Cited by 1,009Evolution and Genetic DynamicsMathematical and Theoretical Epidemiology and Ecology ModelsRNA and protein synthesis mechanisms

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Viral Quasispecies Evolution

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Domingo, Esteban, Sheldon, Julie, Perales, Celia·2012·Microbiology and Molecular Biology Reviews

DOI 10.1128/mmbr.05023-11PMC PMC3372249

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Abstract

SUMMARY: Evolution of RNA viruses occurs through disequilibria of collections of closely related mutant spectra or mutant clouds termed viral quasispecies. Here we review the origin of the quasispecies concept and some biological implications of quasispecies dynamics. Two main aspects are addressed: (i) mutant clouds as reservoirs of phenotypic variants for virus adaptability and (ii) the internal interactions that are established within mutant spectra that render a virus ensemble the unit of selection. The understanding of viruses as quasispecies has led to new antiviral designs, such as lethal mutagenesis, whose aim is to drive viruses toward low fitness values with limited chances of fitness recovery. The impact of quasispecies for three salient human pathogens, human immunodeficiency virus and the hepatitis B and C viruses, is reviewed, with emphasis on antiviral treatment strategies. Finally, extensions of quasispecies to nonviral systems are briefly mentioned to emphasize the broad applicability of quasispecies theory.

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Hallmarks of Cancer: The Next Generation
Hanahan, D., & Weinberg, R. A. (2011) · Cell · doi:10.1016/j.cell.2011.02.013 · Cited by 66,590
The Tragedy of the Commons: The population problem has no technical solution; it requires a fundamental extension in morality.
Hardin, G. (1968) · Science · doi:10.1126/science.162.3859.1243 · Cited by 25,167
A Statistical Distribution Function of Wide Applicability
Weibull, W. (1951) · Journal of Applied Mechanics · doi:10.1115/1.4010337 · Cited by 11,646
EVOLUTION IN MENDELIAN POPULATIONS
Wright, S. (1931) · Genetics · doi:10.1093/genetics/16.2.97 · Cited by 9,237
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
The Neutral Theory of Molecular Evolution
Kimura, M. (1983) · Cambridge University Press eBooks · doi:10.1017/cbo9780511623486 · Cited by 6,300
DNA Repair and Mutagenesis
Friedberg, E. C., Walker, G. C., Siede, W., Wood, R. D., Schultz, R. A., & Ellenberger, T. (2005) · doi:10.1128/9781555816704 · Cited by 5,683
5-Fluorouracil: mechanisms of action and clinical strategies
Longley, D. B., Harkin, D. P., & Johnston, P. G. (2003) · Nature Reviews Cancer · doi:10.1038/nrc1074 · Cited by 5,332
The HCV Life Cycle: In vitro Tissue Culture Systems and Therapeutic Targets
Gerold, G., & Pietschmann, T. (2014) · Digestive Diseases · doi:10.1159/000360830 · Cited by 4,871
Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infection
Ho, D. D., Neumann, A. U., Perelson, A. S., Chen, W., Leonard, J. M., & Markowitz, M. H. (1995) · Nature · doi:10.1038/373123a0 · Cited by 4,261

Show all 888 references

Research works printed but not linked: 29

BergelsonJM. 2010. Receptors, p 73–86. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
BiebricherCK EigenM. 1988. Kinetics of RNA replication by Q.β replicase, p 1–21. In DomingoE HollandJJ AhlquistP (ed), RNA genetics, vol I. CRC Press, Boca Raton, FL.
ClotetB. 2011. The HIV and hepatitis. Drug resistance and PK guide, 11th ed. Fundació Lluita contra la SIDA, Badalona, Spain.
CrowellRL Lonberg-HolmK (ed). 1986. Virus attachment and entry into cells. ASM, Washington, DC.
De PalmaAM NeytsJ. 2010. Antiviral drugs, p 461–482. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington DC.
DomingoE (ed). 2006. Quasispecies: concepts and implications for virology Curr. Top. Microbiol. Immunol. 299:1–422.
DomingoE. 2007. Virus evolution, p 389–421. In KnipeDM HowleyPM (ed), Fields virology, 5th ed. Lippincott Williams & Wilkins Philadelphia, PA.
DomingoE. 2006. Genomics of viruses, p 369–388. In HackerJ DobrindtU (ed), Pathogenomics: genome analysis of pathogenic microbes. Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany.
DomingoE HollandJJ. 1988. High error rates population equilibrium, and evolution of RNA replication systems, p 3–36. In DomingoE HollandJJ AhlquistP (ed), RNA genetics, vol III. CRC Press, Boca Raton, FL.
DomingoE HollandJJ. 2005. The origin and evolution of viruses, p 11–23. In MahyBWJ ter MeulenV (ed), Topley and Wilson's microbiology and microbial infections, 10th ed, vol 1. Virology. Hodder Arnold, London, United Kingdom.
10.1016/B978-0-12-374153-0.00004-7 · DOI
DomingoE. 2010. Mutation, quasispecies and lethal mutagenesis, p 197–211. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
EigenM BiebricherCK. 1988. Sequence space and quasispecies distribution, p 211–245. In DomingoE AhlquistP HollandJJ (ed), RNA genetics, vol 3. CRC Press, Boca Raton, FL.
FengZ LemonSM. 2010. Hepatitis A virus, p 383–396. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
FrankSA. 1996. The design of natural and artificial adaptive systems, p 451–505. In RoseMR LauderGV (ed), Adaptation. Academic Press, San Diego, CA.
FutuymaDJ SlatkinM (ed). 1983. Coevolution. Sinauer Associates Inc. Sunderland, MA.
KingAMQ LefkowitzEJ AdamsMJ CarstensEB (ed). 2011. Virus taxonomy. Ninth report of the International Committee on Taxonomy of Viruses. Elsevier Academic Press, San Diego, CA.
KnowlesNJ HoviT KingAMQ StanwayG. 2010. Overview of taxonomy, p 19–32. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
MateuMG VerdaguerN. 2004. Functional and structural aspects of the interaction of foot-and-mouth disease virus with antibodies, p 223–260. In SobrinoF DomingoE (ed), Foot-and-mouth disease. Current perspectives. Horizon Bioscience, Wymondham, United Kingdom.
Maynard-SmithJ. 1976. The evolution of sex. Cambridge University Press, Cambridge, United Kingdom.
PetersCJ. 2007. Emerging viral diseases, p 605–625. In KnipeDM HowleyPM (ed), Fields virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
SalemiM AMVandamme (ed). 2004. The phylogeny handbook. A practical approach to DNA and protein phylogeny. Cambridge University Press Cambridge United Kingdom.
SeegerC ZoulimF MasonWS. 2007. Hepadnaviruses, p 2977–3027. In KnipeDM HowleyPM (ed), Fields virology, 5th ed. Lippincott Williams & Wilkins, Philadelphia, PA.
SellersRF. 1971. Quantitative aspects of the spread of foot-and-mouth disease. Vet. Bull. 41:431–439.
SimmondsP. 2010. Recombination in the evolution of picornaviruses, p 229–238. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
TracyS ObersteMS DrescherKM. 2008. Group B coxsackievirus. Curr. Top. Microbiol. Immunol. 323:1–340.
VignuzziM AndinoR. 2010. Biological implications of picornavirus fidelity mutants, p 213–228. In EhrenfeldE DomingoE RoosRF (ed), The picornaviruses. ASM Press, Washington, DC.
WimmerE PaulAV. 2010. The making of a picornavirus genome, p 33–58. In EhrenfeldE DomingoE RoosRP (ed), The picornaviruses. ASM Press, Washington, DC.
WrightS. 1932. The roles of mutation, inbreeding, crossbreading, and selection in evolution, p. 356–366. In Proceedings of the VI International Congress of Genetics, vol 1. Brooklyn Botanic Garden, Brooklyn, NY

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Authors: Domingo, E., Sheldon, J., & Perales, C.
Affiliations: Consejo Superior de Investigaciones Científicas (ES)
ORCID: Domingo, Esteban
Sheldon, Julie
Perales, Celia
Venue: Microbiology and Molecular Biology Reviews
Publisher: American Society for Microbiology
Published: 2012-06
Volume: 76
Issue: 2
Pages: 159-216
ISSN: 1092-2172 (ISSN-L)
1098-5557
DOI: 10.1128/mmbr.05023-11
PMC: PMC3372249
OpenAlex: W2073918065
Cited by: 1,009
References: 888
Citations by year: 2026: 51 · 2025: 38 · 2024: 56 · 2023: 55 · 2022: 58 · 2021: 130 · 2020: 104 · 2019: 96 · 2018: 76 · 2017: 76 · 2016: 77 · 2015: 75 · 2014: 63 · 2013: 38 · 2012: 15
FWCI: 7.47
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Microbiology and Molecular Biology Reviews (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Physical Sciences › Mathematics › Applied Mathematics › Mathematical and Theoretical Epidemiology and Ecology Models
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: viral quasispecies, RNA viruses, units of selection, lethal mutagenesis, antiviral strategies, HIV, hepatitis B virus, hepatitis C virus
MeSH terms: Hepatitis B virus, HIV, Humans, RNA Viruses, Selection, Genetic, Virus Diseases, Genome, Viral, Evolution, Molecular

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Viral Quasispecies Evolution

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