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Virus as populations = composition, complexity, quasispecies, dynamics, and biological implications /

Record Type:	Language materials, printed : Monograph/item
Title/Author:	Virus as populations/ Esteban Domingo.
Reminder of title:	composition, complexity, quasispecies, dynamics, and biological implications /
Author:	Domingo, Esteban,
Published:	London, England :Academic Press, : 2020.,
Description:	1 online resource (428 p.)
Subject:	Viruses. -
Online resource:	https://www.sciencedirect.com/science/book/9780128163313
ISBN:	9780128163320 (electronic bk.)

Virus as populations = composition, complexity, quasispecies, dynamics, and biological implications /
Domingo, Esteban,

Virus as populationscomposition, complexity, quasispecies, dynamics, and biological implications /[electronic resource] :Esteban Domingo. - Second edition. - London, England :Academic Press,2020. - 1 online resource (428 p.)

Includes bibliographical references and indexes.

Machine generated contents note: 1.Introduction to virus origins and their role in biological evolution -- Abbreviations -- 1.1.Considerations on biological diversity -- 1.2.Some questions of current virology and the scope of this book -- 1.3.The staggering ubiquity and diversity of viruses: limited morphotypes -- 1.4.Origin of life: a brief historical account and current views -- 1.4.1.Early synthesis of oligonucleotides: a possible ancestral positive selection -- 1.4.2.A primitive RNA world -- 1.4.3.Life from mistakes, information from noninformation: origin of replicons -- 1.4.4.Uptake of energy and a second primitive positive selection -- 1.4.5.Definitions of life -- 1.5.Theories of the origins of viruses -- 1.5.1.Viruses are remnants of primeval genetic elements -- 1.5.2.Viruses are the result of regressive microbial evolution -- 1.5.3.Viruses are liberated autonomous entities -- 1.5.4.Viruses are elements for long-term coevolution -- 1.5.5.Viruses from vesicles --

ISBN: 9780128163320 (electronic bk.)Subjects--Topical Terms:

579004
Viruses.
Index Terms--Genre/Form:

761329
Electronic books

LC Class. No.: QR360 / .D665 2020

Dewey Class. No.: 579.2

National Library of Medicine Call No.: 2020 B-717

Virus as populations = composition, complexity, quasispecies, dynamics, and biological implications /
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245 1 0 $a Virus as populations $h [electronic resource] : $b composition, complexity, quasispecies, dynamics, and biological implications / $c Esteban Domingo.
250 $a Second edition.
260 $a London, England : $b Academic Press, $c 2020.
300 $a 1 online resource (428 p.)
504 $a Includes bibliographical references and indexes.
505 0 $a Machine generated contents note: 1.Introduction to virus origins and their role in biological evolution -- Abbreviations -- 1.1.Considerations on biological diversity -- 1.2.Some questions of current virology and the scope of this book -- 1.3.The staggering ubiquity and diversity of viruses: limited morphotypes -- 1.4.Origin of life: a brief historical account and current views -- 1.4.1.Early synthesis of oligonucleotides: a possible ancestral positive selection -- 1.4.2.A primitive RNA world -- 1.4.3.Life from mistakes, information from noninformation: origin of replicons -- 1.4.4.Uptake of energy and a second primitive positive selection -- 1.4.5.Definitions of life -- 1.5.Theories of the origins of viruses -- 1.5.1.Viruses are remnants of primeval genetic elements -- 1.5.2.Viruses are the result of regressive microbial evolution -- 1.5.3.Viruses are liberated autonomous entities -- 1.5.4.Viruses are elements for long-term coevolution -- 1.5.5.Viruses from vesicles --
505 0 $a Note continued: 1.6.Teachings from mycoviruses -- 1.7.Being alive versus being part of life -- 1.7.1.Role of viruses in the evolution of the biosphere -- 1.7.2.Current exchanges of genetic material -- 1.7.3.Symbiotic relationships -- 1.8.Virus and disease -- 1.9.Viral and cellular dynamics and the tree of life -- 1.10.Overview and concluding remarks -- References -- 2.Molecular basis of genetic variation of viruses: error-prone replication -- Abbreviations -- 2.1.Universal need for genetic variation -- 2.2.Molecular basis of mutation -- 2.3.Types and effects of mutations -- 2.4.Inferences on evolution drawn from mutation types -- 2.5.Mutation rates and frequencies for DNA and RNA genomes -- 2.5.1.Undesired consequences of the confusion between mutation rates and mutation frequencies -- 2.6.Evolutionary origins, evolvability, and consequences of high mutation rates: fidelity mutants --
505 0 $a Note continued: 2.7.Hypermutagenesis and its application to generating a variation: APOBEC and ADAR activities -- 2.8.Error-prone replication and maintenance of genetic information: instability of laboratory viral constructs -- 2.9.Recombination in DNA and RNA viruses -- 2.9.1.Molecular occurrence versus observed recombination -- 2.10.Genome segment reassortment -- 2.11.Transition toward viral genome segmentation: implications for general evolution -- 2.12.Mutation, recombination, and reassortment as individual and combined evolutionary forces -- 2.12.1.Mechanistically unavoidable versus evolutionarily relevant genetic variation -- 2.13.Overview and concluding remarks -- References -- 3.Darwinian principles acting on highly mutable viruses -- Abbreviations -- 3.1.Theoretical frameworks to approach virus evolution -- 3.1.1.Theory and experiment -- 3.2.Genetic variation, competition, and selection -- 3.3.Mutant distributions during DNA and RNA virus infections --
505 0 $a Note continued: 3.4.Positive versus negative selection: two sides of the same coin -- 3.5.Selection and random drift -- 3.6.Viral quasispecies -- 3.6.1.The origins of quasispecies theory -- 3.6.2.Deterministic versus stochastic quasispecies -- 3.6.3.Mutant spectra, master genomes, and consensus sequences -- 3.6.4.Measurement of quasispecies complexity -- 3.6.5.Some key points on the impact of quasispecies in virology -- 3.7.Sequence space and state transitions -- 3.7.1.Virus evolution as a movement in sequence space -- 3.7.2.Exploration of sequence space and the sampling problem: viral population size as a key parameter -- 3.8.Modulating effects of mutant spectra: interference, cooperation and complementation. An ensemble as the unit of selection -- 3.8.1.Molecular mechanisms of complementation and interference -- 3.8.2.Individual versus group selection -- 3.8.3.Stochastic effects in selected collectivities --
505 0 $a Note continued: 3.9.Viral populations in connection with biological complexity -- 3.10.Overview and concluding remarks -- References -- 4.Interaction of virus populations with their hosts -- Abbreviations -- 4.1.Contrasting viral and host population numbers -- 4.1.1.Productive power of some viral infections -- 4.1.2.Population size limitations and the effect of bottlenecks: the effective population size -- 4.2.Types of constraints and evolutionary trade' offs in virus-host interactions -- 4.2.1.Long-term history dictates basal constraints -- 4.2.2.Cell-dependent constraints: No free lunch -- 4.2.3.Constraints in host organisms: contrast with man-made antiviral interventions -- 4.3.Codon usage as a selective constraint: virus attenuation through codon and codon-pair deoptimization -- 4.3.1.The synonymous codon space can affect an evolutionary outcome -- 4.4.Modifications of host cell tropism and host range --
505 0 $a Note continued: 4.4.1.Nonstructural viral proteins and RNA in cell tropism and host range of viruses -- 4.5.Trait coevolution: mutual influences between antigenic variation and tropism change -- 4.6.Escape from antibody and cytotoxic T cell responses in viral persistence: fitness cost -- 4.7.Antigenic variation in the absence of immune selection -- 4.8.Constraints as a demand on mutation rate levels -- 4.9.Multifunctional viral proteins in interaction with host factors: joker substitutions -- 4.10.Alternating selective pressures: the case of arboviruses -- 4.10.1.The sophistication of pathogen-vector-host interactions in plant viruses -- 4.11.Overview and concluding remarks -- References -- 5.Viral fitness as a measure of adaptation -- Abbreviations -- 5.1.Origin of the fitness concept and its relevance to viruses -- 5.1.1.Measurement of viral fitness -- 5.1.2.Power and limitations of fitness measurements -- 5.1.3.Dissection of fitness determinants --
505 0 $a Note continued: 5.2.The challenge of fitness in vivo -- 5.3.Fitness landscapes -- 5.3.1.Justification of ruggedness in fitness landscapes for viruses -- 5.4.Population factors on fitness variations: collective fitness and perturbations by environmental heterogeneity -- 5.5.Quasispecies memory and fitness recovery -- 5.5.1.Implications of quasispecies memory: harbinger mutations -- 5.6.The relationship between fitness and virulence -- 5.7.Fitness landscapes for survival: the advantage of the flattest -- 5.8.Fitness and function -- 5.8.1.Very low fitness versus lethality -- 5.9.Epidemiological fitness -- 5.10.Overview and concluding remarks -- References -- 6.Virus population dynamics examined with experimental model systems -- Abbreviations -- 6.1.Value of experimental evolution -- 6.2.Experimental systems in cell culture and in vivo -- 6.2.1."To culture is to disturb" -- 6.2.2.Experimental evolution in vivo --
505 0 $a Note continued: 6.3.Viral dynamics in controlled environments: alterations of viral subpopulations -- 6.4.Persistent infections in cell culture: virus-cell coevolution -- 6.4.1.Back again 4000 million years: contingency in evolution-- 6.5.Teachings from plaque-to-plaque transfers -- 6.5.1.Muller's ratchet and the advantage of sex -- 6.5.2.Molecular basis of fitness decrease: deep fluctuations, massive extinctions, and rare survivors -- 6.6.Limits to fitness gain and loss -- 6.7.Competitive exclusion principle and Red Queen hypothesis -- 6.7.1.Contingent neutrality in virus -- 6.8.Studies with reconstructed quasispecies -- 6.9.Quasispecies dynamics in cell culture and in vivo -- 6.10.Overview and concluding remarks -- References -- 7.Long-term virus evolution in nature -- Abbreviations -- 7.1.Introduction to the spread of viruses. Outbreaks, epidemics, and pandemics -- 7.2.Reproductive ratio as a predictor of epidemic potential. Indeterminacies in transmission events --
505 0 $a Note continued: 7.3.Rates of virus evolution in nature -- 7.3.1.Influence of the time of sampling -- 7.3.2.Interhost versus intrahost rate of evolution -- 7.3.3.Rate discrepancies and the clock hypothesis -- 7.4.Long-term antigenic diversification of viruses -- 7.4.1.Widely different number of serotypes among genetically variable viruses -- 7.4.2.Similar frequencies of monoclonal antibody-escape mutants in viruses differing in antigenic diversity -- 7.5.Comparing viral genomes. Sequence alignments and databases -- 7.6.Phylogenetic relationships among viruses. Evolutionary models -- 7.7.Extinction, survival, and emergence of viral pathogens. Back to the mutant clouds -- 7.7.1.Factors in viral emergence -- 7.7.2.Complexity revisited -- 7.8.Overview and concluding remarks -- References -- 8.Quasispecies dynamics in disease prevention and control -- Abbreviations -- 8.1.Medical interventions as selective constraints --
505 0 $a Note continued: 8.2.Different manifestations of virus evolution in the prevention and treatment of viral disease -- 8.3.Antiviral vaccines and the adaptive potential of viruses -- 8.3.1.Some requirements for the design of vaccines to control highly variable viruses -- 8.3.2.Vaccination-induced evolution -- 8.4.Resistance to antiviral inhibitors -- 8.4.1.Replicative load and antiviral resistance -- 8.4.2.Barriers to drug resistance -- 8.4.3.Drug efficacy, mutant frequencies, and selection of escape mutants -- 8.4.4.Phenotypic barrier and selective strength -- 8.4.5.Multiple pathways and evolutionary history in the acquisition of drug resistance -- 8.5.Molecular mechanisms of antiviral resistance -- 8.5.1.Some examples with HIV-1 -- 8.5.2.Mutation site and functional barrier -- 8.5.3.Additional considerations on escape mutant frequencies -- 8.6.Antiviral resistance without prior exposure to antiviral agents --
505 0 $a Note continued: 8.7.Fitness or a fitness-associated trait as a multidrug-resistance mechanism -- 8.8.Viral load, fitness, and disease progression -- 8.9.Limitations of simplified reagents and small molecules as antiviral agents -- 8.10."Hit early, hit hard" -- 8.11.Information and global action -- 8.12.Overview and concluding remarks -- References -- 9.Trends in antiviral strategies -- Abbreviations -- 9.1.The challenge -- 9.1.1.Virus as moving targets -- 9.2.Practiced and proposed strategies to confront the moving target challenge with antiviral inhibitors -- 9.2.1.Combination treatments -- 9.2.2.Split treatments -- 9.2.3.Targeting cellular functions -- 9.2.4.Use of drugs that stimulate the host innateimmune system -- 9.2.5.Combined use of immunotherapy and chemotherapy -- 9.3.Lethal mutagenesis and the error threshold -- 9.3.1.Reconciliation of theory and experiment: a proposal -- 9.4.Virus extinction by mutagenic agents --
505 0 $a Note continued: 9.4.1.The search for new mutagenic nucleotide analogs -- 9.5.Lethal mutagenesis in vivo: complications derived from multiple mechanisms of drug action -- the case of ribavirin -- 9.5.1.Favipiravir as antiviral inhibitor and mutagen -- 9.6.Virus resistance to mutagenic agents: multiple mechanisms and evidence of abortive escape pathways -- 9.6.1.Unpredictable effects of some polymerase substitutions -- 9.6.2.Polymerase fidelity and modulation of nucleotide incorporation -- 9.7.Virus extinction as the outcome of replacement of virus subpopulations: tempo and mode of mutation acquisition -- 9.8.The interplay between inhibitors and mutagenic agents in viral populations: sequential versus combination treatments -- 9.9.Prospects for a clinical application of lethal mutagenesis -- 9.10.Some atypical proposals -- 9.11.Overview and concluding remarks -- References -- 10.Collective population effects in nonviral systems -- Abbreviations --
505 0 $a Note continued: 10.1.Concept generalization -- 10.2.Viruses and cells: the genome size-mutation-time coordinates revisited -- 10.2.1.A comparison of antiviral and antibiotic resistance -- 10.3.Darwinian principles and intrapopulation interactions acting on bacterial cell populations -- 10.4.The dynamics of unicellular parasites in the control of parasitic disease -- 10.5.Cancer dynamics: heterogeneity and group behavior -- 10.5.1.The two-component theory of cancer: similarities with other biological systems, and therapeutic implications -- 10.6.Collective behavior of prions -- 10.7.Molecular mechanisms of variation and clonality in evolution -- 10.8.Genomes, clones, consortia, and networks -- 10.8.1.Interacting networks and power laws -- 10.9.An additional level of virus vulnerability? -- 10.10.Overview and concluding remarks -- References.
588 $a Description based on print version record
650 0 $a Viruses. $3 579004
650 2 $a Virus Physiological Phenomena. $3 1344302
655 4 $a Electronic books $2 local. $3 761329
856 4 0 $u https://www.sciencedirect.com/science/book/9780128163313