Viral quasispecies evolution
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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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Some mutations in SARS-CoV-2 will be advantageous and subject to rapid natural selection.
“although most will be detrimental or confer no advantage to the virus, some will be advantageous and be the subject of rapid natural selection (Domingo et al., 2012; Rambaut et al., 2020).”
From Reduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum (2021) · cites this paper as Domingo et al., 2012
Cites
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 · see citing works
Hardin, G. (1968) · Science · doi:10.1126/science.162.3859.1243 · Cited by 25,167 · see citing works
A Statistical Distribution Function of Wide Applicability
Weibull, W. (1951) · Journal of Applied Mechanics · doi:10.1115/1.4010337 · Cited by 11,666 · see citing works
EVOLUTION IN MENDELIAN POPULATIONS
Wright, S. (1931) · Genetics · doi:10.1093/genetics/16.2.97 · Cited by 9,078 · see citing works
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 · see citing works
The Neutral Theory of Molecular Evolution
Kimura, M. (1983) · Cambridge University Press eBooks · doi:10.1017/cbo9780511623486 · Cited by 6,300 · see citing works
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 · see citing works
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 · see citing works
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 4,854 · see citing works
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 · see citing works
Selforganization of matter and the evolution of biological macromolecules
Eigen, M. (1971) · Die Naturwissenschaften · doi:10.1007/bf00623322 · Cited by 3,788 · see citing works
HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation Time
Perelson, A. S., Neumann, A. U., Markowitz, M. H., Leonard, J. M., & Ho, D. D. (1996) · Science · doi:10.1126/science.271.5255.1582 · Cited by 3,533 · see citing works
Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance
Ge, D., Fellay, J., Thompson, A. J. V., Simon, J. S., Shianna, K. V., Urban, T. J., Heinzen, E. L., Qiu, P., Bertelsen, A. H., Muir, A. J., et al. (2009) · Nature · doi:10.1038/nature08309 · Cited by 3,510 · see citing works
Gauze, G. F. (1934) · doi:10.5962/bhl.title.4489 · Cited by 3,321 · see citing works
Viral dynamics in human immunodeficiency virus type 1 infection
Wei, X., Ghosh, S. K., Taylor, M. E., Johnson, V. A., Emini, E. A., Deutsch, P., Lifson, J. D., Bonhoeffer, S., Nowak, M. A., Hahn, B. H., et al. (1995) · Nature · doi:10.1038/373117a0 · Cited by 3,259 · see citing works
Punctuated equilibria: an alternative to phyletic gradualism
Eldredge, N., Gould, S. J., & Schöpf, T. J. M. (1972) · Cited by 3,132 · see citing works
Global epidemiology of hepatitis C virus infection
Shepard, C. W., Finelli, L., & Alter, M. J. (2005) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(05)70216-4 · Cited by 2,758 · see citing works
Competition and Biodiversity in Spatially Structured Habitats
Tilman, D. G. (1994) · Ecology · doi:10.2307/1939377 · Cited by 2,747 · see citing works
The relation of recombination to mutational advance
Muller, H. J. (1964) · Mutation Research · doi:10.1016/0027-5107(64)90047-8 · Cited by 2,512 · see citing works
Valen, L. V. (1973) · Medical Entomology and Zoology · Cited by 2,468 · see citing works
Evolutionary Dynamics: Exploring the Equations of Life
NOWAK, M. A. (2006) · doi:10.2307/j.ctvjghw98 · Cited by 2,438 · see citing works
Antibody neutralization and escape by HIV-1
Wei, X., Decker, J. M., Wang, S., Hui, H., Kappes, J. C., Wu, X., Salazar-Gonzalez, J. F., Salazar, M. G., Kilby, J. M., Saag, M. S., et al. (2003) · Nature · doi:10.1038/nature01470 · Cited by 2,421 · see citing works
Control of Viremia in Simian Immunodeficiency Virus Infection by CD8 + Lymphocytes
Schmitz, J. E., Kuroda, M. J., Santra, S., Sasseville, V. G., Simon, M. A., Lifton, M. A., Rácz, P., Tenner‐Racz, K., Dalesandro, M. R., Scallon, B. J., et al. (1999) · Science · doi:10.1126/science.283.5403.857 · Cited by 2,167 · see citing works
Hepatitis C Viral Dynamics in Vivo and the Antiviral Efficacy of Interferon-α Therapy
Neumann, A. U., Lam, N. P., Dahari, H., Gretch, D. R., Wiley, T. E., Layden, T. J., & Perelson, A. S. (1998) · Science · doi:10.1126/science.282.5386.103 · Cited by 2,111 · see citing works
Binding of Hepatitis C Virus to CD81
Pileri, P., Uematsu, Y., Campagnoli, S., Galli, G., Falugi, F., Petracca, R., Weiner, A. J., Houghton, M., Rosa, D., Grandi, G., et al. (1998) · Science · doi:10.1126/science.282.5390.938 · Cited by 2,059 · see citing works
The impact of next-generation sequencing technology on genetics
Mardis, E. R. (2008) · Trends in Genetics · doi:10.1016/j.tig.2007.12.007 · Cited by 2,050 · see citing works
HIV Population Dynamics in Vivo: Implications for Genetic Variation, Pathogenesis, and Therapy
Coffin, J. M. (1995) · Science · doi:10.1126/science.7824947 · Cited by 1,963 · see citing works
The Hypercycle: A principle of natural self-organization
Eigen, M., & Schuster, P. M. (1979) · Cited by 1,906 · see citing works
King, J. L., & Jukes, T. H. (1969) · Science · doi:10.1126/science.164.3881.788 · Cited by 1,776 · see citing works
Immunological memory and protective immunity: understanding their relation
Ahmed, R., & Gray, D. (1996) · Science · doi:10.1126/science.272.5258.54 · Cited by 1,775 · see citing works
A principle of natural self-organization: Part A: Emergence of the hypercycle
Eigen, M., & Schuster, P. (1977) · Naturwissenschaften · doi:10.1007/bf00450633 · Cited by 1,752 · see citing works
UPDATE ON DRUG RESISTANCE MUTATIONS IN HIV-1
&NA; (2001) · Infectious Diseases in Clinical Practice · doi:10.1097/00019048-200106000-00020 · Cited by 1,685 · see citing works
Coevolution of hosts and parasites
Anderson, R. M., & May, R. M. (1982) · Parasitology · doi:10.1017/s0031182000055360 · Cited by 1,658 · see citing works
RNA VIRUS MUTATIONS AND FITNESS FOR SURVIVAL
Domingo, E., & Holland, J. J. (1997) · Annual Review of Microbiology · doi:10.1146/annurev.micro.51.1.151 · Cited by 1,514 · see citing works
Self-citationRapid Evolution of RNA Genomes
Holland, J. J., Spindler, K. R., Horodyski, F. M., Grabau, E. A., Nichol, S. T., & VandePol, S. (1982) · Science · doi:10.1126/science.7041255 · Cited by 1,478 · see citing works
Seeger, C., & Mason, W. S. (2000) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.64.1.51-68.2000 · Cited by 1,457 · see citing works
Bioorganic and Medicinal Chemistry of Fluorine
Bégué, J., & Bonnet‐Delpon, D. (2007) · Wiley eBooks · doi:10.1002/9780470281895 · Cited by 1,417 · see citing works
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens
Grenfell, B. T., Pybus, O. G., Gog, J. R., Wood, J. L. N., Daly, J. M., MUMFORD, J. A., & Holmes, E. C. (2004) · Science · doi:10.1126/science.1090727 · Cited by 1,370 · see citing works
Mechanisms Underlying Lineage Commitment and Plasticity of Helper CD4 + T Cells
O’Shea, J. J., & Paul, W. E. (2010) · Science · doi:10.1126/science.1178334 · Cited by 1,338 · see citing works
Molecular Basis for High Virulence of Hong Kong H5N1 Influenza A Viruses
Hatta, M., Gao, P., Halfmann, P., & Kawaoka, Y. (2001) · Science · doi:10.1126/science.1062882 · Cited by 1,336 · see citing works
Functions and Regulation of RNA Editing by ADAR Deaminases
Nishikura, K. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060208-105251 · Cited by 1,303 · see citing works
Sanjuán, R., Nebot, M. R., Chirico, N., Mansky, L. M., & Belshaw, R. D. (2010) · Journal of Virology · doi:10.1128/jvi.00694-10 · Cited by 1,247 · see citing works
Muller, H. (1932) · American Naturalist · doi:10.1086/280418 · Cited by 1,242 · see citing works
Claudin-1 is a hepatitis C virus co-receptor required for a late step in entry
Evans, M. J., von Hahn, T., Tscherne, D. M., Syder, A. J., Panis, M., Wölk, B., Hatziioannou, T., McKeating, J. A., Bieniasz, P. D., & Rice, C. M. (2007) · Nature · doi:10.1038/nature05654 · Cited by 1,233 · see citing works
Rapid evolution of the neutralizing antibody response to HIV type 1 infection
Richman, D. D., Wrin, T., Little, S. J., & Petropoulos, C. J. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0630530100 · Cited by 1,196 · see citing works
Snijder, E. J., Bredenbeek, P. J., Dobbe, J. C., Thiel, V., Ziebuhr, J., Poon, L. L. M., Guan, Y., Rozanov, M. N., Spaan, W. J. M., & Gorbalenya, A. E. (2003) · Journal of Molecular Biology · doi:10.1016/s0022-2836(03)00865-9 · Cited by 1,188 · see citing works
Marsh, M., & Helenius, A. (2006) · Cell · doi:10.1016/j.cell.2006.02.007 · Cited by 1,186 · see citing works
Borrow, P., Lewicki, H. A., Wei, X., Horwitz, M. S., Peffer, N. J., Meyers, H. L., Nelson, J. A., Gairin, J. E., Hahn, B. H., Oldstone, M. B. A., et al. (1997) · Nature Medicine · doi:10.1038/nm0297-205 · Cited by 1,181 · see citing works
Mansky, L. M., & Temin, H. M. (1995) · Journal of Virology · doi:10.1128/jvi.69.8.5087-5094.1995 · Cited by 1,154 · see citing works
Mutation rates among RNA viruses
Drake, J. W., & Holland, J. J. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.24.13910 · Cited by 1,143 · see citing works
The role of parenteral antischistosomal therapy in the spread of hepatitis C virus in Egypt
Frank, C., Mohamed, M. K., Strickland, G. T., Lavanchy, D., Arthur, R. R., Magder, L. S., Khoby, T. E., Abdel-Wahab, Y., Ohn, E. S. A., Anwar, W., et al. (2000) · The Lancet · doi:10.1016/s0140-6736(99)06527-7 · Cited by 1,131 · see citing works
Vignuzzi, M., Stone, J. K., Arnold, J. J., Cameron, C. E., & Andino, R. (2006) · Nature · doi:10.1038/nature04388 · Cited by 1,116 · see citing works
Course and outcome of hepatitis C
Hoofnagle, J. H. (2002) · Hepatology · doi:10.1002/hep.1840360704 · Cited by 1,083 · see citing works
Tian, K., Yu, X., Zhao, T., Feng, Y., Cao, Z., Wang, C., Hu, Y., Chen, X., Hu, D., Tian, X., et al. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000526 · Cited by 1,063 · see citing works
A General Model of Prion Strains and Their Pathogenicity
Collinge, J., & Clarke, A. R. (2007) · Science · doi:10.1126/science.1138718 · Cited by 1,058 · see citing works
Viral dynamics in hepatitis B virus infection.
Nowak, M. A., Bonhoeffer, S., Hill, A. M., Boehme, R. E., Thomas, H. C., & McDade, H. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.9.4398 · Cited by 1,043 · see citing works
Accelerated evolution and Muller’s Rachet in endosymbiotic bacteria
Moran, N. A. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.7.2873 · Cited by 1,017 · see citing works
Human immunodeficiency virus genetic variation that can escape cytotoxic T cell recognition
Phillips, R. E., Rowland-Jones, S. L., Nixon, D. F., Gotch, F. M., Edwards, J. P., Ogunlesi, A. O., Elvin, J. G., Rothbard, J. B., Bangham, C. R. M., Rizza, C. R., et al. (1991) · Nature · doi:10.1038/354453a0 · Cited by 1,015 · see citing works
Enomoto, N., Sakuma, I., Asahina, Y., Kurosaki, M., Murakami, T., Yamamoto, C., Ogura, Y., Izumi, N., Marumo, F., & Sato, C. (1996) · New England Journal of Medicine · doi:10.1056/nejm199601113340203 · Cited by 997 · see citing works
THE MAINTENANCE OF THE ACCURACY OF PROTEIN SYNTHESIS AND ITS RELEVANCE TO AGEING
Orgel, L. E. (1963) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.49.4.517 · Cited by 968 · see citing works
The Population Genetics of dN/dS
Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962 · see citing works
Human occludin is a hepatitis C virus entry factor required for infection of mouse cells
Ploß, A., Evans, M. J., Gaysinskaya, V. A., Panis, M., You, H., de Jong, Y. P., & Rice, C. M. (2009) · Nature · doi:10.1038/nature07684 · Cited by 940 · see citing works
A single amino acid in the PB2 gene of influenza A virus is a determinant of host range
Subbarao, K., London, W. T., & Murphy, B. R. (1993) · Journal of Virology · doi:10.1128/jvi.67.4.1761-1764.1993 · Cited by 936 · see citing works
Martell, M., Esteban, J. I., Quer, J., Genescà, J., Weiner, A. J., Esteban, R., Guàrdia, J., & Gómez, J. (1992) · Journal of Virology · doi:10.1128/jvi.66.5.3225-3229.1992 · Cited by 929 · see citing works
Shankarappa, R., Margolick, J. B., Gange, S. J., Rodrigo, A. G., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C. R., Learn, G. H., He, X., et al. (1999) · Journal of Virology · doi:10.1128/jvi.73.12.10489-10502.1999 · Cited by 926 · see citing works
The Outcome of Acute Hepatitis C Predicted by the Evolution of the Viral Quasispecies
Farci, P., Shimoda, A., Coiana, A., Diaz, G., Peddis, G., Melpolder, J. C., Strazzera, A., Chien, D. Y., Muñoz, S. J., Balestrieri, A., et al. (2000) · Science · doi:10.1126/science.288.5464.339 · Cited by 882 · see citing works
Biological and biomedical implications of the co-evolution of pathogens and their hosts
Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B., & Levin, B. R. (2002) · Nature Genetics · doi:10.1038/ng1202-569 · Cited by 869 · see citing works
Self-citationThe three-dimensional structure of foot-and-mouth disease virus at 2.9 Å resolution
Acharya, R., Fry, E. E., Stuart, D. I., Fox, G., Rowlands, D. J., & Brown, F. (1989) · Nature · doi:10.1038/337709a0 · Cited by 866 · see citing works
Genetic diversity and evolution of hepatitis C virus – 15 years on
Peter Simmonds, K. (2004) · Journal of General Virology · doi:10.1099/vir.0.80401-0 · Cited by 863 · see citing works
RNA virus error catastrophe: Direct molecular test by using ribavirin
Crotty, S., Cameron, C. E., & Andino, R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.111085598 · Cited by 853 · see citing works
Genetic Heterogeneity of Hepatitis C Virus: Quasispecies and Genotypes
Bukh, J., Miller, R. H., & Purcell, R. H. (1995) · Seminars in Liver Disease · doi:10.1055/s-2007-1007262 · Cited by 843 · see citing works
Quasispecies Theory and the Behavior of RNA Viruses
Lauring, A. S., & Andino, R. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001005 · Cited by 840 · see citing works
Fiers, W. C., Contreras, R., Duerinck, F., Haegeman, G., Iserentant, D., Merregaert, J., Jou, W. M., Molemans, F., Raeymaekers, A., den Berghe, A. V., et al. (1976) · Nature · doi:10.1038/260500a0 · Cited by 814 · see citing works
Gale, M., Korth, M. J., Tang, N., Tan, S., Hopkins, D. A., Dever, T. E., Polyak, S. J., Gretch, D. R., & Katze, M. G. (1997) · Virology · doi:10.1006/viro.1997.8493 · Cited by 810 · see citing works
Bioinformatics: sequence and genome analysis
(2001) · Choice Reviews Online · doi:10.5860/choice.39-0923 · Cited by 766 · see citing works
Salazar-Gonzalez, J. F., Salazar, M. G., Keele, B. F., Learn, G. H., Giorgi, E. E., Li, H., Decker, J. M., Wang, S., Baalwa, J., Kraus, M. H., et al. (2009) · The Journal of Experimental Medicine · doi:10.1084/jem.20090378 · Cited by 763 · see citing works
Woese, C. R. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.132266999 · Cited by 762 · see citing works
Viral Infections of Humans. Epidemiology and Control.
Evans, A. S. 1.-1. (1983) · Annals of Internal Medicine · doi:10.7326/0003-4819-98-2-273_2 · Cited by 753 · see citing works
Graham, R. L., & Baric, R. S. (2009) · Journal of Virology · doi:10.1128/jvi.01394-09 · Cited by 738 · see citing works
Virus attenuation by genome-scale changes in codon pair bias
Coleman, J. R., Papamichail, D., Skiena, S., Futcher, B., Wimmer, E., & Mueller, S. (2008) · Science · doi:10.1126/science.1155761 · Cited by 715 · see citing works
Hepatitis B Virus Resistance to Nucleos(t)ide Analogues
Zoulim, F., & LOCARNINI, S. A. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.08.063 · Cited by 707 · see citing works
Shafritz, D. A., Shouval, D., Sherman, H. I., Hadziyannis, S. J., & Kew, M. C. (1981) · New England Journal of Medicine · doi:10.1056/nejm198110293051807 · Cited by 706 · see citing works
THE NATURAL-SELECTION THEORY OF ANTIBODY FORMATION
Jerne, N. K. (1955) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.41.11.849 · Cited by 702 · see citing works
The Hypercycle: A principle of natural self-organization Part B: The abstract hypercycle
Eigen, M., & Schuster, P. (1978) · Naturwissenschaften · doi:10.1007/bf00420631 · Cited by 702 · see citing works
The viral polymerase mediates adaptation of an avian influenza virus to a mammalian host
Gabriel, G., Dauber, B., Wolff, T., Planz, O., Klenk, H., & Stech, J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0507415102 · Cited by 693 · see citing works
Eigen, M., McCaskill, J., & Schuster, P. (1988) · The Journal of Physical Chemistry · doi:10.1021/j100335a010 · Cited by 670 · see citing works
Prisoner's dilemma in an RNA virus
Turner, P. E., & Chao, L. (1999) · Nature · doi:10.1038/18913 · Cited by 659 · see citing works
Temporal fluctuations in HIV quasispecies in vivo are not reflected by sequential HIV isolations
Meyerhans, A., Cheynier, R., Albert, J., Seth, M., Kwok, S. Y., Sninsky, J. J., Morfeldt-Månson, L., Åsjö, B., & Wain–Hobson, S. (1989) · Cell · doi:10.1016/0092-8674(89)90942-2 · Cited by 652 · see citing works
Treating viral hepatitis C: efficacy, side effects, and complications
Manns, M. P., Wedemeyer, H., & Cornberg, M. (2006) · Gut · doi:10.1136/gut.2005.076646 · Cited by 650 · see citing works
Viral and immunological determinants of hepatitis C virus clearance, persistence, and disease
Thimme, R., Bukh, J., Spangenberg, H. C., Wieland, S. F., Pemberton, J., Steiger, C., Govindarajan, S., Purcell, R. H., & Chisari, F. V. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.202608299 · Cited by 639 · see citing works
Evolution of digital organisms at high mutation rates leads to survival of the flattest
Wilke, C. O., Wang, J. L., Ofria, C., Lenski, R. E., & Adami, C. (2001) · Nature · doi:10.1038/35085569 · Cited by 636 · see citing works
Virus dynamics and drug therapy
Bonhoeffer, S., May, R. M., Shaw, G. M., & Nowak, M. A. (1997) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.94.13.6971 · Cited by 630 · see citing works
Minskaia, E., Hertzig, T., Gorbalenya, A., Campanacci, V., Cambillau, C., Canard, B., & Ziebuhr, J. (2006) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0508200103 · Cited by 618 · see citing works
Microbial Threats to Health: Emergence, Detection, and Response
Smolinski, M. S., Hamburg, M. A., & Lederberg, J. (2003) · Cited by 616 · see citing works
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus.
Sanjuán, R., Moya, A., & Elena, S. F. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0400146101 · Cited by 582 · see citing works
Systems biology and combination therapy in the quest for clinical efficacy
Fitzgerald, J. B., Schoeberl, B., Nielsen, U. B., & Sorger, P. K. (2006) · Nature Chemical Biology · doi:10.1038/nchembio817 · Cited by 570 · see citing works
Nucleotide sequence heterogeneity of an RNA phage population
Domingo, E., Sabo, D. L., Taniguchi, T., & Weissmann, C. (1978) · Cell · doi:10.1016/0092-8674(78)90223-4 · Cited by 565 · see citing works
Self-citationGenetic Variation in HTLV-III/LAV Over Time in Patients with AIDS or at Risk for AIDS
Hahn, B. H., Shaw, G. M., Taylor, M. E., Redfield, R. R., Markham, P., Salahuddin, S. Z., Wong‐Staal, F., Gallo, R. C., Parks, E. S., & Parks, W. P. (1986) · Science · doi:10.1126/science.3012778 · Cited by 564 · see citing works
Hepatitis B e antigen-negative chronic hepatitis B
Hadziyannis, S. J., & Vassilopoulos, D. (2001) · Hepatology · doi:10.1053/jhep.2001.27834 · Cited by 558 · see citing works
Control of cccDNA function in hepatitis B virus infection
Levrero, M., Pollicino, T., Petersen, J., Belloni, L., Raimondo, G., & Dandri, M. (2009) · Journal of Hepatology · doi:10.1016/j.jhep.2009.05.022 · Cited by 552 · see citing works
Origin and Evolution of Viruses
Holland, J. J., & Domingo, E. (1998) · Virus Genes · doi:10.1023/a:1007989407305 · Cited by 524 · see citing works
Self-citationThe role of evolution in the emergence of infectious diseases
Antia, R., Regoes, R. R., Koella, J. C., & Bergstrom, C. T. (2003) · Nature · doi:10.1038/nature02104 · Cited by 511 · see citing works
Course and outcome of hepatitis C
Hoofnagle, J. H. (2002) · Hepatology · doi:10.1053/jhep.2002.36227 · Cited by 509 · see citing works
Resistance to Direct Antiviral Agents in Patients With Hepatitis C Virus Infection
Sarrazin, C., & Zeuzem, S. (2009) · Gastroenterology · doi:10.1053/j.gastro.2009.11.055 · Cited by 506 · see citing works
An integrated view of protein evolution
Pál, C., Papp, B., & Lercher, M. J. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1838 · Cited by 502 · see citing works
de Jong, J. J., de Ronde, A., Keulen, W., Tersmette, M., & Goudsmit, J. (1992) · Journal of Virology · doi:10.1128/jvi.66.11.6777-6780.1992 · Cited by 500 · see citing works
Domingo, E., Martı́nez-Salas, E., Sobrino, F., de la Torre, J. C., Portela, A., Ortı́n, J., López‐Galíndez, C., Pérez‐Breña, P., Villanueva, N., Nájera, R., et al. (1985) · Gene · doi:10.1016/0378-1119(85)90017-4 · Cited by 499 · see citing works
Self-citationMUTATION LOAD AND THE SURVIVAL OF SMALL POPULATIONS
Lynch, M. F., & Gabriel, W. (1990) · Evolution · doi:10.1111/j.1558-5646.1990.tb05244.x · Cited by 492 · see citing works
Denison, M. R., Graham, R. L., Donaldson, E., Eckerle, L. D., & Baric, R. S. (2011) · RNA Biology · doi:10.4161/rna.8.2.15013 · Cited by 490 · see citing works
The accumulation of deleterious genes in a population—Muller's Ratchet
Haigh, J. (1978) · Theoretical Population Biology · doi:10.1016/0040-5809(78)90027-8 · Cited by 489 · see citing works
Eckerle, L. D., Becker, M. M., Halpin, R., Li, K., Venter, E., Lu, X., Scherbakova, S., Graham, R. L., Baric, R. S., Stockwell, T. B., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000896 · Cited by 489 · see citing works
Natural Selection and the Concept of a Protein Space
Smith, J. (1970) · Nature · doi:10.1038/225563a0 · Cited by 488 · see citing works
Fitness of RNA virus decreased by Muller’s ratchet
Chao, L. (1990) · Nature · doi:10.1038/348454a0 · Cited by 488 · see citing works
The Hypercycle: A principle of natural self-organization Part C: The realistic hypercycle
Eigen, M., & Schuster, P. (1978) · The Science of Nature · doi:10.1007/bf00439699 · Cited by 487 · see citing works
Polymorphism due to selection of varying direction
Haldane, J. B. S., & Jayakar, S. D. (1963) · Journal of Genetics · doi:10.1007/bf02986143 · Cited by 483 · see citing works
Hu, W. S., & Temin, H. M. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.4.1556 · Cited by 476 · see citing works
RIP: the evolutionary cost of genome defense
Galagan, J. E., & Selker, E. U. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.07.007 · Cited by 464 · see citing works
Cupples, C. G., & Miller, J. H. (1989) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.86.14.5345 · Cited by 453 · see citing works
Metabolism and mechanism of action of 5-fluorouracil
Parker, W. B., & Cheng, Y. C. (1990) · Pharmacology & Therapeutics · doi:10.1016/0163-7258(90)90056-8 · Cited by 450 · see citing works
Martínez‐Picado, J., Prado, J. G., Fry, E. E., Pfafferott, K. J., Leslie, A. J., Chetty, S., Thobakgale, C., Honeyborne, I., Crawford, H., Matthews, P. C., et al. (2006) · Journal of Virology · doi:10.1128/jvi.80.7.3617-3623.2006 · Cited by 447 · see citing works
Multiply infected spleen cells in HIV patients
Jung, A., Maier, R., Vartanian, J., Bocharov, G. A., Jung, V., Fischer, U., Meese, E. U., Wain–Hobson, S., & Meyerhans, A. (2002) · Nature · doi:10.1038/418144a · Cited by 437 · see citing works
Dynamics of HIV-1 recombination in its natural target cells
Levy, D. N., Aldrovandi, G. M., Kutsch, O., & Shaw, G. M. (2004) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0306764101 · Cited by 437 · see citing works
Time to Hit HIV, Early and Hard
Ho, D. D. (1995) · New England Journal of Medicine · doi:10.1056/nejm199508173330710 · Cited by 434 · see citing works
Darwinian Evolution of Prions in Cell Culture
Li, J., Browning, S. R., Mahal, S. P., Oelschlegel, A. M., & Weissmann, C. (2009) · Science · doi:10.1126/science.1183218 · Cited by 434 · see citing works
Molecular Epidemiology and Evolution of Enterovirus 71 Strains Isolated from 1970 to 1998
Brown, B. A., Oberste, M. S., Alexander, J. P., Kennett, M., & Pallansch, M. A. (1999) · Journal of Virology · doi:10.1128/jvi.73.12.9969-9975.1999 · Cited by 431 · see citing works
Discovery of an Ebolavirus-Like Filovirus in Europe
Negredo, A., Palacios, G. F., Vázquez‐Morón, S., González, F., Dopazo, H., Molero, F., Javier Juste, B., Quetglas, J., Savji, N., Martínez, M. D. L. C., et al. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002304 · Cited by 430 · see citing works
von Hahn, T., Yoon, J. C., Alter, H. J., Rice, C. M., Rehermann, B., Balfe, P., & McKeating, J. A. (2006) · Gastroenterology · doi:10.1053/j.gastro.2006.12.008 · Cited by 424 · see citing works
Erickson, A. L., Kimura, Y., Igarashi, S., Eichelberger, J. S., Houghton, M., Sidney, J., McKinney, D. M., Sette, A., Hughes, A. L., & Walker, C. M. (2001) · Immunity · doi:10.1016/s1074-7613(01)00245-x · Cited by 411 · see citing works
Ageing of Clones of Mammalian Cells
Orgel, L. E. (1973) · Nature · doi:10.1038/243441a0 · Cited by 410 · see citing works
Wang, C., Mitsuya, Y., Gharizadeh, B., Ronaghi, M., & Shafer, R. W. (2007) · Genome Research · doi:10.1101/gr.6468307 · Cited by 408 · see citing works
Pfeiffer, J. K., & Kirkegaard, K. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1232294100 · Cited by 405 · see citing works
Chun, T., Davey, R. T., Ostrowski, M., Justement, J. S., Engel, D., Mullins, J. I., & Fauci, A. S. (2000) · Nature Medicine · doi:10.1038/77481 · Cited by 403 · see citing works
Origins of CD4+ effector and central memory T cells
Pepper, M., & Jenkins, M. K. (2011) · Nature Immunology · doi:10.1038/ni.2038 · Cited by 401 · see citing works
HIV-1 can escape from RNA interference by evolving an alternative structure in its RNA genome
Westerhout, E. M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki220 · Cited by 400 · see citing works
Bioinformatics: Sequence and Genome Analysis
Romero, P. R. (2004) · Briefings in Bioinformatics · doi:10.1093/bib/5.4.393-a · Cited by 397 · see citing works
Replicative Fitness of Protease Inhibitor-Resistant Mutants of Human Immunodeficiency Virus Type 1
Martínez‐Picado, J., Savara, A. V., Sutton, L., & D’Aquila, R. T. (1999) · Journal of Virology · doi:10.1128/jvi.73.5.3744-3752.1999 · Cited by 396 · see citing works
Simen, B. B., Simons, J. F., Hullsiek, K. H., Novak, R. M., MacArthur, R. D., Baxter, J. D., Huang, C., Lubeski, C. K., Turenchalk, G. S., Braverman, M. S., et al. (2009) · The Journal of Infectious Diseases · doi:10.1086/596736 · Cited by 391 · see citing works
Increased Fidelity Reduces Poliovirus Fitness and Virulence under Selective Pressure in Mice
Pfeiffer, J. K., & Kirkegaard, K. (2005) · PLoS Pathogens · doi:10.1371/journal.ppat.0010011 · Cited by 383 · see citing works
High Rate of Recombination throughout the Human Immunodeficiency Virus Type 1 Genome
Jetzt, A. E., Yu, H., Klarmann, G. J., Ron, Y., Preston, B. D., & Dougherty, J. P. (2000) · Journal of Virology · doi:10.1128/jvi.74.3.1234-1240.2000 · Cited by 379 · see citing works
Johnson, J. A., Jin-fen, L., Wei, X., Lipscomb, J. T., Irlbeck, D. M., Craig, C., Smith, A. J., Bennett, D., Monsour, M., Sandstrom, P. A., et al. (2008) · PLoS Medicine · doi:10.1371/journal.pmed.0050158 · Cited by 372 · see citing works
Jackson, T., Ellard, F. M., ABU-GHAZALEH, R., Brookes, S. M., Blakemore, W. E., Corteyn, A., Stuart, D. I., Newman, J. W. I., & King, A. M. Q. (1996) · Journal of Virology · doi:10.1128/jvi.70.8.5282-5287.1996 · Cited by 372 · see citing works
MULLER'S RATCHET AND MUTATIONAL MELTDOWNS
Gabriel, W., Lynch, M., & Bürger, R. (1993) · Evolution · doi:10.1111/j.1558-5646.1993.tb01266.x · Cited by 371 · see citing works
Nijhuis, M., Schuurman, R., de Jong, D. C. M., Erickson, J. W., Gustchina, E., Albert, J., Schipper, P. J., Gulnik, S., & Boucher, C. A. (1999) · AIDS · doi:10.1097/00002030-199912030-00006 · Cited by 364 · see citing works
The Fecal Viral Flora of Wild Rodents
Phan, T., Kapusinszky, B., Wang, C., Rose, R. K., Lipton, H., & Delwart, E. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1002218 · Cited by 363 · see citing works
Swetina, J., & Schuster, P. M. (1982) · Biophysical Chemistry · doi:10.1016/0301-4622(82)87037-3 · Cited by 361 · see citing works
Lethal mutagenesis of HIV with mutagenic nucleoside analogs
Loeb, L. A., Essigmann, J. M., Kazazi, F., Zhang, J., Rose, K. D., & Mullins, J. I. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.4.1492 · Cited by 357 · see citing works
A BACTERIOPHAGE CONTAINING RNA
Loeb, T., & Zinder, N. D. (1961) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.47.3.282 · Cited by 354 · see citing works
Functional classification of drugs by properties of their pairwise interactions
Yeh, P. J., Tschumi, A. I., & Kishony, R. (2006) · Nature Genetics · doi:10.1038/ng1755 · Cited by 350 · see citing works
Kuntzen, T., Timm, J., Berical, A. C., Lennon, N. J., Berlin, A. M., Young, S., Lee, B., Heckerman, D. E., Carlson, J. M., Reyor, L. L., et al. (2008) · Hepatology · doi:10.1002/hep.22549 · Cited by 348 · see citing works
Long-term therapy of chronic hepatitis B with lamivudine
Lau, D., Khokhar, F., Doo, E. C., Ghany, M. G., Herion, D. W., Park, Y., Kleiner, D. E., Schmid, P., Condreay, L. D., Gauthier, J., et al. (2000) · Hepatology · doi:10.1053/jhep.2000.17912 · Cited by 345 · see citing works
HIV-1 adaptation to NK-cell-mediated immune pressure
Alter, G., Heckerman, D. E., Schneidewind, A., Fadda, L., Kadie, C. M., Carlson, J. M., Oniangue-Ndza, C., Martin, M. P., Li, B., Khakoo, S. I., et al. (2011) · Nature · doi:10.1038/nature10237 · Cited by 343 · see citing works
Haaland, R. E., Hawkins, P. A., Salazar-Gonzalez, J. F., Johnson, A., Tichacek, A., Karita, E., Manigart, O., Mulenga, J., Keele, B. F., Shaw, G. M., et al. (2009) · PLoS Pathogens · doi:10.1371/journal.ppat.1000274 · Cited by 342 · see citing works
Error catastrophe and antiviral strategy
Eigen, M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.212514799 · Cited by 339 · see citing works
Making sense of cancer genomic dataPreprint
Chin, L., Hahn, W. C., Getz, G. A., & Meyerson, M. M. (2011) · Genes & Development · doi:10.1101/gad.2017311 · Cited by 336 · see citing works
Weiner, A. J., Erickson, A. L., Kansopon, J., Crawford, K., Muchmore, E., Hughes, A. L., Houghton, M., & Walker, C. M. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.7.2755 · Cited by 334 · see citing works
The Origins of Life: <i>From the birth of life to the origin of language</i>
Maynard Smith, J., & SzathmáRy, E. (1999) · doi:10.1093/oso/9780198504931.001.0001 · Cited by 334 · see citing works
Antibody‐dependent enhancement of viral infection: molecular mechanisms and in vivo implications
Takada, A., & Kawaoka, Y. (2003) · Reviews in Medical Virology · doi:10.1002/rmv.405 · Cited by 332 · see citing works
Rapid fitness losses in mammalian RNA virus clones due to Muller’s ratchet
Duarte, E., Clarke, D., Moya, A., Domingo, E., & Holland, J. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.13.6015 · Cited by 331 · see citing works
Self-citationOhAinle, M., Balmaseda, Á., Macalalad, A. R., Téllez, Y., Zody, M. C., SABORÍO, S. I., Nuñez, A., Lennon, N. J., Birren, B. W., Gordon, A. L., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3003084 · Cited by 330 · see citing works
High Fidelity of Murine Hepatitis Virus Replication Is Decreased in nsp14 Exoribonuclease Mutants
Eckerle, L. D., Lu, X., Sperry, S. M., Choi, L., & Denison, M. R. (2007) · Journal of Virology · doi:10.1128/jvi.01296-07 · Cited by 328 · see citing works
Unifying Evolutionary Dynamics
Page, K. M., & Nowak, M. A. (2002) · Journal of Theoretical Biology · doi:10.1006/jtbi.2002.3112 · Cited by 322 · see citing works
Evolution of foot-and-mouth disease virus
Domingo, E., Escarmı́s, C., Baranowski, É., Ruiz-Jarabo, C. M., Carrillo, E. C., Núñez, J. I., & Sobrino, F. (2003) · Virus Research · doi:10.1016/s0168-1702(02)00259-9 · Cited by 321 · see citing works
Self-citationBiological and Structural Characterization of a Host-Adapting Amino Acid in Influenza Virus
Yamada, S., Hatta, M., Staker, B. L., Watanabe, S., Imai, M., Shinya, K., Sakai‐Tagawa, Y., Ito, M., Ozawa, M., Watanabe, T., et al. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1001034 · Cited by 319 · see citing works
Korber, B., Kunstman, K., Patterson, B. K., Furtado, M. R., McEvilly, M. M., Levy, R. M., & Wolinsky, S. M. (1994) · Journal of Virology · doi:10.1128/jvi.68.11.7467-7481.1994 · Cited by 318 · see citing works
Johnson, P. R., Schnepp, B. C., Zhang, J., Connell, M. J., Greene, S. M., Yuste, E., Desrosiers, R. C., & Clark, K. R. (2009) · Nature Medicine · doi:10.1038/nm.1967 · Cited by 310 · see citing works
Modelling T-cell memory by genetic marking of memory T cells in vivo
Jacob, J., & Baltimore, D. (1999) · Nature · doi:10.1038/21208 · Cited by 308 · see citing works
Hepatitis C virus resistance to protease inhibitors
Halfon, P., & Locarnini, S. (2011) · Journal of Hepatology · doi:10.1016/j.jhep.2011.01.011 · Cited by 306 · see citing works
Rapid Evolution of Pandemic Noroviruses of the GII.4 Lineage
Bull, R. A., Eden, J., Rawlinson, W. D., & White, P. A. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000831 · Cited by 301 · see citing works
Enhanced Fidelity of 3TC-Selected Mutant HIV-1 Reverse Transcriptase
Wainberg, M. A., Drosopoulos, W. C., Salomón, H., Hsu, M., Borkow, G., Parniak, M. A., Gu, Z., Song, Q., Manne, J., Islam, S. A., et al. (1996) · Science · doi:10.1126/science.271.5253.1282 · Cited by 301 · see citing works
Sá‐Carvalho, D., Rieder, E. A., Baxt, B., Rodarte, R. S., Tanuri, A., & Mason, P. W. (1997) · Journal of Virology · doi:10.1128/jvi.71.7.5115-5123.1997 · Cited by 299 · see citing works
EXPERIMENTAL ANALYSIS OF VITO VOLTERRA'S MATHEMATICAL THEORY OF THE STRUGGLE FOR EXISTENCE
Gause, G. F. (1934) · Science · doi:10.1126/science.79.2036.16-a · Cited by 299 · see citing works
Zuñiga, R., Lucchetti, A., Galvan, P., Sanchez, S., Sánchez, C. N., Hernández, A. G., Sanchez, H., Frahm, N., Linde, C., Hewitt, H. S., et al. (2006) · Journal of Virology · doi:10.1128/jvi.80.6.3122-3125.2006 · Cited by 294 · see citing works
Borrow, P., Evans, C. F., & Oldstone, M. B. (1995) · Journal of Virology · doi:10.1128/jvi.69.2.1059-1070.1995 · Cited by 293 · see citing works
HIV rebounds from latently infected cells, rather than from continuing low-level replication
Joos, B., Fischer, M., Kuster, H., Pillai, S. K., Wong, J. K., Böni, J., Hirschel, B. J., Weber, R. K., Trkola, A., Günthard, H. F., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0804192105 · Cited by 291 · see citing works
Hepatitis C and liver transplantation
Berenguer, M., López‐Labrador, F. X., & Wright, T. L. (2001) · Journal of Hepatology · doi:10.1016/s0168-8278(01)00179-9 · Cited by 290 · see citing works
Bartosch, B., Verney, G., Dreux, M., Donot, P., Morice, Y., Pénin, F., Pawlotsky, J., Lavillette, D., & Cosset, F. (2005) · Journal of Virology · doi:10.1128/jvi.79.13.8217-8229.2005 · Cited by 290 · see citing works
Viruses as Quasispecies: Biological Implications
Domingo, E., Martín, V., Perales, C., Grande-Pérez, A., García-Arriaza, J., & Arias, A. (2006) · Current Topics in Microbiology and Immunology · doi:10.1007/3-540-26397-7_3 · Cited by 290 · see citing works
Self-citationZeng, Q., Langereis, M. A., van Vliet, A. L. W., Huizinga, E. G., & de Groot, R. J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800502105 · Cited by 289 · see citing works
Kaplan, G. G., Totsuka, A., Thompson, P., Akatsuka, T., Moritsugu, Y., & Feinstone, S. M. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00803.x · Cited by 285 · see citing works
Mutagen-directed Attenuation of Rift Valley Fever Virus as a Method for Vaccine Development
Caplen, H., Peters, C. J., & Bishop, D. H. L. (1985) · Journal of General Virology · doi:10.1099/0022-1317-66-10-2271 · Cited by 283 · see citing works
Maag, D., Castro, C. D., Hong, Z., & Cameron, C. E. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.c100349200 · Cited by 282 · see citing works
Antibody recognition of picornaviruses and escape from neutralization: a structural view
Mateu, M. G. (1995) · Virus Research · doi:10.1016/0168-1702(95)00048-u · Cited by 282 · see citing works
Theory of lethal mutagenesis for viruses
Bull, J. J., Sanjuán, R., & Wilke, C. O. (2007) · Journal of Virology · doi:10.1128/jvi.01624-06 · Cited by 281 · see citing works
Wong, J. K., Ignacio, C. C., Torriani, F. J., Havlir, D. V., Fitch, N. J. S., & Richman, D. D. (1997) · Journal of Virology · doi:10.1128/jvi.71.3.2059-2071.1997 · Cited by 280 · see citing works
Evolution of Cell Recognition by Viruses
Baranowski, É., Ruiz-Jarabo, C. M., & Domingo, E. (2001) · Science · doi:10.1126/science.1058613 · Cited by 279 · see citing works
Self-citationHepatitis B virus genetic variability and evolution
Kay, A., & Zoulim, F. (2007) · Virus Research · doi:10.1016/j.virusres.2007.02.021 · Cited by 278 · see citing works
Evolvability of an RNA virus is determined by its mutational neighbourhood
Burch, C. L., & Chao, L. (2000) · Nature · doi:10.1038/35020564 · Cited by 276 · see citing works
Fischer, W., Ganusov, V. V., Giorgi, E. E., Hraber, P., Keele, B. F., Leitner, T., Han, C. S., Gleasner, C. D., Green, L., Lo, C., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012303 · Cited by 276 · see citing works
APOBEC proteins and intrinsic resistance to HIV-1 infection
Malim, M. H. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0185 · Cited by 276 · see citing works
Quasispecies theory in the context of population genetics
Wilke, C. O. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-44 · Cited by 276 · see citing works
Live attenuated influenza virus vaccines by computer-aided rational design
Mueller, S., Coleman, J. R., Papamichail, D., Ward, C. B., Nimnual, A., Futcher, B., Skiena, S., & Wimmer, E. (2010) · Nature Biotechnology · doi:10.1038/nbt.1636 · Cited by 275 · see citing works
Quantitation of relative fitness and great adaptability of clonal populations of RNA viruses
Holland, J. J., de la Torre, J. C., Clarke, D. K., & Duarte, E. A. (1991) · Journal of Virology · doi:10.1128/jvi.65.6.2960-2967.1991 · Cited by 274 · see citing works
Parrish, C. R., & Kawaoka, Y. (2005) · Annual Review of Microbiology · doi:10.1146/annurev.micro.59.030804.121059 · Cited by 270 · see citing works
Exponential increases of RNA virus fitness during large population transmissions.
Novella, I. S., Duarte, E. A., Elena, S. F., Moyá, A., Domingo, E., & Holland, J. J. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.13.5841 · Cited by 270 · see citing works
Self-citationShukla, D. D., & Ward, C. W. (1988) · Journal of General Virology · doi:10.1099/0022-1317-69-11-2703 · Cited by 269 · see citing works
Spontaneous Mutation: Comparative Rates of Spontaneous Mutation
Drake, J. W. (1969) · Nature · doi:10.1038/2211132a0 · Cited by 269 · see citing works
Nakamura, S., Yang, C.-S., Sakon, N., Ueda, M., Tougan, T., Yamashita, A., Goto, N., Takahashi, K., Yasunaga, T., Ikuta, K., et al. (2009) · PLoS ONE · doi:10.1371/journal.pone.0004219 · Cited by 267 · see citing works
Sobrino, F., Dávila, M., Ortı́n, J., & Domingo, E. (1983) · Virology · doi:10.1016/0042-6822(83)90258-1 · Cited by 267 · see citing works
Self-citationOn the nature of virus quasispecies
Eigen, M. (1996) · Trends in Microbiology · doi:10.1016/0966-842x(96)20011-3 · Cited by 266 · see citing works
Single amino-acid changes in HIV envelope affect viral tropism and receptor binding
Cordonnier, A. M., Montagnier, L., & Emerman, M. (1989) · Nature · doi:10.1038/340571a0 · Cited by 265 · see citing works
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Liu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2021) · Cell Host & Microbe · doi:10.1016/j.chom.2021.01.014 · Cited by 725 · see citing works
“We did not directly address the fitness of the mutants generated in this study, and any studies of the fitness of the VSVSARS-CoV-2 variants would pertain to their relative replicative fitness measured in cell culture (Domingo et al., 2012).”
BackgroundReduced neutralization of SARS-CoV-2 B.1.617 by vaccine and convalescent serum
Liu, C., Ginn, H. M., Dejnirattisai, W., Supasa, P., Wang, B., Tuekprakhon, A., Nutalai, R., Zhou, D., Mentzer, A. J., Zhao, Y., et al. (2021) · Cell · doi:10.1016/j.cell.2021.06.020 · Cited by 669 · see citing works
Subissi, L., Posthuma, C. C., Collet, A., Zevenhoven-Dobbe, J. C., Gorbalenya, A. E., Decroly, É., Snijder, E. J., Canard, B., & Imbert, I. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1323705111 · Cited by 580 · see citing works
Malone, B., Urakova, N., Snijder, E. J., & Campbell, E. A. (2021) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-021-00432-z · Cited by 538 · see citing works
Shen, Z., Xiao, Y., Kang, L., Ma, W., Shi, L., Zhang, L., Zhou, Z., Yang, J., Zhong, J., Yang, D., et al. (2020) · Clinical Infectious Diseases · doi:10.1093/cid/ciaa203 · Cited by 513 · see citing works
Smith, E. C., Blanc, H., Vignuzzi, M., & Denison, M. R. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003565 · Cited by 428 · see citing works
Bosch, A., Pintó, R., & Guix, S. (2014) · Clinical Microbiology Reviews · doi:10.1128/cmr.00013-14 · Cited by 311 · see citing works
Andino, R., & Domingo, E. (2015) · Virology · doi:10.1016/j.virol.2015.03.022 · Cited by 374 · see citing works
Self-citationDomingo, E., & Perales, C. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008271 · Cited by 330 · see citing works
Self-citationAgostini, M. L., Pruijssers, A. J. P., Chappell, J. D., Gribble, J., Lu, X., Andres, E. L., Bluemling, G. R., Lockwood, M. A., Sheahan, T. P., Sims, A. M., et al. (2019) · Journal of Virology · doi:10.1128/jvi.01348-19 · Cited by 328 · see citing works
Ogando, N. S., Zevenhoven-Dobbe, J. C., van der Meer, Y., Bredenbeek, P. J., Posthuma, C. C., & Snijder, E. J. (2020) · Journal of Virology · doi:10.1128/jvi.01246-20 · Cited by 276 · see citing works
Functions and consequences of AID/APOBEC-mediated DNA and RNA deamination
Pecori, R., Giorgio, S. D., Lorenzo, J. P., & Papavasiliou, F. N. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00459-8 · Cited by 254 · see citing works
Elevated virulence of an emerging viral genotype as a driver of honeybee loss
McMahon, D. P., Natsopoulou, M. E., Doublet, V., Fürst, M. A., Weging, S., Brown, M. J. F., Gogol‐Döring, A., & Paxton, R. J. (2016) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2016.0811 · Cited by 244 · see citing works
Evolutionary consequences of drug resistance: shared principles across diverse targets and organisms
Hughes, D., & Andersson, D. I. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3922 · Cited by 243 · see citing works
Hepatitis E Virus Genotypes and Evolution: Emergence of Camel Hepatitis E Variants
Sridhar, S., Teng, J. L. L., Chiu, T.-H., Lau, S. K. P., & Woo, P. C. Y. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18040869 · Cited by 238 · see citing works
New strategies against drug resistance to herpes simplex virus
Jiang, Y., Feng, H., Lin, Y., & Guo, X. (2016) · International Journal of Oral Science · doi:10.1038/ijos.2016.3 · Cited by 227 · see citing works
Virological and Immunological Outcomes of Coinfections
Kumar, N., Sharma, S., Barua, S., Tripathi, B. N., & Rouse, B. T. (2018) · Clinical Microbiology Reviews · doi:10.1128/cmr.00111-17 · Cited by 226 · see citing works
Diversification of self-replicating molecules
Sadownik, J. W., Mattia, E., Nowak, P., & Otto, S. (2016) · Nature Chemistry · doi:10.1038/nchem.2419 · Cited by 214 · see citing works
Mordecai, G. J., Wilfert, L., Martin, S. J., Jones, I. M., & Schroeder, D. C. (2015) · The ISME Journal · doi:10.1038/ismej.2015.178 · Cited by 205 · see citing works
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities
Chiara, M., D’Erchia, A. M., Gissi, C., Manzari, C., Parisi, A., Resta, N., Zambelli, F., Picardi, E., Pavesi, G., Horner, D. S., et al. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa297 · Cited by 202 · see citing works
Duque-Valencia, J., Sarute, N., Olarte‐Castillo, X. A., & Ruíz-Saenz, J. (2019) · Viruses · doi:10.3390/v11070582 · Cited by 197 · see citing works
Advantages of genome sequencing by long-read sequencer using SMRT technology in medical area
Nakano, K., Shiroma, A., Shimoji, M., Tamotsu, H., Ashimine, N., Ohki, S., Shinzato, M., Minami, M., Nakanishi, T., Teruya, K., et al. (2017) · Human Cell · doi:10.1007/s13577-017-0168-8 · Cited by 182 · see citing works
Hepatitis A virus: Host interactions, molecular epidemiology and evolution
Vaughan, G., Rossi, L. M. G., Forbi, J. C., de Paula, V. S., Purdy, M. A., Xia, G., & Khudyakov, Y. E. (2013) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2013.10.023 · Cited by 169 · see citing works
Citrus tristeza virus: evolution of complex and varied genotypic groups
Harper, S. J. (2013) · Frontiers in Microbiology · doi:10.3389/fmicb.2013.00093 · Cited by 169 · see citing works
Genetic conflicts: the usual suspects and beyond
McLaughlin, R. N., & Malik, H. S. (2017) · Journal of Experimental Biology · doi:10.1242/jeb.148148 · Cited by 167 · see citing works
Vector competence of European mosquitoes for West Nile virus
Vogels, C. B. F., Göertz, G. P., Pijlman, G. P., & Koenraadt, C. J. M. (2017) · Emerging Microbes & Infections · doi:10.1038/emi.2017.82 · Cited by 164 · see citing works
Virus factories: biogenesis and structural design
de Castro, I. F., Volonté, L., & Risco, C. (2012) · Cellular Microbiology · doi:10.1111/cmi.12029 · Cited by 156 · see citing works
A comprehensive review on the antiviral activities of chalcones
Elkhalifa, D. H., Al‐Hashimi, I., Moustafa, A. A., & Khalil, A. A. (2020) · Journal of drug targeting · doi:10.1080/1061186x.2020.1853759 · Cited by 156 · see citing works
Favipiravir elicits antiviral mutagenesis during virus replication in vivo
Arias, A., Thorne, L., & Goodfellow, I. (2014) · eLife · doi:10.7554/elife.03679 · Cited by 150 · see citing works
Delmont, T. O., Kiefl, E., Kilinc, O., Esen, Ö. C., Uysal, I., Rappé, M. S., Giovannoni, S. J., & Eren, A. M. (2019) · eLife · doi:10.7554/elife.46497 · Cited by 137 · see citing works
Xiao, M., Liu, X., Ji, J., Li, M., Li, J., Yang, L., Sun, W., Ren, P., Yang, G., Zhao, J., et al. (2020) · Genome Medicine · doi:10.1186/s13073-020-00751-4 · Cited by 137 · see citing works
Full-length haplotype reconstruction to infer the structure of heterogeneous virus populations
Giallonardo, F. D., Töpfer, A., Rey, M., Prabhakaran, S., Duport, Y., Leemann, C., Schmutz, S., Campbell, N. K., Joos, B., Lecca, M. R., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku537 · Cited by 136 · see citing works
Technology dictates algorithms: recent developments in read alignment
Alser, M., Rotman, J., Deshpande, D., Taraszka, K., Shi, H., Baykal, P. I., Yang, H. T., Xue, V., Knyazev, S., Singer, B. D., et al. (2021) · Genome Biology · doi:10.1186/s13059-021-02443-7 · Cited by 144 · see citing works
Syller, J., & Grupa, A. (2015) · Molecular Plant Pathology · doi:10.1111/mpp.12322 · Cited by 131 · see citing works
Hepatitis E: an underestimated emerging threat
Webb, G. W., & Dalton, H. R. (2019) · Therapeutic Advances in Infectious Disease · doi:10.1177/2049936119837162 · Cited by 127 · see citing works
Recombination in Enteroviruses, a Multi-Step Modular Evolutionary Process
Muslin, C., Kain, A. M., Bessaud, M., Blondel, B., & Delpeyroux, F. (2019) · Viruses · doi:10.3390/v11090859 · Cited by 127 · see citing works
Thinking Outside the Triangle: Replication Fidelity of the Largest RNA Viruses
Smith, E. C., Sexton, N. R., & Denison, M. R. (2014) · Annual Review of Virology · doi:10.1146/annurev-virology-031413-085507 · Cited by 125 · see citing works
Intra-host variation and evolutionary dynamics of SARS-CoV-2 populations in COVID-19 patients
Wang, Y., Wang, D., Zhang, L., Sun, W., Zhang, Z., Chen, W., Zhu, A., Huang, Y., Xiao, F., Yao, J., et al. (2021) · Genome Medicine · doi:10.1186/s13073-021-00847-5 · Cited by 124 · see citing works
Measles Virus Fusion Protein: Structure, Function and Inhibition
Plattet, P., Alves, L. C., Herren, M., & Aguilar, H. C. (2016) · Viruses · doi:10.3390/v8040112 · Cited by 122 · see citing works
Schweizer, M., & Peterhans, E. (2013) · Annual Review of Animal Biosciences · doi:10.1146/annurev-animal-022513-114209 · Cited by 115 · see citing works
Viral quasispecies complexity measures
Gregori, J., Perales, C., Rodríguez‐Frias, F., Esteban, J. I., Quer, J., & Domingo, E. (2016) · Virology · doi:10.1016/j.virol.2016.03.017 · Cited by 109 · see citing works
Self-citationFoxtail mosaic virus : A Viral Vector for Protein Expression in Cereals
Bouton, C. R., King, R. C., Chen, H., Azhakanandam, K., Bieri, S., Hammond-Kosack, K. E., & Kanyuka, K. (2018) · PLANT PHYSIOLOGY · doi:10.1104/pp.17.01679 · Cited by 109 · see citing works
Pfaller, C. K., Mastorakos, G. M., Matchett, W. E., Ma, X., Samuel, C. E., & Cattaneo, R. (2015) · Journal of Virology · doi:10.1128/jvi.01017-15 · Cited by 108 · see citing works
Ryabov, E. V., Childers, A. K., Lopez, D., Grubbs, K., Posada-Flórez, F. J., Weaver, D., Girten, W., vanEngelsdorp, D., Chen, Y., & Evans, J. D. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000502 · Cited by 108 · see citing works
Coronaviruses as DNA Wannabes: A New Model for the Regulation of RNA Virus Replication Fidelity
Smith, E. C., & Denison, M. R. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003760 · Cited by 107 · see citing works
De Novo Reconstruction of Consensus Master Genomes of Plant RNA and DNA Viruses from siRNAs
Séguin, J., Rajeswaran, R., Malpica-López, N., Martín, R. R., Kasschau, K. D., Dolja, V. V., Otten, P., Farinelli, L., & Pooggin, M. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088513 · Cited by 105 · see citing works
Dengue drug discovery: Progress, challenges and outlook
Lim, S. P. (2018) · Antiviral Research · doi:10.1016/j.antiviral.2018.12.016 · Cited by 105 · see citing works
Use of Host-like Peptide Motifs in Viral Proteins Is a Prevalent Strategy in Host-Virus Interactions
Hagai, T., Azia, A., Babu, M. M., & Andino, R. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.04.052 · Cited by 105 · see citing works
De novo assembly of viral quasispecies using overlap graphsPreprint
Baaijens, J. A., Aabidine, A. Z. E., Rivals, É., & Schönhuth, A. (2017) · Genome Research · doi:10.1101/gr.215038.116 · Cited by 105 · see citing works
Dinis, J. M., Florek, K. R., Fatola, O. O., Moncla, L. H., Mutschler, J. P., Charlier, O. K., Meece, J. K., Belongia, E. A., & Friedrich, T. C. (2016) · Journal of Virology · doi:10.1128/jvi.03248-15 · Cited by 103 · see citing works
Liu, Z., VanBlargan, L. A., Bloyet, L.-M., Rothlauf, P. W., Chen, R. E., Stumpf, S., Zhao, H., Errico, J. M., Theel, E. S., Liebeskind, M. J., et al. (2020) · doi:10.1101/2020.11.06.372037 · Cited by 135 · see citing works
Within-Host Viral Diversity: A Window into Viral Evolution
Lauring, A. S. (2020) · Annual Review of Virology · doi:10.1146/annurev-virology-010320-061642 · Cited by 101 · see citing works
Walz, P. H., Chamorro, M. F., Falkenberg, S. M., Passler, T., van der Meer, F. J. U. M., & Woolums, A. R. (2020) · Journal of Veterinary Internal Medicine · doi:10.1111/jvim.15816 · Cited by 101 · see citing works
Viral Quasispecies Assembly via Maximal Clique Enumeration
Töpfer, A., Marschall, T., Bull, R. A., Luciani, F., Schönhuth, A., & Beerenwinkel, N. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003515 · Cited by 94 · see citing works
Within host RNA virus persistence: mechanisms and consequences
Randall, R. E., & Griffin, D. E. (2017) · Current Opinion in Virology · doi:10.1016/j.coviro.2017.03.001 · Cited by 90 · see citing works
The pepper virome: natural co-infection of diverse viruses and their quasispecies
Jo, Y., Choi, H., Kim, S., Kim, S., Lee, B. C., & Cho, W. K. (2017) · BMC Genomics · doi:10.1186/s12864-017-3838-8 · Cited by 90 · see citing works
Poliovirus intrahost evolution is required to overcome tissue-specific innate immune responses
Xiao, Y., Dolan, P., Goldstein, E. F., Li, M., Farkov, M., Brodsky, L., & Andino, R. (2017) · Nature Communications · doi:10.1038/s41467-017-00354-5 · Cited by 89 · see citing works
Recent Progress in Studies of Porcine Reproductive and Respiratory Syndrome Virus 1 in China
Sun, Q., Xu, H., An, T., Cai, X., Tian, Z., & Zhang, H. (2023) · Viruses · doi:10.3390/v15071528 · Cited by 88 · see citing works
Kevill, J. L., Highfield, A. C., Mordecai, G. J., Martin, S. J., & Schroeder, D. C. (2017) · Viruses · doi:10.3390/v9110314 · Cited by 86 · see citing works
Tabachnick, W. J. (2016) · Annual Review of Virology · doi:10.1146/annurev-virology-110615-035630 · Cited by 86 · see citing works
Stenglein, M. D., Jacobson, E. R., Chang, L.-W., Sanders, C. J., Hawkins, M. G., Guzman, D. S.-M., Drazenovich, T. L., Dunker, F. H., Kamaka, E. K., Fisher, D., et al. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1004900 · Cited by 85 · see citing works
Knyazev, S., Tsyvina, V., Shankar, A., Melnyk, A., Artyomenko, A., Malygina, T., Porozov, Y. B., Campbell, E. M., Switzer, W. M., Skums, P., et al. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab576 · Cited by 84 · see citing works
Three dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex
de Castro, I. F., Fernández, J., Barajas, D., Nagy, P. D., & Risco, C. (2016) · Journal of Cell Science · doi:10.1242/jcs.181586 · Cited by 84 · see citing works
Luczo, J. M., Stambas, J., Durr, P. A., Michalski, W. P., & Bingham, J. (2015) · Reviews in Medical Virology · doi:10.1002/rmv.1846 · Cited by 83 · see citing works
Perelygina, L. M., Chen, M., Suppiah, S., Adebayo, A., Abernathy, E. S., Dorsey, M. J., Bercovitch, L. G., Paris, K., White, K. P., Krol, A. L., et al. (2019) · PLoS Pathogens · doi:10.1371/journal.ppat.1008080 · Cited by 83 · see citing works
Intra-host dynamics of Ebola virus during 2014
Ni, M., Chen, C., Qian, J., Xiao, H., Shi, W., Luo, Y., Wang, H., Li, Z., Wu, J. F., Xu, P., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.151 · Cited by 82 · see citing works
Diversity, Distribution, and Evolution of Tomato Viruses in China Uncovered by Small RNA Sequencing
Xu, C., Sun, X., Taylor, A., Jiao, C., Xu, Y., Cai, X., Wang, X., Ge, C., Pan, G., Wang, Q., et al. (2017) · Journal of Virology · doi:10.1128/jvi.00173-17 · Cited by 82 · see citing works
Extracellular vesicles: Vehicles of en bloc viral transmission
Altan‐Bonnet, N., Perales, C., & Domingo, E. (2019) · Virus Research · doi:10.1016/j.virusres.2019.03.023 · Cited by 82 · see citing works
Self-citationIncreased Replicative Fitness Can Lead to Decreased Drug Sensitivity of Hepatitis C Virus
Sheldon, J., Beach, N. M., Moreno, E., Gallego, I., Piñeiro, D., Martı́nez-Salas, E., Gregori, J., Quer, J., Esteban, J. I., Rice, C. M., et al. (2014) · Journal of Virology · doi:10.1128/jvi.01860-14 · Cited by 82 · see citing works
Self-citationTowards improvements in foot-and-mouth disease vaccine performance
Belsham, G. J. (2020) · Acta veterinaria Scandinavica · doi:10.1186/s13028-020-00519-1 · Cited by 80 · see citing works
Axonal spread of neuroinvasive viral infections
Taylor, M. P., & Enquist, L. W. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.01.002 · Cited by 80 · see citing works
Perales, C., Beach, N. M., Gallego, I., Soria, M. E., Quer, J., Esteban, J. I., Rice, C. M., Domingo, E., & Sheldon, J. (2013) · Journal of Virology · doi:10.1128/jvi.02824-12 · Cited by 78 · see citing works
Self-citationWithin-Host Diversity of SARS-CoV-2 in COVID-19 Patients With Variable Disease Severities
Al-Khatib, H. A., Benslimane, F. M., Elbashir, I., Coyle, P. V., Maslamani, M. A. R. S. A., Al‐Khal, A., Thani, A. A. A., & Yassine, H. M. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.575613 · Cited by 75 · see citing works
Graudenzi, A., Maspero, D., Angaroni, F., Piazza, R., & Ramazzotti, D. (2021) · iScience · doi:10.1016/j.isci.2021.102116 · Cited by 75 · see citing works
Unfolded protein response in hepatitis C virus infection
Chan, S. (2014) · Frontiers in Microbiology · doi:10.3389/fmicb.2014.00233 · Cited by 74 · see citing works
Baaijens, J. A., Zulli, A., Ott, I. M., Nika, I., van der Lugt, M. J., Petrone, M. E., Alpert, T., Fauver, J. R., Kalinich, C. C., Vogels, C. B. F., et al. (2022) · Genome biology · doi:10.1186/s13059-022-02805-9 · Cited by 73 · see citing works
Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir
de Ávila, A. I., Gallego, I., Soria, M. E., Gregori, J., Quer, J., Esteban, J. I., Rice, C. M., Domingo, E., & Perales, C. (2016) · PLoS ONE · doi:10.1371/journal.pone.0164691 · Cited by 73 · see citing works
Self-citationMolecular epidemiology, evolution and phylogeny of foot-and-mouth disease virus
Jamal, S. M., & Belsham, G. J. (2018) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2018.01.020 · Cited by 72 · see citing works
Pathogen evolution and the immunological niche
Cobey, S. E. (2014) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.12493 · Cited by 72 · see citing works
Graepel, K. W., Lu, X., Case, J. B., Sexton, N. R., Smith, E. C., & Denison, M. R. (2017) · mBio · doi:10.1128/mbio.01503-17 · Cited by 71 · see citing works
Extinction of Hepatitis C Virus by Ribavirin in Hepatoma Cells Involves Lethal Mutagenesis
Ortega‐Prieto, A. M., Sheldon, J., Grande-Pérez, A., Tejero, H., Gregori, J., Quer, J., Esteban, J. I., Domingo, E., & Perales, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071039 · Cited by 71 · see citing works
Self-citationHepatitis E virus treatment and ribavirin therapy: viral mechanisms of nonresponse
Tödt, D., Meister, T. L., & Steinmann, E. (2018) · Current Opinion in Virology · doi:10.1016/j.coviro.2018.10.001 · Cited by 70 · see citing works
Yan, T., Zhu, J.-R., Di, D., Gao, Q., Zhang, Y., Zhang, A., Yan, C., Miao, H., & Wang, X. (2015) · Virology · doi:10.1016/j.virol.2014.12.042 · Cited by 69 · see citing works
Accurate Genetic Detection of Hepatitis C Virus Transmissions in Outbreak Settings
Campo, D. S., Xia, G.-L., Dimitrova, Z., Lin, Y., Forbi, J. C., Ganova-Raeva, L. M., Punkova, L., Ramachandran, S., Thai, H. T. C., Skums, P., et al. (2015) · The Journal of Infectious Diseases · doi:10.1093/infdis/jiv542 · Cited by 69 · see citing works
Evolutionary ecology of virus emergence
Dennehy, J. J. (2016) · Annals of the New York Academy of Sciences · doi:10.1111/nyas.13304 · Cited by 69 · see citing works
QUENTIN: reconstruction of disease transmissions from viral quasispecies genomic data
Skums, P., Zelikovsky, A., Singh, R., Gussler, W., Dimitrova, Z., Knyazev, S., Mandric, I., Ramachandran, S., Campo, D. S., Jha, D., et al. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btx402 · Cited by 69 · see citing works
Domingo, E., & Perales, C. (2018) · European Biophysics Journal · doi:10.1007/s00249-018-1282-6 · Cited by 68 · see citing works
Self-citationKutnjak, D., Rupar, M., Gutiérrez‐Aguirre, I., Curk, T., Kreuze, J. F., & Ravnikar, M. (2015) · Journal of Virology · doi:10.1128/jvi.03685-14 · Cited by 68 · see citing works
Hapuarachchi, H. C., Koo, C., Kek, R., Xu, H., Lai, Y. L., Liu, L., Kok, S. Y., Shi, Y., Lee, R. T. C., Lee, K.-S., et al. (2016) · Scientific Reports · doi:10.1038/srep22592 · Cited by 67 · see citing works
Inference with viral quasispecies diversity indices: clonal and NGS approaches
Gregori, J., Salicrú, M., Domingo, E., Sánchez‐Pla, Á., Esteban, J. I., Rodríguez‐Frias, F., & Quer, J. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btt768 · Cited by 64 · see citing works
Self-citationA Comparison of Deformed Wing Virus in Deformed and Asymptomatic Honey Bees
Brettell, L. E., Mordecai, G. J., Schroeder, D. C., Jones, I. M., Silva, J. D. T., Vicente-Rubiano, M., & Martin, S. J. (2017) · Insects · doi:10.3390/insects8010028 · Cited by 64 · see citing works
Virus population dynamics during infection
Poirier, E. Z., & Vignuzzi, M. (2017) · Current Opinion in Virology · doi:10.1016/j.coviro.2017.03.013 · Cited by 64 · see citing works
Elrashdy, F., Redwan, E. M. M. M., & Uversky, V. N. (2020) · Biomolecules · doi:10.3390/biom10091312 · Cited by 64 · see citing works
Dengue Virus Evolution under a Host-Targeted Antiviral
Plummer, E. M., Buck, M. D., Sanchez, M., Greenbaum, J., Turner, J., Grewal, R., Klose, B., Sampath, A., Warfield, K. L., Peters, B., et al. (2015) · Journal of Virology · doi:10.1128/jvi.00028-15 · Cited by 63 · see citing works
Tödt, D., Wälter, S., Brown, R. J. P., & Steinmann, E. (2016) · Viruses · doi:10.3390/v8100283 · Cited by 63 · see citing works
The global population of SARS-CoV-2 is composed of six major subtypes
Morais, I. J., Polveiro, R. C., Souza, G. M., Bortolin, D. I., Sassaki, F. T., & Lima, A. T. M. (2020) · Scientific Reports · doi:10.1038/s41598-020-74050-8 · Cited by 62 · see citing works
Boys, I. N., Xu, E., Mar, K. B., Cruz-Rivera, P. C. D. L., Eitson, J. L., Moon, B., & Schoggins, J. W. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.09.014 · Cited by 63 · see citing works
Dolan, P., Taguwa, S., Rangel, M. A., Acevedo, A., Hagai, T., Andino, R., & Frydman, J. (2021) · eLife · doi:10.7554/elife.61921 · Cited by 62 · see citing works
Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake
López-Bueno, A., Rastrojo, A., Peiró‐Pastor, R., Arenas, M., & Alcamı́, A. (2015) · Molecular Ecology · doi:10.1111/mec.13321 · Cited by 62 · see citing works
Pilosof, S., He, Q., Tiedje, K. E., Ruybal‐Pesántez, S., Day, K. P., & Pascual, M. (2019) · PLoS Biology · doi:10.1371/journal.pbio.3000336 · Cited by 61 · see citing works
- Authors
- Domingo, E., Sheldon, J., & Perales, C.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- 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
- 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
- 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
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › 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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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