Research Topics
| Rafael SanjuanSummaryAffiliation: University of Valencia Country: Spain Publications
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Detail Information
Publications
Experimental evolution of RNA versus DNA virusesPilar Domingo-Calap
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain Departament de Genètica, Universitat de Valencia, Spain Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública CSISP, Valencia, Spain E mail
Evolution 65:2987-94. 2011..The results are therefore consistent with the observation that, despite their lower mutation rates, ssDNA viruses can sometimes match the evolvability of RNA viruses...
From molecular genetics to phylodynamics: evolutionary relevance of mutation rates across virusesRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Paterna, Spain
PLoS Pathog 8:e1002685. 2012..The model is consistent with data from replication kinetics, selection strength and chemical mutagenesis studies...- Mutational fitness effects in RNA and single-stranded DNA viruses: common patterns revealed by site-directed mutagenesis studiesRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departamento de Genética, Universitat de Valencia, C Catedrático Agustín Escardino 9, Valencia 46980, Spain
Philos Trans R Soc Lond B Biol Sci 365:1975-82. 2010..20-0.41). Other summary statistics are provided. These generalizations about the distribution of mutational fitness effects can help us to better understand the evolution of RNA and single-stranded DNA viruses... - Viral mutation ratesRafael Sanjuan
Institut Cavanilles de Biodiversitat y Biologia Evolutiva, Departament de Genetica, Universitat de Valencia, C Catedrático Agustín Escardino 9, Paterna 46980, Valencia, Spain
J Virol 84:9733-48. 2010..A regularly updated virus mutation rate data set will be available at www.uv.es/rsanjuan/virmut... - Interplay between RNA structure and protein evolution in HIV-1Rafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departamento de Genética, Universitat de Valencia, Spain
Mol Biol Evol 28:1333-8. 2011..Characterizing the evolutionary trade-offs between the selective pressures acting at the RNA and protein levels will help us to better understand the variability and evolution of HIV-1... 
Weighted least-squares likelihood ratio test for branch testing in phylogenies reconstructed from distance measuresRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Edifici d Instituts de Paterna Apartat 2085 R S, Valencia, 46071, Spain
Syst Biol 54:218-29. 2005..This point is illustrated by analyzing the relationships between human immunodeficiency virus type 1 (HIV-1) sequences isolated from various organs of different individuals...- The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virusRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Proc Natl Acad Sci U S A 101:8396-401. 2004..The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations... - A network model for the correlation between epistasis and genomic complexityRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
PLoS ONE 3:e2663. 2008.... - Epistasis and the adaptability of an RNA virusRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
Genetics 170:1001-8. 2005..Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution... - In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairsRafael Sanjuan
Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Valencia, Spain
Mol Biol Evol 23:2123-30. 2006..In good agreement with our previous finding of an evolutionary trend toward increased robustness, we now found a trend toward reduced antagonistic epistasis... - Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable regionRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
Evolution 58:1185-94. 2004..In contrast, positive selection does not seem to be the mechanism responsible for the evolution of patient-specific sequences... - The cost of replication fidelity in an RNA virusVictoria Furió
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Proc Natl Acad Sci U S A 102:10233-7. 2005..We demonstrate that the observed mutation rate in vesicular stomatitis virus can be explained by a trade-off between replication rate and replication fidelity... - In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutationsRafael Sanjuan
Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Avenida de los Naranjos s n, Valencia, Spain
Mol Biol Evol 23:1427-36. 2006..We also show that genomic redundancy can contribute to the robustness of these simple RNA genomes... - The contribution of epistasis to the architecture of fitness in an RNA virusRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Proc Natl Acad Sci U S A 101:15376-9. 2004..In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components... - The fitness effects of random mutations in single-stranded DNA and RNA bacteriophagesPilar Domingo-Calap
Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Valencia, Spain
PLoS Genet 5:e1000742. 2009..Mutational fitness effects are important for understanding processes of fitness decline, but also of neutral evolution and adaptation. As such, these findings can contribute to explain the evolution of ssDNA and ssRNA viruses... - The effect of genetic robustness on evolvability in digital organismsSantiago F Elena
Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Valencia, Spain
BMC Evol Biol 8:284. 2008..However, several issues related to robustness remain poorly understood, such as its implications for evolvability (the ability to produce adaptive evolutionary innovations)... - Relationship between within-host fitness and virulence in the vesicular stomatitis virus: correlation with partial decouplingVictoria Furió
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Spain
J Virol 86:12228-36. 2012.... - Effect of ribavirin on the mutation rate and spectrum of hepatitis C virus in vivoJosé M Cuevas
Departamento de Genetica, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
J Virol 83:5760-4. 2009..This result is consistent with the known in vitro mutagenic effect of ribavirin and suggests that the antiviral effect of ribavirin plus interferon treatment is at least partly exerted through lethal mutagenesis... - The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virusFrancy Y E Carrillo
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
Infect Genet Evol 7:69-73. 2007.... - Selection for robustness in mutagenized RNA virusesRafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
PLoS Genet 3:e93. 2007..These results show that selection can directly favor mutational robustness and reveal a novel viral resistance mechanism against treatment by lethal mutagenesis... - Nucleoside analogue mutagenesis of a single-stranded DNA virus: evolution and resistancePilar Domingo-Calap
Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Valencia, Spain
J Virol 86:9640-6. 2012..We hypothesize that regulation of lysis time may allow the virus to optimize progeny size in cells showing defects in DNA synthesis... - The cost of replication fidelity in human immunodeficiency virus type 1Victoria Furió
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
Proc Biol Sci 274:225-30. 2007..Since in RNA viruses fast replication is critical for survival, this could impose a high cost of fidelity and favour the evolution of high mutation rates... - Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virusFrancy Y E Carrillo
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Infect Genet Evol 8:614-20. 2008..Further studies are needed to discern whether infections involving different viruses could have an increased ability to escape antiviral strategies... - Point mutation rate of bacteriophage PhiX174José M Cuevas
Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departamento de Genética, Universitat de Valencia, 46071 Valencia, Spain
Genetics 183:747-9. 2009..0x10(-6) substitutions per base per round of copying, which is consistent with Drake's rule (0.003 mutations per genome per round of copying in DNA-based microorganisms)... - Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virusJosé M Cuevas
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
Infect Genet Evol 5:55-65. 2005..Evolution in presence of sub-inhibitory concentrations of antivirals compensated for the reduction in fitness in presence of antiviral therapy... - Distribution of fitness effects caused by single-nucleotide substitutions in bacteriophage f1Joan B Peris
Departament de Genetica, Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, 46980 Valencia, Spain
Genetics 185:603-9. 2010..Our results confirm that high mutational sensitivity is a general property of viruses with small genomes, including RNA and single-strand DNA viruses infecting animals, plants, and bacteria... - Immune Activation Promotes Evolutionary Conservation of T-Cell Epitopes in HIV-1Rafael Sanjuan
Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, Valencia, Spain Departament de Genètica, Universitat de Valencia, Valencia, Spain
PLoS Biol 11:e1001523. 2013..Our results also support the view that some pathogens draw benefits from the immune response and suggest that vaccination strategies based on conserved TH epitopes may be counterproductive... - Mutation rate of bacteriophage ΦX174 modified through changes in GATC sequence contextJosé M Cuevas
Instituto Cavanilles de Biodiversidad y Biología Evolutiva and Departamento de Genética, Universitat de Valencia, Spain
Infect Genet Evol 11:1820-2. 2011..A thirty-fold reduction in the mutation rate was achieved by introducing seven GATC sequences in its genome. This motif allows for methyl-directed mismatch repair and is strongly avoided in nature by ΦX174 and other phages... - The fitness effects of synonymous mutations in DNA and RNA virusesJosé M Cuevas
Mol Biol Evol 29:17-20. 2012..4% and 0%, respectively. In contrast, the effects of nonsynonymous substitutions appear to be similar in ssRNA and ssDNA viruses... - Unequal distribution of RT-PCR artifacts along the E1-E2 region of Hepatitis C virusPilar Domingo-Calap
Instituto Cavanilles de Biodiversidad y Biologia Evolutiva, Universitat de Valencia, Spain
J Virol Methods 161:136-40. 2009..The data suggest that the RNA sequence context or secondary structure can determine the fidelity of in vitro transcription or reverse transcription. Potentially, these factors might also modify the fidelity of the viral polymerase... - [Short-term prognosis of patients admitted for probable acute coronary syndrome without ST-segment elevation. Role of new myocardial damage markers and acute-phase reactants]Vicent Bodi
Servei de Cardiologia, Hospital Clinic i Universitari, Valencia, Universitat de Valencia, Spain
Rev Esp Cardiol 55:823-30. 2002..The relative value of classic markers, myocardial damage variables, and levels of acute-phase reactants in establishing the pre-discharge prognosis of acute coronary syndrome without ST-segment elevation was analyzed...