application Research (ADEAR) Training Program, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kimberly Schmitt
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Leila Remling-Mulder
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Ryan Moriarty
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - John J. Baczenas
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Kelly Goff
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
| | - Shelby O’Connor
- Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Mark Stenglein
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Preston A. Marx
- Department of Tropical Medicine, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA, USA
- Tulane National Primate Research Center, Covington, LA, USA
| | - Ramesh Akkina
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA
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14
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Deigin Y, Segreto R. The genetic structure of SARS-CoV-2 is consistent with both natural or laboratory origin: Response to Tyshkovskiy and Panchin (10.1002/bies.202000325). Bioessays 2021; 43:e2100137. [PMID: 34327738 DOI: 10.1002/bies.202100137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/06/2021] [Accepted: 07/09/2021] [Indexed: 11/10/2022]
Abstract
Tyshkovskiy and Panchin have recently published a commentary on our paper in which they outline several "points of disagreement with the Segreto/Deigin hypothesis." As our paper is titled "The genetic structure of SARS-CoV-2 does not rule out a laboratory origin," points of disagreement should provide evidence that rules out a laboratory origin. However, Tyshkovskiy and Panchin provide no such evidence and instead attempt to criticize our arguments that highlight aspects of SARS-CoV-2 that could be consistent with the lab leak hypothesis. Strikingly, Tyshkovskiy and Panchin's main point of criticism is based on a false premise that we have claimed RaTG13 to be a direct progenitor of SARS-CoV-2, and their other points of criticism are either not valid, based on flawed mathematical analysis, or are unrelated to our hypotheses. Thus, the genetic structure of SARS-CoV-2 remains consistent with both natural or laboratory origin, which means that both the zoonotic and the lab leak hypothesis need to be investigated equally thoroughly.
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Affiliation(s)
- Yuri Deigin
- Youthereum Genetics Inc., Toronto, Ontario, Canada
| | - Rossana Segreto
- Department of Microbiology, University of Innsbruck, Innsbruck, Tyrol, Austria
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15
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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: 34] [Impact Index Per Article: 11.3] [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.
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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
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16
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Computational based design and tracking of synthetic variants of Porcine circovirus reveal relations between silent genomic information and viral fitness. Sci Rep 2021; 11:10620. [PMID: 34012100 PMCID: PMC8134455 DOI: 10.1038/s41598-021-89918-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/29/2021] [Indexed: 12/17/2022] Open
Abstract
Viral genomes not only code the protein content, but also include silent, overlapping codes which are important to the regulation of the viral life cycle and affect its evolution. Due to the high density of these codes, their non-modular nature and the complex intracellular processes they encode, the ability of current approaches to decipher them is very limited. We describe the first computational-experimental pipeline for studying the effects of viral silent and non-silent information on its fitness. The pipeline was implemented to study the Porcine Circovirus type 2 (PCV2), the shortest known eukaryotic virus, and includes the following steps: (1) Based on the analyses of 2100 variants of PCV, suspected silent codes were inferred. (2) Five hundred variants of the PCV2 were designed to include various ‘smart’ silent mutations. (3) Using state of the art synthetic biology approaches, the genomes of these five hundred variants were generated. (4) Competition experiments between the variants were performed in Porcine kidney-15 (PK15) cell-lines. (5) The variant titers were analyzed based on novel next-generation sequencing (NGS) experiments. (6) The features related to the titer of the variants were inferred and their analyses enabled detection of various novel silent functional sequence and structural motifs. Furthermore, we demonstrate that 50 of the silent variants exhibit higher fitness than the wildtype in the analyzed conditions.
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17
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De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. Mutation Rates and Selection on Synonymous Mutations in SARS-CoV-2. Genome Biol Evol 2021; 13:evab087. [PMID: 33895815 PMCID: PMC8135539 DOI: 10.1093/gbe/evab087] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2021] [Indexed: 12/23/2022] Open
Abstract
The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G →U and C →U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. Although previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
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Affiliation(s)
- Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, United Kingdom
| | - Conor R Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, United Kingdom
- Department of Genetics, University of Cambridge, United Kingdom
| | - Yatish Turakhia
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, California, USA
- Genomics Institute, University of California, Santa Cruz, California, USA
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridgeshire, United Kingdom
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18
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Wisotsky SR, Kosakovsky Pond SL, Shank SD, Muse SV. Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril. Mol Biol Evol 2021; 37:2430-2439. [PMID: 32068869 PMCID: PMC7403620 DOI: 10.1093/molbev/msaa037] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Most molecular evolutionary studies of natural selection maintain the decades-old assumption that synonymous substitution rate variation (SRV) across sites within genes occurs at levels that are either nonexistent or negligible. However, numerous studies challenge this assumption from a biological perspective and show that SRV is comparable in magnitude to that of nonsynonymous substitution rate variation. We evaluated the impact of this assumption on methods for inferring selection at the molecular level by incorporating SRV into an existing method (BUSTED) for detecting signatures of episodic diversifying selection in genes. Using simulated data we found that failing to account for even moderate levels of SRV in selection testing is likely to produce intolerably high false positive rates. To evaluate the effect of the SRV assumption on actual inferences we compared results of tests with and without the assumption in an empirical analysis of over 13,000 Euteleostomi (bony vertebrate) gene alignments from the Selectome database. This exercise reveals that close to 50% of positive results (i.e., evidence for selection) in empirical analyses disappear when SRV is modeled as part of the statistical analysis and are thus candidates for being false positives. The results from this work add to a growing literature establishing that tests of selection are much more sensitive to certain model assumptions than previously believed.
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Affiliation(s)
- Sadie R Wisotsky
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC.,Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | | | - Stephen D Shank
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Spencer V Muse
- Bioinformatics Research Center, North Carolina State University, Raleigh, NC.,Department of Statistics, North Carolina State University, Raleigh, NC
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19
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Favipiravir antiviral efficacy against SARS-CoV-2 in a hamster model. Nat Commun 2021; 12:1735. [PMID: 33741945 PMCID: PMC7979801 DOI: 10.1038/s41467-021-21992-w] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 01/28/2021] [Indexed: 12/24/2022] Open
Abstract
Despite no or limited pre-clinical evidence, repurposed drugs are massively evaluated in clinical trials to palliate the lack of antiviral molecules against SARS-CoV-2. Here we use a Syrian hamster model to assess the antiviral efficacy of favipiravir, understand its mechanism of action and determine its pharmacokinetics. When treatment is initiated before or simultaneously to infection, favipiravir has a strong dose effect, leading to reduction of infectious titers in lungs and clinical alleviation of the disease. Antiviral effect of favipiravir correlates with incorporation of a large number of mutations into viral genomes and decrease of viral infectivity. Antiviral efficacy is achieved with plasma drug exposure comparable with those previously found during human clinical trials. Notably, the highest dose of favipiravir tested is associated with signs of toxicity in animals. Thereby, pharmacokinetic and tolerance studies are required to determine whether similar effects can be safely achieved in humans.
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20
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Genome Number and Size Polymorphism in Zika Virus Infectious Units. J Virol 2021; 95:JVI.00787-20. [PMID: 33328311 PMCID: PMC8094933 DOI: 10.1128/jvi.00787-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 12/04/2020] [Indexed: 12/18/2022] Open
Abstract
The arthropod-borne Zika virus (ZIKV) infects humans and can cause severe neurological sequelae, particularly in fetuses infected in utero. How this virus has been able to spread across vast geological ranges and evolve in new host populations is not yet understood. Zika virus (ZIKV; Flaviviridae, Flavivirus) is an arthropod-borne infection that can result in severe outcomes, particularly in fetuses infected in utero. It has been assumed that infection by ZIKV, as well as other viruses, is largely initiated by individual virus particles binding to and entering a cell. However, recent studies have demonstrated that multiple virus particles are frequently delivered to a cell simultaneously and that this collective particle delivery enhances infection. ZIKV is maintained in nature between Aedes aegypti mosquitos and vertebrate hosts, including humans. Human infection is initiated through the injection of a relatively small initial inoculum comprised of a genetically complex virus population. Since most mutations decrease virus fitness, collective particle transmission could benefit ZIKV and other arthropod-borne diseases by facilitating the maintenance of genetic complexity and adaptability during infection or through other mechanisms. Therefore, we utilized a barcoded ZIKV to quantify the number of virus genomes that initiate a plaque. We found that individual plaques contain a mean of 10 infecting viral genomes (range, 1 to 212). Few plaques contained more than two dominant genomes. To determine whether multigenome infectious units consist of collectively transmitting virions, infectious units of ZIKV were then separated mechanically by centrifugation, and heavier fractions were found to contain more genomes per plaque-forming unit, with larger diameters. Finally, larger/heavier infectious units reformed after removal. These data suggest that ZIKV populations consist of a variety of infectious unit sizes, likely mostly made up of aggregates, and only rarely begin with a single virus genome. IMPORTANCE The arthropod-borne Zika virus (ZIKV) infects humans and can cause severe neurological sequelae, particularly in fetuses infected in utero. How this virus has been able to spread across vast geological ranges and evolve in new host populations is not yet understood. This research demonstrates a novel mechanism of ZIKV transmission through multigenome aggregates, providing insight into ZIKV evolution, immunologic evasion, and better future therapeutic design. This study shows that ZIKV plaques result from collections of genomes rather than individual genomes, increasing the potential for interactions between ZIKV genotypes.
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21
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De Maio N, Walker CR, Turakhia Y, Lanfear R, Corbett-Detig R, Goldman N. Mutation rates and selection on synonymous mutations in SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.01.14.426705. [PMID: 33469589 PMCID: PMC7814826 DOI: 10.1101/2021.01.14.426705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The COVID-19 pandemic has seen an unprecedented response from the sequencing community. Leveraging the sequence data from more than 140,000 SARS-CoV-2 genomes, we study mutation rates and selective pressures affecting the virus. Understanding the processes and effects of mutation and selection has profound implications for the study of viral evolution, for vaccine design, and for the tracking of viral spread. We highlight and address some common genome sequence analysis pitfalls that can lead to inaccurate inference of mutation rates and selection, such as ignoring skews in the genetic code, not accounting for recurrent mutations, and assuming evolutionary equilibrium. We find that two particular mutation rates, G→U and C→U, are similarly elevated and considerably higher than all other mutation rates, causing the majority of mutations in the SARS-CoV-2 genome, and are possibly the result of APOBEC and ROS activity. These mutations also tend to occur many times at the same genome positions along the global SARS-CoV-2 phylogeny (i.e., they are very homoplasic). We observe an effect of genomic context on mutation rates, but the effect of the context is overall limited. While previous studies have suggested selection acting to decrease U content at synonymous sites, we bring forward evidence suggesting the opposite.
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Affiliation(s)
- Nicola De Maio
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Conor R Walker
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Yatish Turakhia
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Robert Lanfear
- Department of Ecology and Evolution, Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA 95064, USA
| | - Nick Goldman
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
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22
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Lythgoe KA, Lumley SF, Pellis L, McKeating JA, Matthews PC. Estimating hepatitis B virus cccDNA persistence in chronic infection. Virus Evol 2021; 7:veaa063. [PMID: 33732502 PMCID: PMC7947180 DOI: 10.1093/ve/veaa063] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Hepatitis B virus (HBV) infection is a major global health problem with over 240 million infected individuals at risk of developing progressive liver disease and hepatocellular carcinoma. HBV is an enveloped DNA virus that establishes its genome as an episomal, covalently closed circular DNA (cccDNA) in the nucleus of infected hepatocytes. Currently, available standard-of-care treatments for chronic hepatitis B (CHB) include nucleos(t)ide analogues (NAs) that suppress HBV replication but do not target the cccDNA and hence rarely cure infection. There is considerable interest in determining the lifespan of cccDNA molecules to design and evaluate new curative treatments. We took a novel approach to this problem by developing a new mathematical framework to model changes in evolutionary rates during infection which, combined with previously determined within-host evolutionary rates of HBV, we used to determine the lifespan of cccDNA. We estimate that during HBe-antigen positive (HBeAgPOS) infection the cccDNA lifespan is 61 (36-236) days, whereas during the HBeAgNEG phase of infection it is only 26 (16-81) days. We found that cccDNA replicative capacity declined by an order of magnitude between HBeAgPOS and HBeAgNEG phases of infection. Our estimated lifespan of cccDNA is too short to explain the long durations of chronic infection observed in patients on NA treatment, suggesting that either a sub-population of long-lived hepatocytes harbouring cccDNA molecules persists during therapy, or that NA therapy does not suppress all viral replication. These results provide a greater understanding of the biology of the cccDNA reservoir and can aid the development of new curative therapeutic strategies for treating CHB.
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Affiliation(s)
- Katrina A Lythgoe
- Big Data Institute, University of Oxford, Old Road Campus, Oxford OX3 7LF, UK
- Department of Zoology, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK
| | - Sheila F Lumley
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
| | - Lorenzo Pellis
- Department of Mathematics, Alan Turing Building, Oxford Rd, Manchester M13 9PL, UK
| | - Jane A McKeating
- Nuffield Department of Medicine Research Building, University of Oxford, Oxford OX3 7LF, UK
| | - Philippa C Matthews
- Nuffield Department of Medicine, University of Oxford, Medawar Building, South Parks Road, Oxford OX1 3SY, UK
- Department of Infectious Diseases and Microbiology, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
- NIHR Biomedical Research Centre, John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK
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23
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Marano JM, Chuong C, Weger-Lucarelli J. Rolling circle amplification: A high fidelity and efficient alternative to plasmid preparation for the rescue of infectious clones. Virology 2020; 551:58-63. [PMID: 33032077 PMCID: PMC7521378 DOI: 10.1016/j.virol.2020.08.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/25/2020] [Accepted: 08/31/2020] [Indexed: 11/19/2022]
Abstract
Alphaviruses (genus Alphavirus; family Togaviridae) are a medically relevant family of viruses that include chikungunya virus and Mayaro virus. Infectious cDNA clones of these viruses are necessary molecular tools to understand viral biology. Traditionally, rescuing virus from an infectious cDNA clone requires propagating plasmids in bacteria, which can result in mutations in the viral genome due to bacterial toxicity or recombination and requires specialized equipment and knowledge to propagate the bacteria. Here, we present an alternative- rolling circle amplification (RCA), an in vitro technology. We demonstrate that the viral yield of transfected RCA product is comparable to midiprepped plasmid, albeit with a slight delay in kinetics. RCA, however, is cheaper and less time-consuming. Further, sequential RCA did not introduce mutations into the viral genome, subverting the need for glycerol stocks and retransformation. These results indicate that RCA is a viable alternative to traditional plasmid-based approaches to viral rescue.
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Affiliation(s)
- Jeffrey M Marano
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA; Translational Biology, Medicine, and Health Graduate Program, Virginia Tech, Blacksburg, VA, USA
| | - Christina Chuong
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA
| | - James Weger-Lucarelli
- Department of Biomedical Sciences and Pathobiology, Virginia Tech, VA-MD Regional College of Veterinary Medicine, Blacksburg, VA, USA.
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24
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Weckworth JK, Davis BW, Roelke-Parker ME, Wilkes RP, Packer C, Eblate E, Schwartz MK, Mills LS. Identifying Candidate Genetic Markers of CDV Cross-Species Pathogenicity in African Lions. Pathogens 2020; 9:E872. [PMID: 33114123 PMCID: PMC7690837 DOI: 10.3390/pathogens9110872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/16/2020] [Accepted: 10/19/2020] [Indexed: 12/17/2022] Open
Abstract
Canine distemper virus (CDV) is a multi-host pathogen with variable clinical outcomes of infection across and within species. We used whole-genome sequencing (WGS) to search for viral markers correlated with clinical distemper in African lions. To identify candidate markers, we first documented single-nucleotide polymorphisms (SNPs) differentiating CDV strains associated with different clinical outcomes in lions in East Africa. We then conducted evolutionary analyses on WGS from all global CDV lineages to identify loci subject to selection. SNPs that both differentiated East African strains and were under selection were mapped to a phylogenetic tree representing global CDV diversity to assess if candidate markers correlated with documented outbreaks of clinical distemper in lions (n = 3). Of 54 SNPs differentiating East African strains, ten were under positive or episodic diversifying selection and 20 occurred in the clinical strain despite strong purifying selection at those loci. Candidate markers were in functional domains of the RNP complex (n = 19), the matrix protein (n = 4), on CDV glycoproteins (n = 5), and on the V protein (n = 1). We found mutations at two loci in common between sequences from three CDV outbreaks of clinical distemper in African lions; one in the signaling lymphocytic activation molecule receptor (SLAM)-binding region of the hemagglutinin protein and another in the catalytic center of phosphodiester bond formation on the large polymerase protein. These results suggest convergent evolution at these sites may have a functional role in clinical distemper outbreaks in African lions and uncover potential novel barriers to pathogenicity in this species.
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Affiliation(s)
- Julie K. Weckworth
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA;
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - Brian W. Davis
- Department of Veterinary Integrative Biosciences, Texas A&M University College of Veterinary Medicine, College Station, TX 77843, USA;
| | - Melody E. Roelke-Parker
- Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA;
| | - Rebecca P. Wilkes
- Department of Comparative Pathobiology, Animal Disease Diagnostic Laboratory, Purdue University College of Veterinary Medicine, West Lafayette, IN 47907, USA;
| | - Craig Packer
- Department of Ecology, Evolution and Behavior, University of Minnesota, St. Paul, MN 55108, USA;
| | - Ernest Eblate
- Tanzania Wildlife Research Institute, Arusha, Tanzania;
| | - Michael K. Schwartz
- Wildlife Biology Program, Department of Ecosystem and Conservation Sciences, W. A. Franke College of Forestry and Conservation, University of Montana, Missoula, MT 59812, USA;
- United States Department of Agriculture, Forest Service, National Genomics Center for Wildlife and Fish Conservation, Rocky Mountain Research Station, Missoula, MT 59801, USA
| | - L. Scott Mills
- Fisheries, Wildlife, and Conservation Biology Program, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA;
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25
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Abstract
The evolutionary dynamics of a virus can differ within hosts and across populations. Studies of within-host evolution provide an important link between experimental studies of virus evolution and large-scale phylodynamic analyses. They can determine the extent to which global processes are recapitulated on local scales and how accurately experimental infections model natural ones. They may also inform epidemiologic models of disease spread and reveal how host-level dynamics contribute to a virus's evolution at a larger scale. Over the last decade, advances in viral sequencing have enabled detailed studies of viral genetic diversity within hosts. I review how within-host diversity is sampled, measured, and expressed, and how comparative studies of viral diversity can be leveraged to elucidate a virus's evolutionary dynamics. These concepts are illustrated with detailed reviews of recent research on the within-host evolution of influenza virus, dengue virus, and cytomegalovirus.
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Affiliation(s)
- Adam S Lauring
- Division of Infectious Diseases, Department of Internal Medicine, and Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA;
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26
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Dench J, Hinz A, Aris‐Brosou S, Kassen R. Identifying the drivers of computationally detected correlated evolution among sites under antibiotic selection. Evol Appl 2020; 13:781-793. [PMID: 32211067 PMCID: PMC7086105 DOI: 10.1111/eva.12900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/02/2019] [Accepted: 11/14/2019] [Indexed: 11/29/2022] Open
Abstract
The ultimate causes of correlated evolution among sites in a genome remain difficult to tease apart. To address this problem directly, we performed a high-throughput search for correlated evolution among sites associated with resistance to a fluoroquinolone antibiotic using whole-genome data from clinical strains of Pseudomonas aeruginosa, before validating our computational predictions experimentally. We show that for at least two sites, this correlation is underlain by epistasis. Our analysis also revealed eight additional pairs of synonymous substitutions displaying correlated evolution underlain by physical linkage, rather than selection associated with antibiotic resistance. Our results provide direct evidence that both epistasis and physical linkage among sites can drive the correlated evolution identified by high-throughput computational tools. In other words, the observation of correlated evolution is not by itself sufficient evidence to guarantee that the sites in question are epistatic; such a claim requires additional evidence, ideally coming from direct estimates of epistasis, based on experimental evidence.
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Affiliation(s)
- Jonathan Dench
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
| | - Aaron Hinz
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
| | - Stéphane Aris‐Brosou
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
- Department of Mathematics and StatisticsUniversity of OttawaOttawaOntarioCanada
| | - Rees Kassen
- Department of BiologyUniversity of OttawaOttawaOntarioCanada
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27
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Pham JY, Ogbunugafor CB, Nguyen Ba AN, Hartl DL. Experimental evolution for niche breadth in bacteriophage T4 highlights the importance of structural genes. Microbiologyopen 2020; 9:e968. [PMID: 31778298 PMCID: PMC7002106 DOI: 10.1002/mbo3.968] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/24/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022] Open
Abstract
Ecologists have long studied the evolution of niche breadth, including how variability in environments can drive the evolution of specialism and generalism. This concept is of particular interest in viruses, where niche breadth evolution may explain viral disease emergence, or underlie the potential for therapeutic measures like phage therapy. Despite the significance and potential applications of virus-host interactions, the genetic determinants of niche breadth evolution remain underexplored in many bacteriophages. In this study, we present the results of an evolution experiment with a model bacteriophage system, Escherichia virus T4, in several host environments: exposure to Escherichia coli C, exposure to E. coli K-12, and exposure to both E. coli C and E. coli K-12. This experimental framework allowed us to investigate the phenotypic and molecular manifestations of niche breadth evolution. First, we show that selection on different hosts led to measurable changes in phage productivity in all experimental populations. Second, whole-genome sequencing of experimental populations revealed signatures of selection. Finally, clear and consistent patterns emerged across the host environments, especially the presence of new mutations in phage structural genes-genes encoding proteins that provide morphological and biophysical integrity to a virus. A comparison of mutations found across functional gene categories revealed that structural genes acquired significantly more mutations than other categories. Our findings suggest that structural genes are central determinants in bacteriophage niche breadth.
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Affiliation(s)
- Jenny Y. Pham
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | | | - Alex N. Nguyen Ba
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
| | - Daniel L. Hartl
- Department of Organismic and Evolutionary BiologyHarvard UniversityCambridgeMAUSA
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28
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Goz E, Zafrir Z, Tuller T. Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code. Bioinformatics 2019; 34:3241-3248. [PMID: 29718236 PMCID: PMC7109696 DOI: 10.1093/bioinformatics/bty351] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 04/27/2018] [Indexed: 01/09/2023] Open
Abstract
Motivation Understanding how viruses co-evolve with their hosts and adapt various genomic level strategies in order to ensure their fitness may have essential implications in unveiling the secrets of viral evolution, and in developing new vaccines and therapeutic approaches. Here, based on a novel genomic analysis of 2625 different viruses and 439 corresponding host organisms, we provide evidence of universal evolutionary selection for high dimensional ‘silent’ patterns of information hidden in the redundancy of viral genetic code. Results Our model suggests that long substrings of nucleotides in the coding regions of viruses from all classes, often also repeat in the corresponding viral hosts from all domains of life. Selection for these substrings cannot be explained only by such phenomena as codon usage bias, horizontal gene transfer and the encoded proteins. Genes encoding structural proteins responsible for building the core of the viral particles were found to include more host-repeating substrings, and these substrings tend to appear in the middle parts of the viral coding regions. In addition, in human viruses these substrings tend to be enriched with motives related to transcription factors and RNA binding proteins. The host-repeating substrings are possibly related to the evolutionary pressure on the viruses to effectively interact with host's intracellular factors and to efficiently escape from the host's immune system. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Eli Goz
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel
| | - Zohar Zafrir
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel Aviv University, Tel Aviv, Israel.,SynVaccineLtd, Ramat Hachayal, Tel Aviv, Israel.,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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29
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Kemble H, Nghe P, Tenaillon O. Recent insights into the genotype-phenotype relationship from massively parallel genetic assays. Evol Appl 2019; 12:1721-1742. [PMID: 31548853 PMCID: PMC6752143 DOI: 10.1111/eva.12846] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/21/2019] [Accepted: 07/02/2019] [Indexed: 12/20/2022] Open
Abstract
With the molecular revolution in Biology, a mechanistic understanding of the genotype-phenotype relationship became possible. Recently, advances in DNA synthesis and sequencing have enabled the development of deep mutational scanning assays, capable of scoring comprehensive libraries of genotypes for fitness and a variety of phenotypes in massively parallel fashion. The resulting empirical genotype-fitness maps pave the way to predictive models, potentially accelerating our ability to anticipate the behaviour of pathogen and cancerous cell populations from sequencing data. Besides from cellular fitness, phenotypes of direct application in industry (e.g. enzyme activity) and medicine (e.g. antibody binding) can be quantified and even selected directly by these assays. This review discusses the technological basis of and recent developments in massively parallel genetics, along with the trends it is uncovering in the genotype-phenotype relationship (distribution of mutation effects, epistasis), their possible mechanistic bases and future directions for advancing towards the goal of predictive genetics.
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Affiliation(s)
- Harry Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Philippe Nghe
- École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), UMR CNRS‐ESPCI CBI 8231PSL Research UniversityParis Cedex 05France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, Unité Mixte de Recherche 1137Université Paris Diderot, Université Paris NordParisFrance
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30
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Lebeuf-Taylor E, McCloskey N, Bailey SF, Hinz A, Kassen R. The distribution of fitness effects among synonymous mutations in a gene under directional selection. eLife 2019; 8:45952. [PMID: 31322500 PMCID: PMC6692132 DOI: 10.7554/elife.45952] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 07/18/2019] [Indexed: 12/21/2022] Open
Abstract
The fitness effects of synonymous mutations, nucleotide changes that do not alter the encoded amino acid, have often been assumed to be neutral, but a growing body of evidence suggests otherwise. We used site-directed mutagenesis coupled with direct measures of competitive fitness to estimate the distribution of fitness effects among synonymous mutations for a gene under directional selection and capable of adapting via synonymous nucleotide changes. Synonymous mutations had highly variable fitness effects, both deleterious and beneficial, resembling those of nonsynonymous mutations in the same gene. This variation in fitness was underlain by changes in transcription linked to the creation of internal promoter sites. A positive correlation between fitness and the presence of synonymous substitutions across a phylogeny of related Pseudomonads suggests these mutations may be common in nature. Taken together, our results provide the most compelling evidence to date that synonymous mutations with non-neutral fitness effects may in fact be commonplace.
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Affiliation(s)
| | - Nick McCloskey
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Susan F Bailey
- Department of Biology, Clarkson University, Potsdam, United States
| | - Aaron Hinz
- Department of Biology, University of Ottawa, Ottawa, Canada
| | - Rees Kassen
- Department of Biology, University of Ottawa, Ottawa, Canada
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31
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Huang SW, Hung SJ, Wang JR. Application of deep sequencing methods for inferring viral population diversity. J Virol Methods 2019; 266:95-102. [PMID: 30690049 DOI: 10.1016/j.jviromet.2019.01.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 01/11/2019] [Accepted: 01/24/2019] [Indexed: 12/13/2022]
Abstract
The first deep sequencing method was announced in 2005. Due to an increasing number of sequencing data and a reduction in the costs of each sequencing dataset, this innovative technique was soon applied to genetic investigations of viral genome diversity in various viruses, particularly RNA viruses. These deep sequencing findings documented viral epidemiology and evolution and provided high-resolution data on the genetic changes in viral populations. Here, we review deep sequencing platforms that have been applied in viral quasispecies studies. Further, we discuss recent deep sequencing studies on viral inter- and intrahost evolution, drug resistance, and humoral immune selection, especially in emerging and re-emerging viruses. Deep sequencing methods are becoming the standard for providing comprehensive results of viral population diversity, and their applications are discussed.
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Affiliation(s)
- Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Su-Jhen Hung
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan; National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan.
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32
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Mohamed Ali S, Amroun A, de Lamballerie X, Nougairède A. Evolution of Chikungunya virus in mosquito cells. Sci Rep 2018; 8:16175. [PMID: 30385797 PMCID: PMC6212429 DOI: 10.1038/s41598-018-34561-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/22/2018] [Indexed: 01/23/2023] Open
Abstract
It has been observed that replication of Chikungunya virus (CHIKV) in C6/36 Aedes albopictus cells has little effect on virus evolution. To characterize evolutionary patterns associated with CHIKV replication in mosquito cells, we performed serial passages of the LR2006 strain in Ae. albopictus cells (75 and 30 passages in C6/36 and U4.4 respectively) and Ae. aegypti cells (100 passages in AA-A20 and in AE) and studied genotypic changes accompanying adaptation during this evolutionary process. Quantitative analysis revealed cell specific patterns: low mutation rates in C6/36 cells except when a CHIKV strain pre-adapted to mammalian was used and typical features of adaptation to cell culture conditions with a high number of fixed mutations in AE and AA-A20 cells probably due to the weak permissiveness of these latter cell lines. Altogether, these results suggested that both cell line and viral strain influence rates of viral evolution. In contrast, characteristics and distribution of mutations were qualitatively very similar in all mosquito cells with a high level of parallel evolution including 4 deletion mutations. Serial passage in mammalian cells of viruses pre-adapted to mosquito cells revealed disappearance of almost all shared mutations suggesting that many of these mutational patterns are vector-specific.
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Affiliation(s)
- Souand Mohamed Ali
- Unité des virus Émergents (UVE; Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Abdennour Amroun
- Unité des virus Émergents (UVE; Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Xavier de Lamballerie
- Unité des virus Émergents (UVE; Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France
| | - Antoine Nougairède
- Unité des virus Émergents (UVE; Aix-Marseille Univ - IRD 190 - Inserm 1207 - IHU Méditerranée Infection), Marseille, France.
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33
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Domingo-Calap P, Schubert B, Joly M, Solis M, Untrau M, Carapito R, Georgel P, Caillard S, Fafi-Kremer S, Paul N, Kohlbacher O, González-Candelas F, Bahram S. An unusually high substitution rate in transplant-associated BK polyomavirus in vivo is further concentrated in HLA-C-bound viral peptides. PLoS Pathog 2018; 14:e1007368. [PMID: 30335851 PMCID: PMC6207329 DOI: 10.1371/journal.ppat.1007368] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/30/2018] [Accepted: 09/28/2018] [Indexed: 11/18/2022] Open
Abstract
Infection with human BK polyomavirus, a small double-stranded DNA virus, potentially results in severe complications in immunocompromised patients. Here, we describe the in vivo variability and evolution of the BK polyomavirus by deep sequencing. Our data reveal the highest genomic evolutionary rate described in double-stranded DNA viruses, i.e., 10−3–10−5 substitutions per nucleotide site per year. High mutation rates in viruses allow their escape from immune surveillance and adaptation to new hosts. By combining mutational landscapes across viral genomes with in silico prediction of viral peptides, we demonstrate the presence of significantly more coding substitutions within predicted cognate HLA-C-bound viral peptides than outside. This finding suggests a role for HLA-C in antiviral immunity, perhaps through the action of killer cell immunoglobulin-like receptors. The present study provides a comprehensive view of viral evolution and immune escape in a DNA virus. Little is known about the mechanisms of evolution and viral immune escape in double-stranded DNA (dsDNA) viruses. Here, we study the evolution of BK polyomavirus and observe the highest genomic evolutionary rate described so far for a dsDNA virus, in the range of RNA viruses, which usually evolve rapidly. Furthermore, the prediction of viral peptides to determine immune escape suggests a specific role of HLA-C in antiviral immunity. These findings are helpful for future advances in antiviral therapies and provide a step forward in our understanding of in vivo viral evolution in humans.
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Affiliation(s)
- Pilar Domingo-Calap
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- * E-mail: (PDC); (SB)
| | - Benjamin Schubert
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
| | - Mélanie Joly
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Morgane Solis
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Meiggie Untrau
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Raphael Carapito
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
| | - Philippe Georgel
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Sophie Caillard
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Service de Néphrologie et Transplantation Rénale, Hôpitaux Universitaires de Strasbourg, France
| | - Samira Fafi-Kremer
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire de Virologie, Plateau Technique de Microbiologie, Pôle de Biologie, Hôpitaux Universitaires de Strasbourg, France
| | - Nicodème Paul
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
| | - Oliver Kohlbacher
- Center for Bioinformatics, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, Tübingen, Germany
- Quantitative Biology Center, Tübingen, Germany
- Faculty of Medicine, University of Tübingen, Tübingen, Germany
- Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Institute for Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany
| | - Fernando González-Candelas
- Unidad Mixta Infección y Salud Pública FISABIO/Universitat de València, Institute for Integrative Systems Biology I2SysBio (CSIC-UV) and CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - Seiamak Bahram
- Plateforme GENOMAX, Laboratoire d’ImmunoRhumatologie Moléculaire, INSERM UMR_S1109, LabEx Transplantex, Centre de Recherche d’Immunologie et d’Hématologie, Faculté de Médecine, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Université de Strasbourg, Strasbourg, France
- Fédération Hospitalo-Universitaire, OMICARE, Centre de Recherche d’Immunologie et d’Hématologie, Strasbourg, France
- Laboratoire Central d’Immunologie, Plateau Technique de Biologie, Nouvel Hôpital Civil, France
- * E-mail: (PDC); (SB)
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34
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Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet 2018; 14:e1007615. [PMID: 30148850 PMCID: PMC6128649 DOI: 10.1371/journal.pgen.1007615] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 09/07/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023] Open
Abstract
Synonymous mutations do not alter the specified amino acid but may alter the structure or function of an mRNA in ways that impact fitness. There are few examples in the literature, however, in which the effects of synonymous mutations on microbial growth rates have been measured, and even fewer for which the underlying mechanism is understood. We evolved four populations of a strain of Salmonella enterica in which a promiscuous enzyme has been recruited to replace an essential enzyme. A previously identified point mutation increases the enzyme’s ability to catalyze the newly needed reaction (required for arginine biosynthesis) but decreases its ability to catalyze its native reaction (required for proline biosynthesis). The poor performance of this enzyme limits growth rate on glucose. After 260 generations, we identified two synonymous mutations in the first six codons of the gene encoding the weak-link enzyme that increase growth rate by 41 and 67%. We introduced all possible synonymous mutations into the first six codons and found substantial effects on growth rate; one doubles growth rate, and another completely abolishes growth. Computational analyses suggest that these mutations affect either the stability of a stem-loop structure that sequesters the start codon or the accessibility of the region between the Shine-Dalgarno sequence and the start codon. Thus, these mutations would be predicted to affect translational efficiency and thereby indirectly affect mRNA stability because translating ribosomes protect mRNA from degradation. Experimental data support these hypotheses. We conclude that the effects of the synonymous mutations are due to a combination of effects on mRNA stability and translation efficiency that alter levels of the weak-link enzyme. These findings suggest that synonymous mutations can have profound effects on fitness under strong selection and that their importance in evolution may be under-appreciated. When a new enzyme is needed, microbes often recruit a pre-existing enzyme with a promiscuous activity corresponding to the newly needed activity. Such enzymes are often the “weak-link” in metabolism because they have not evolved to efficiently catalyze the new reaction. Under these circumstances, increasing the level of the weak-link enzyme can improve fitness. We evolved a strain of S. enterica in which a weak-link enzyme–E383A ProA–serves essential functions in synthesis of proline and arginine for 260 generations and then sequenced the genomes of several evolved strains. A mutation in the promoter of the operon encoding E383A ProA increased growth rate 9-fold. More surprisingly, a mutation upstream of the start codon and two synonymous mutations within the first six codons also increased growth rate by up to 68%. Introduction of all possible synonymous mutations in the first six codons showed that some doubled growth rate, while others slowed or even prevented growth. Computational and experimental data suggest that these effects were due to enhanced translational efficiency of the weak-link enzyme. These results show that synonymous mutations, once assumed to be selectively neutral, can have strong impacts on fitness when growth rate is limited by a weak-link enzyme.
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Affiliation(s)
- JohnCarlo Kristofich
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Andrew B. Morgenthaler
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Wallis R. Kinney
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
| | - Christopher C. Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Daniel J. Snyder
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - William M. Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
| | - Vaughn S. Cooper
- University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Shelley D. Copley
- Department of Molecular, Cellular and Developmental Biology, University of Colorado Boulder, Boulder, CO, United States of America
- Cooperative Institute for Research in Environmental Sciences, University of Colorado Boulder, Boulder, CO, United States of America
- * E-mail:
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35
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Bilska K, Jurczak S, Kulik T, Ropelewska E, Olszewski J, Żelechowski M, Zapotoczny P. Species Composition and Trichothecene Genotype Profiling of Fusarium Field Isolates Recovered from Wheat in Poland. Toxins (Basel) 2018; 10:E325. [PMID: 30103473 PMCID: PMC6115980 DOI: 10.3390/toxins10080325] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 07/29/2018] [Accepted: 08/07/2018] [Indexed: 12/20/2022] Open
Abstract
Fusarium head blight (FHB) of cereals is the major head disease negatively affecting grain production worldwide. In 2016 and 2017, serious outbreaks of FHB occurred in wheat crops in Poland. In this study, we characterized the diversity of Fusaria responsible for these epidemics using TaqMan assays. From a panel of 463 field isolates collected from wheat, four Fusarium species were identified. The predominant species were F. graminearum s.s. (81%) and, to a lesser extent, F. avenaceum (15%). The emergence of the 15ADON genotype was found ranging from 83% to 87% of the total trichothecene genotypes isolated in 2016 and 2017, respectively. Our results indicate two dramatic shifts within fungal field populations in Poland. The first shift is associated with the displacement of F. culmorum by F. graminearum s.s. The second shift resulted from a loss of nivalenol genotypes. We suggest that an emerging prevalence of F. graminearum s.s. may be linked to boosted maize production, which has increased substantially over the last decade in Poland. To detect variation within Tri core clusters, we compared sequence data from randomly selected field isolates with a panel of strains from geographically diverse origins. We found that the newly emerged 15ADON genotypes do not exhibit a specific pattern of polymorphism enabling their clear differentiation from the other European strains.
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Affiliation(s)
- Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Sebastian Jurczak
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Ewa Ropelewska
- Department of Systems Engineering, Faculty of Engineering, University of Warmia and Mazury in Olsztyn, Heweliusza 14, 10-718 Olsztyn, Poland.
| | - Jacek Olszewski
- Experimental Education Unit, Oczapowskiego 8, 10-719 Olsztyn, Poland.
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Piotr Zapotoczny
- Department of Systems Engineering, Faculty of Engineering, University of Warmia and Mazury in Olsztyn, Heweliusza 14, 10-718 Olsztyn, Poland.
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36
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Lyons DM, Lauring AS. Evidence for the Selective Basis of Transition-to-Transversion Substitution Bias in Two RNA Viruses. Mol Biol Evol 2018; 34:3205-3215. [PMID: 29029187 PMCID: PMC5850290 DOI: 10.1093/molbev/msx251] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The substitution rates of transitions are higher than expected by chance relative to those of transversions. Many have argued that selection disfavors transversions, as nonsynonymous transversions are less likely to conserve biochemical properties of the original amino acid. Only recently has it become feasible to directly test this selective hypothesis by comparing the fitness effects of a large number of transition and transversion mutations. For example, a recent study of six viruses and one beta-lactamase gene did not find evidence supporting the selective hypothesis. Here, we analyze the relative fitness effects of transition and transversion mutations from our recently published genome-wide study of mutational fitness effects in influenza virus. In contrast to prior work, we find that transversions are significantly more detrimental than transitions. Using what we believe to be an improved statistical framework, we also identify a similar trend in two HIV data sets. We further demonstrate a fitness difference in transition and transversion mutations using four deep mutational scanning data sets of influenza virus and HIV, which provided adequate statistical power. We find that three of the most commonly cited radical/conservative amino acid categories are predictive of fitness, supporting their utility in studies of positive selection and codon usage bias. We conclude that selection is a major contributor to the transition:transversion substitution bias in viruses and that this effect is only partially explained by the greater likelihood of transversion mutations to cause radical as opposed to conservative amino acid changes.
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Affiliation(s)
- Daniel M Lyons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI
| | - Adam S Lauring
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI.,Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI
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37
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Abstract
Many viruses evolve rapidly. This is due, in part, to their high mutation rates. Mutation rate estimates for over 25 viruses are currently available. Here, we review the population genetics of virus mutation rates. We specifically cover the topics of mutation rate estimation, the forces that drive the evolution of mutation rates, and how the optimal mutation rate can be context-dependent.
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38
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Kula A, Saelens J, Cox J, Schubert AM, Travisano M, Putonti C. The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host. Sci Rep 2018; 8:8350. [PMID: 29844443 PMCID: PMC5974221 DOI: 10.1038/s41598-018-25914-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/01/2018] [Indexed: 12/05/2022] Open
Abstract
Viruses rely upon their hosts for biosynthesis of viral RNA, DNA and protein. This dependency frequently engenders strong selection for virus genome compatibility with potential hosts, appropriate gene regulation and expression necessary for a successful infection. While bioinformatic studies have shown strong correlations between codon usage in viral and host genomes, the selective factors by which this compatibility evolves remain a matter of conjecture. Engineered to include codons with a lesser usage and/or tRNA abundance within the host, three different attenuated strains of the bacterial virus ФX174 were created and propagated via serial transfers. Molecular sequence data indicate that biosynthetic compatibility was recovered rapidly. Extensive computational simulations were performed to assess the role of mutational biases as well as selection for translational efficiency in the engineered phage. Using bacteriophage as a model system, we can begin to unravel the evolutionary processes shaping codon compatibility between viruses and their host.
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Affiliation(s)
- Alexander Kula
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, University of Miami, Coral Gables, FL, USA
| | - Joseph Saelens
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
| | - Jennifer Cox
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Alyxandria M Schubert
- Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA.,Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA
| | - Michael Travisano
- Department of Ecology, Evolution and Behavior, University of Minnesota, Saint Paul, MN, USA.,BioTechnology Institute, University of Minnesota, Saint Paul, MN, USA
| | - Catherine Putonti
- Department of Biology, Loyola University Chicago, Chicago, IL, USA. .,Bioinformatics Program, Loyola University Chicago, Chicago, IL, USA. .,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA.
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39
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Amini HR, Ajaki A, Farahi M, Heidari M, Pirali A, Forouzanfar M, Eghbalsaied S. The novel T755C mutation in <i>BMP15</i> is associated with the litter size of Iranian Afshari, Ghezel, and Shal breeds. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-153-2018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Abstract. The present study was conducted to determine the molecular genetic variation
in bone morphogenetic protein 15 (BMP15) of some selected Iranian sheep breeds and
aims to provide relevant genetic information for twin-birth lambing.
Therefore, a total of 44 rams and 213 ewes with single-, twin-, and
triplet-birth lambing were used from Shal, Ghezel, Afshari and
Lori-Bakhtiari sheep breeds. Three primer pairs were used for amplification of
exons 1 and 2 of the BMP15 gene. The sequencing result
of distinctive single-strand conformation polymorphism
(SSCP)
patterns showed segregation
of the T755C mutation and the ensuing non-conservative substitution of L252P
in the BMP15 propeptide. All three ewes with triplet-birth lambing and two
sterile ewes were heterozygotic for this mutation. Association analysis
revealed that this mutation was significantly related to the ewe's litter
size, so that ewes with the CT genotype had 0.24 and 0.30 more lambs than
those with the CC (p < 0.05) and TT (p < 0.01)
genotypes, respectively. The mutation effect on the litter size was
incomplete dominance in Afshari breed and over-dominance in Shal and Ghezel
breeds. In conclusion, the findings in this experiment suggested synergistic
effects of the T755C mutation and other unknown mutations in other effective
genes which cause infertility and higher litter size in two different ways.
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40
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Abstract
Reproduction of RNA viruses is typically error-prone due to the infidelity of their replicative machinery and the usual lack of proofreading mechanisms. The error rates may be close to those that kill the virus. Consequently, populations of RNA viruses are represented by heterogeneous sets of genomes with various levels of fitness. This is especially consequential when viruses encounter various bottlenecks and new infections are initiated by a single or few deviating genomes. Nevertheless, RNA viruses are able to maintain their identity by conservation of major functional elements. This conservatism stems from genetic robustness or mutational tolerance, which is largely due to the functional degeneracy of many protein and RNA elements as well as to negative selection. Another relevant mechanism is the capacity to restore fitness after genetic damages, also based on replicative infidelity. Conversely, error-prone replication is a major tool that ensures viral evolvability. The potential for changes in debilitated genomes is much higher in small populations, because in the absence of stronger competitors low-fit genomes have a choice of various trajectories to wander along fitness landscapes. Thus, low-fit populations are inherently unstable, and it may be said that to run ahead it is useful to stumble. In this report, focusing on picornaviruses and also considering data from other RNA viruses, we review the biological relevance and mechanisms of various alterations of viral RNA genomes as well as pathways and mechanisms of rehabilitation after loss of fitness. The relationships among mutational robustness, resilience, and evolvability of viral RNA genomes are discussed.
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41
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Vrancken B, Suchard MA, Lemey P. Accurate quantification of within- and between-host HBV evolutionary rates requires explicit transmission chain modelling. Virus Evol 2017; 3:vex028. [PMID: 29026650 PMCID: PMC5632516 DOI: 10.1093/ve/vex028] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512–22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the ‘colonization–adaptation–transmission’ model can explain the differential impact of transmission on synonymous and non-synonymous substitution rates. Here, we revisit this dataset using a full probabilistic Bayesian phylogenetic framework that adequately accounts for the non-independence of sequence data when estimating evolutionary parameters. Examination of the transmission chain data under a flexible coalescent prior reveals a general inconsistency between the estimated timings and clustering patterns and the known transmission history, highlighting the need to incorporate host transmission information in the analysis. Using an explicit genealogical transmission chain model, we find strong support for a transmission-associated decrease of the overall evolutionary rate. However, in contrast to the initially reported larger transmission effect on non-synonymous substitution rate, we find a similar decrease in both non-synonymous and synonymous substitution rates that cannot be adequately explained by the colonization-adaptation-transmission model. An alternative explanation may involve a transmission/establishment advantage of hepatitis B virus variants that have accumulated fewer within-host substitutions, perhaps by spending more time in the covalently closed circular DNA state between each round of viral replication. More generally, this study illustrates that ignoring phylogenetic relationships can lead to misleading evolutionary estimates.
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Affiliation(s)
- Bram Vrancken
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
| | - Marc A Suchard
- Department of Biomathematics, University of California, Los Angeles, CA 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, CA 90095, USA.,Department of Biostatistics, UCLA Fielding School of Public Health, University of California, Los Angeles, CA 90095, USA
| | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute for Medical Research, KU Leuven - University of Leuven, B-3000 Leuven, Belgium
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42
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Moratorio G, Henningsson R, Barbezange C, Carrau L, Bordería AV, Blanc H, Beaucourt S, Poirier EZ, Vallet T, Boussier J, Mounce BC, Fontes M, Vignuzzi M. Attenuation of RNA viruses by redirecting their evolution in sequence space. Nat Microbiol 2017; 2:17088. [PMID: 28581455 PMCID: PMC7098180 DOI: 10.1038/nmicrobiol.2017.88] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 04/27/2017] [Indexed: 12/18/2022]
Abstract
RNA viruses pose serious threats to human health. Their success relies on their capacity to generate genetic variability and, consequently, on their adaptive potential. We describe a strategy to attenuate RNA viruses by altering their evolutionary potential. We rationally altered the genomes of Coxsackie B3 and influenza A viruses to redirect their evolutionary trajectories towards detrimental regions in sequence space. Specifically, viral genomes were engineered to harbour more serine and leucine codons with nonsense mutation targets: codons that could generate Stop mutations after a single nucleotide substitution. Indeed, these viruses generated more Stop mutations both in vitro and in vivo, accompanied by significant losses in viral fitness. In vivo, the viruses were attenuated, generated high levels of neutralizing antibodies and protected against lethal challenge. Our study demonstrates that cornering viruses in ‘risky’ areas of sequence space may be implemented as a broad-spectrum vaccine strategy against RNA viruses. Virus attenuation is used to obtain vaccine strains. Here, the rapid evolution of RNA viruses is exploited by engineering their genomes to encode sites that are a mutation away from a stop codon, a clever method to generate attenuated viruses.
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Affiliation(s)
- Gonzalo Moratorio
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Rasmus Henningsson
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,International Group for Data Analysis, Institut Pasteur, C3BI, USR 3756 IP CNRS, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,Centre for Mathematical Sciences, Lund University, 22100 Lund, Sweden
| | - Cyril Barbezange
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Lucia Carrau
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,Sorbonne Paris Cité, Université Paris Diderot, Cellule Pasteur, 75013 Paris, France
| | - Antonio V Bordería
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,International Group for Data Analysis, Institut Pasteur, C3BI, USR 3756 IP CNRS, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Stephanie Beaucourt
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Enzo Z Poirier
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,Sorbonne Paris Cité, Université Paris Diderot, Cellule Pasteur, 75013 Paris, France
| | - Thomas Vallet
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Jeremy Boussier
- International Group for Data Analysis, Institut Pasteur, C3BI, USR 3756 IP CNRS, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,Unité d'Immunobiologie des Cellules Dendritiques, Institut Pasteur, Inserm 1223, 25 rue du Dr. Roux, 75724 Paris cedex 15, Paris, France.,Ecole doctorale Frontières du vivant, Université Paris Diderot, 75013 Paris, France
| | - Bryan C Mounce
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
| | - Magnus Fontes
- International Group for Data Analysis, Institut Pasteur, C3BI, USR 3756 IP CNRS, 28 rue du Dr. Roux, 75724 Paris cedex 15, France.,Centre for Mathematical Sciences, Lund University, 22100 Lund, Sweden
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724 Paris cedex 15, France
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43
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Morley VJ, Turner PE. Dynamics of molecular evolution in RNA virus populations depend on sudden versus gradual environmental change. Evolution 2017; 71:872-883. [PMID: 28121018 PMCID: PMC5382103 DOI: 10.1111/evo.13193] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/03/2017] [Accepted: 01/12/2017] [Indexed: 12/31/2022]
Abstract
Understanding the dynamics of molecular adaptation is a fundamental goal of evolutionary biology. While adaptation to constant environments has been well characterized, the effects of environmental complexity remain seldom studied. One simple but understudied factor is the rate of environmental change. Here we used experimental evolution with RNA viruses to investigate whether evolutionary dynamics varied based on the rate of environmental turnover. We used whole-genome next-generation sequencing to characterize evolutionary dynamics in virus populations adapting to a sudden versus gradual shift onto a novel host cell type. In support of theoretical models, we found that when populations evolved in response to a sudden environmental change, mutations of large beneficial effect tended to fix early, followed by mutations of smaller beneficial effect; as predicted, this pattern broke down in response to a gradual environmental change. Early mutational steps were highly parallel across replicate populations in both treatments. The fixation of single mutations was less common than sweeps of associated "cohorts" of mutations, and this pattern intensified when the environment changed gradually. Additionally, clonal interference appeared stronger in response to a gradual change. Our results suggest that the rate of environmental change is an important determinant of evolutionary dynamics in asexual populations.
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Affiliation(s)
- Valerie J Morley
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, P. O. Box 208106, New Haven, Connecticut, 06520.,Graduate Program in Microbiology, Yale School of Medicine, New Haven, Connecticut, 06520
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44
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Evolutionary dynamics of dengue virus populations within the mosquito vector. Curr Opin Virol 2016; 21:47-53. [DOI: 10.1016/j.coviro.2016.07.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 07/23/2016] [Accepted: 07/27/2016] [Indexed: 02/05/2023]
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45
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Haddox HK, Dingens AS, Bloom JD. Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV's Envelope Protein on Viral Replication in Cell Culture. PLoS Pathog 2016; 12:e1006114. [PMID: 27959955 PMCID: PMC5189966 DOI: 10.1371/journal.ppat.1006114] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 12/27/2016] [Accepted: 12/07/2016] [Indexed: 11/18/2022] Open
Abstract
HIV is notorious for its capacity to evade immunity and anti-viral drugs through rapid sequence evolution. Knowledge of the functional effects of mutations to HIV is critical for understanding this evolution. HIV's most rapidly evolving protein is its envelope (Env). Here we use deep mutational scanning to experimentally estimate the effects of all amino-acid mutations to Env on viral replication in cell culture. Most mutations are under purifying selection in our experiments, although a few sites experience strong selection for mutations that enhance HIV's replication in cell culture. We compare our experimental measurements of each site's preference for each amino acid to the actual frequencies of these amino acids in naturally occurring HIV sequences. Our measured amino-acid preferences correlate with amino-acid frequencies in natural sequences for most sites. However, our measured preferences are less concordant with natural amino-acid frequencies at surface-exposed sites that are subject to pressures absent from our experiments such as antibody selection. Our data enable us to quantify the inherent mutational tolerance of each site in Env. We show that the epitopes of broadly neutralizing antibodies have a significantly reduced inherent capacity to tolerate mutations, rigorously validating a pervasive idea in the field. Overall, our results help disentangle the role of inherent functional constraints and external selection pressures in shaping Env's evolution.
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Affiliation(s)
- Hugh K. Haddox
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, Washington, United States of America
| | - Adam S. Dingens
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Molecular and Cellular Biology PhD Program, University of Washington, Seattle, Washington, United States of America
| | - Jesse D. Bloom
- Basic Sciences Division and Computational Biology Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
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46
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Palmer BA, Fanning LJ. Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness. PLoS One 2016; 11:e0167089. [PMID: 27880830 PMCID: PMC5120871 DOI: 10.1371/journal.pone.0167089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 11/07/2016] [Indexed: 11/18/2022] Open
Abstract
Hepatitis C virus is a positive-sense single-stranded RNA virus. The gene junction partitioning the viral glycoproteins E1 and E2 displays concurrent sequence evolution with the 3'-end of E1 highly conserved and the 5'-end of E2 highly heterogeneous. This gene junction is also believed to contain structured RNA elements, with a growing body of evidence suggesting that such structures can act as an additional level of viral replication and transcriptional control. We have previously used ultradeep pyrosequencing to analyze an amplicon library spanning the E1/E2 gene junction from a treatment naïve patient where samples were collected over 10 years of chronic HCV infection. During this timeframe maintenance of an in-frame insertion, recombination and humoral immune targeting of discrete virus sub-populations was reported. In the current study, we present evidence of epistatic evolution across the E1/E2 gene junction and observe the development of co-varying networks of codons set against a background of a complex virome with periodic shifts in population dominance. Overtime, the number of codons actively mutating decreases for all virus groupings. We identify strong synonymous co-variation between codon sites in a group of sequences harbouring a 3 bp in-frame insertion and propose that synonymous mutation acts to stabilize the RNA structural backbone.
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Affiliation(s)
- Brendan A. Palmer
- Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
- * E-mail: (LJF); (BAP)
| | - Liam J. Fanning
- Molecular Virology Diagnostic & Research Laboratory, Department of Medicine, University College Cork, Cork, Ireland
- * E-mail: (LJF); (BAP)
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Abstract
A virus’ mutational robustness is described in terms of the strength and distribution of the mutational fitness effects, or MFE. The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution. Here we define the mutational fitness effects in influenza A virus by generating 128 viruses, each with a single nucleotide mutation. In contrast to mutational scanning approaches, this strategy allowed us to unambiguously assign fitness values to individual mutations. The presence of each desired mutation and the absence of additional mutations were verified by next generation sequencing of each stock. A mutation was considered lethal only after we failed to rescue virus in three independent transfections. We measured the fitness of each viable mutant relative to the wild type by quantitative RT-PCR following direct competition on A549 cells. We found that 31.6% of the mutations in the genome-wide dataset were lethal and that the lethal fraction did not differ appreciably between the HA- and NA-encoding segments and the rest of the genome. Of the viable mutants, the fitness mean and standard deviation were 0.80 and 0.22 in the genome-wide dataset and best modeled as a beta distribution. The fitness impact of mutation was marginally lower in the segments coding for HA and NA (0.88 ± 0.16) than in the other 6 segments (0.78 ± 0.24), and their respective beta distributions had slightly different shape parameters. The results for influenza A virus are remarkably similar to our own analysis of CirSeq-derived fitness values from poliovirus and previously published data from other small, single stranded DNA and RNA viruses. These data suggest that genome size, and not nucleic acid type or mode of replication, is the main determinant of viral mutational fitness effects. Like other RNA viruses, influenza virus has a very high mutation rate. While high mutation rates may increase the rate at which influenza virus will adapt to a new host, acquire a new route of transmission, or escape from host immune surveillance, data from model systems suggest that most new viral mutations are either lethal or highly detrimental. Mutational robustness refers to the ability of a virus to tolerate, or buffer, these mutations. The mutational robustness of a virus will determine which mutations are maintained in a population and may have a greater impact on viral evolution than mutation rate. We defined the mutational robustness of influenza A virus by measuring the fitness of a large number of viruses, each with a single point mutation. We found that the overall robustness of influenza was similar to that of poliovirus and other viruses of similar size. Interestingly, mutations appeared to be more easily accommodated in hemagglutinin and neuraminidase than elsewhere in the genome. This work will inform models of influenza evolution at the global and molecular scale.
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Lequime S, Fontaine A, Ar Gouilh M, Moltini-Conclois I, Lambrechts L. Genetic Drift, Purifying Selection and Vector Genotype Shape Dengue Virus Intra-host Genetic Diversity in Mosquitoes. PLoS Genet 2016; 12:e1006111. [PMID: 27304978 PMCID: PMC4909269 DOI: 10.1371/journal.pgen.1006111] [Citation(s) in RCA: 97] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 05/17/2016] [Indexed: 01/15/2023] Open
Abstract
Due to their error-prone replication, RNA viruses typically exist as a diverse population of closely related genomes, which is considered critical for their fitness and adaptive potential. Intra-host demographic fluctuations that stochastically reduce the effective size of viral populations are a challenge to maintaining genetic diversity during systemic host infection. Arthropod-borne viruses (arboviruses) traverse several anatomical barriers during infection of their arthropod vectors that are believed to impose population bottlenecks. These anatomical barriers have been associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. Whether these patterns result from stochastic sampling (genetic drift) rather than natural selection, and/or from the influence of vector genetic heterogeneity has not been elucidated. Here, we used deep sequencing of full-length viral genomes to monitor the intra-host evolution of a wild-type dengue virus isolate during infection of several mosquito genetic backgrounds. We estimated a bottleneck size ranging from 5 to 42 founding viral genomes at initial midgut infection, irrespective of mosquito genotype, resulting in stochastic reshuffling of the variant repertoire. The observed level of genetic diversity increased following initial midgut infection but significantly differed between mosquito genetic backgrounds despite a similar initial bottleneck size. Natural selection was predominantly negative (purifying) during viral population expansion. Taken together, our results indicate that dengue virus intra-host genetic diversity in the mosquito vector is shaped by genetic drift and purifying selection, and point to a novel role for vector genetic factors in the genetic breadth of virus populations during infection. Identifying the evolutionary forces acting on arboviral populations within their arthropod vector provides novel insights into arbovirus evolution. During infection of their arthropod vectors, arthropod-borne viruses (arboviruses) such as dengue viruses traverse several anatomical barriers that are believed to cause dramatic reductions in population size. Such population bottlenecks challenge the maintenance of viral genetic diversity, which is considered critical for fitness and adaptability of arboviruses. Anatomical barriers in the vector were previously associated with both maintenance of arboviral genetic diversity and alteration of the variant repertoire. However, the relative role of random processes and natural selection, and the influence of vector genetic heterogeneity have not been elucidated. In this study, we used high-throughput sequencing to monitor dengue virus genetic diversity during infection of several genetic backgrounds of their mosquito vector. Our results show that initial infection of the vector is randomly founded by only a few tens of individual virus genomes. The overall level of viral genetic diversity generated during infection was predominantly under purifying selection but differed significantly between mosquito genetic backgrounds. Thus, in addition to random evolutionary forces and the purging of deleterious mutations that shape dengue virus genetic diversity during vector infection, our results also point to a novel role for vector genetic factors in the genetic breadth of virus populations.
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Affiliation(s)
- Sebastian Lequime
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- Université Pierre et Marie Curie, Cellule Pasteur UPMC, Paris, France
- * E-mail: (SL); (LL)
| | - Albin Fontaine
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- Equipe Résidente de Recherche d’Infectiologie Tropicale, Division Expertise, Institut de Recherche Biomédicale des Armées, Brétigny-sur-Orge, France
| | - Meriadeg Ar Gouilh
- Unité Environnement et Risques Infectieux, Cellule d’Intervention Biologique d’Urgence, Department of Infection and Epidemiology, Institut Pasteur, Paris, France
- EA4655, Unité Risques Microbiens U2RM, Université de Caen Normandie, Caen, France
| | - Isabelle Moltini-Conclois
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
| | - Louis Lambrechts
- Insect-Virus Interactions Group, Department of Genomes and Genetics, Institut Pasteur, Paris, France
- Centre National de la Recherche Scientifique, Unité de Recherche Associée 3012, Paris, France
- * E-mail: (SL); (LL)
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Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0292. [PMID: 26150658 DOI: 10.1098/rstb.2014.0292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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50
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Hapuarachchi HC, Koo C, Kek R, Xu H, Lai YL, Liu L, Kok SY, Shi Y, Chuen RLT, Lee KS, Maurer-Stroh S, Ng LC. Intra-epidemic evolutionary dynamics of a Dengue virus type 1 population reveal mutant spectra that correlate with disease transmission. Sci Rep 2016; 6:22592. [PMID: 26940650 PMCID: PMC4778070 DOI: 10.1038/srep22592] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/17/2016] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013–2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design.
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Affiliation(s)
| | - Carmen Koo
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Relus Kek
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Helen Xu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yee Ling Lai
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Lilac Liu
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Suet Yheng Kok
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Yuan Shi
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667
| | - Raphael Lee Tze Chuen
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671
| | - Kim-Sung Lee
- School of Life Sciences and Chemical Technology, Ngee Ann Polytechnic, Block 83, #04-00, 535 Clementi Road, Singapore 599489
| | - Sebastian Maurer-Stroh
- Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street #07-01, Matrix Building, Singapore 138671.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551.,National Public Health Laboratory (NPHL), Ministry of Health (MOH), 3 Biopolis Drive, #05-14 to 16, Synapse, Singapore 138623
| | - Lee Ching Ng
- Environmental Health Institute, National Environment Agency, 11, Biopolis Way, #06-05-08, Singapore 138667.,School of Biological Sciences (SBS), Nanyang Technological University (NTU), 60 Nanyang Drive, Singapore 637551
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